Contacts of the helix formed by residues 31 - 71 (chain A) in PDB entry 2GQ3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP 3.9 2.2 + - - -
30A ILE* 1.3 78.8 - - - +
32A PRO* 1.3 71.3 - - - +
33A ASP* 3.4 13.2 + - - +
34A SER* 2.8 39.6 + - - +
35A PHE 2.8 24.4 + - - -
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Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN* 4.4 13.0 - - + +
25A LEU* 3.7 30.7 - - + -
30A ILE 3.6 7.6 - - - +
31A ASP* 1.3 93.1 - - - +
33A ASP* 1.3 60.2 + - - +
35A PHE* 3.5 1.7 - - + +
36A TRP* 3.0 37.6 + - + -
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 5.5 0.5 - - - +
17A TYR* 5.6 1.4 + - - -
31A ASP* 3.3 13.3 + - - +
32A PRO* 1.3 78.8 - - - +
34A SER* 1.3 59.7 + - - +
36A TRP* 3.4 5.5 + - - +
37A ALA* 3.0 28.4 + - - +
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 5.1 3.4 - - - -
31A ASP* 2.8 33.9 + - - +
33A ASP* 1.3 74.7 - - - +
35A PHE* 1.3 68.6 + - - +
37A ALA* 4.2 5.3 - - - +
38A GLY* 2.9 18.5 + - - -
419A VAL* 4.6 4.0 - - - +
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.7 17.7 - - + -
25A LEU* 4.1 20.4 - - + -
30A ILE* 4.1 12.9 - - + +
31A ASP 2.8 15.3 + - - +
32A PRO* 3.5 12.3 - - + +
33A ASP 3.3 0.2 - - - -
34A SER* 1.3 80.7 - - - +
36A TRP* 1.3 75.2 + + - +
38A GLY* 3.0 1.6 + - - -
39A VAL* 2.9 48.9 + - + +
366A LEU* 4.3 8.7 - - + -
367A PHE* 3.7 21.8 - + - -
370A LEU* 3.8 16.6 - - + -
419A VAL* 3.9 18.2 - - + +
420A LEU* 3.7 27.4 - - + -
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Residues in contact with TRP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.6 22.4 - - + +
12A ILE* 3.2 44.4 - - + -
16A LEU* 4.8 0.9 - - + -
17A TYR* 3.5 39.1 - + - -
20A VAL* 3.5 29.8 - - + +
21A ASN* 2.7 24.8 + - - -
25A LEU* 4.3 0.4 - - + +
32A PRO* 3.0 25.6 + - + +
33A ASP* 4.0 5.2 - - - +
35A PHE* 1.3 90.3 - + - +
37A ALA* 1.4 58.6 + - - +
39A VAL* 3.2 23.8 + - + +
40A ASP* 2.9 27.7 + - - +
350A ILE* 4.7 0.4 - - + -
367A PHE* 3.9 30.7 - + - -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.5 5.5 - - + +
33A ASP 3.0 17.2 + - - +
34A SER* 4.2 5.4 - - - +
35A PHE 3.3 0.2 - - - -
36A TRP* 1.4 76.1 - - - +
38A GLY* 1.3 57.6 + - - +
40A ASP* 3.4 8.5 + - - +
41A LYS* 3.0 27.3 + - - +
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A SER 2.9 14.4 + - - -
35A PHE 3.5 3.8 - - - -
37A ALA* 1.3 71.7 - - - +
39A VAL* 1.3 60.8 + - - +
41A LYS* 4.3 6.1 - - - -
42A VAL* 2.8 35.5 + - - +
419A VAL* 3.7 25.4 - - - -
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.9 17.0 - - + -
35A PHE* 2.9 51.5 + - + +
36A TRP* 3.2 29.6 + - + +
38A GLY* 1.3 73.7 - - - +
40A ASP* 1.3 59.6 + - - +
42A VAL* 3.8 0.3 - - - +
43A VAL* 2.9 39.3 + - + +
350A ILE* 4.5 9.4 - - + -
363A MET* 6.2 0.2 - - + -
366A LEU* 4.2 30.5 - - + -
367A PHE* 4.6 4.5 - - + -
419A VAL* 4.5 0.8 - - - +
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.3 8.1 - - + +
8A GLY* 4.1 8.0 - - - -
9A ASN* 3.1 35.5 + - - +
10A LEU* 3.5 24.5 + - + +
36A TRP 2.9 13.5 + - - +
37A ALA* 3.6 12.0 - - - +
38A GLY 3.2 0.2 - - - -
39A VAL* 1.3 79.1 - - - +
41A LYS* 1.3 63.0 + - - +
43A VAL* 4.0 1.6 - - - +
44A ALA* 3.1 27.2 + - - +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA 3.0 17.0 + - - +
38A GLY* 3.3 6.5 + - - +
40A ASP* 1.3 73.9 + - - +
42A VAL* 1.3 63.7 + - + +
44A ALA* 3.2 4.7 + - + +
45A ASP* 2.8 65.5 + - - +
415A ARG* 3.9 15.0 - - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY 2.8 24.4 + - - +
39A VAL 3.9 2.7 - - - +
41A LYS* 1.3 73.2 - - + +
43A VAL* 1.3 61.0 + - - +
46A LEU* 3.1 41.3 + - + +
362A ILE* 4.1 20.0 - - + -
366A LEU* 4.3 14.6 - - + -
412A LEU* 4.3 8.7 - - + -
415A ARG* 4.0 37.0 - - + +
416A VAL* 4.9 0.7 - - + -
419A VAL* 3.8 22.0 - - + -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.0 31.6 - - + -
39A VAL* 2.9 30.8 + - + +
40A ASP 4.0 2.9 - - - +
42A VAL* 1.3 75.0 - - - +
44A ALA* 1.3 63.8 + - - +
47A THR* 2.7 42.3 + - - +
358A VAL* 4.0 30.1 - - + -
362A ILE* 3.9 24.9 - - + -
363A MET* 5.7 1.6 - - + -
366A LEU* 4.6 2.9 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASN* 6.3 2.9 - - + -
40A ASP* 3.1 22.7 + - - +
41A LYS* 3.8 5.8 - - + +
43A VAL* 1.3 78.2 - - + +
45A ASP* 1.3 67.1 + - - +
47A THR* 4.7 0.8 - - - -
48A PRO* 3.4 19.2 - - - +
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 2.8 47.0 + - - +
42A VAL 4.1 2.0 - - - +
44A ALA* 1.3 84.2 - - - +
46A LEU* 1.3 63.4 + - + +
48A PRO* 3.5 12.0 - - - +
49A GLN* 5.0 3.1 + - - +
415A ARG* 2.9 39.6 + - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.1 25.3 + - + +
45A ASP* 1.3 87.3 - - + +
47A THR* 1.3 66.3 + - - +
48A PRO* 3.3 3.1 - - - -
49A GLN* 3.2 6.3 + - + +
50A ASN* 3.0 19.9 + - - +
362A ILE* 3.9 10.8 - - + -
408A PHE* 3.5 24.5 - - + -
411A GLU* 5.0 10.1 - - + +
412A LEU* 3.6 49.8 - - + +
415A ARG* 4.4 19.3 - - + +
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 2.7 34.8 + - - +
44A ALA* 4.7 1.3 - - - -
46A LEU* 1.3 75.8 - - - +
48A PRO* 1.3 72.8 - - + +
50A ASN* 3.2 9.3 + - - +
51A GLN* 2.9 23.6 + - + +
358A VAL* 5.7 0.5 - - - +
359A PHE* 3.9 20.5 + - + +
362A ILE* 4.1 10.3 - - - +
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Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA 3.4 21.3 - - - +
45A ASP 3.5 7.9 - - - +
46A LEU 3.4 4.3 - - - -
47A THR* 1.3 95.6 - - + +
49A GLN* 1.3 55.4 + - - +
51A GLN* 3.4 5.7 + - + +
52A ALA* 2.9 27.9 + - - +
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Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASP 5.0 2.0 + - - +
46A LEU* 3.2 10.5 + - + +
48A PRO* 1.3 77.1 - - - +
50A ASN* 1.3 63.4 + - - +
52A ALA* 3.9 14.6 - - - +
53A LEU* 2.9 45.4 + - - +
404A ALA* 4.9 4.2 - - - +
408A PHE* 3.4 30.2 - - + +
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU 3.0 12.7 + - - +
47A THR* 3.2 8.9 + - - +
49A GLN* 1.3 76.0 - - - +
51A GLN* 1.3 61.6 + - - +
53A LEU* 3.4 5.5 + - - +
54A LEU* 3.1 20.6 + - - +
343A HIS* 3.0 40.9 + - - +
359A PHE* 3.5 38.4 - - + +
361A GLY* 5.9 0.7 - - - -
362A ILE* 3.8 8.2 + - + +
408A PHE* 3.6 27.9 - - + -
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Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A THR* 2.9 19.1 + - + +
48A PRO* 3.7 6.7 - - + +
50A ASN* 1.3 74.1 - - - +
52A ALA* 1.3 60.5 + - - +
54A LEU* 3.1 15.6 + - - +
55A ASN* 2.8 64.3 + - - +
359A PHE* 3.6 22.4 - - + -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO 2.9 18.0 + - - +
49A GLN* 3.7 18.4 - - - +
51A GLN* 1.3 75.6 - - - +
53A LEU* 1.3 59.2 + - - +
55A ASN* 3.4 10.5 + - - +
56A ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN* 2.9 37.8 + - - +
50A ASN* 3.7 6.1 - - - +
52A ALA* 1.3 77.3 - - - +
54A LEU* 1.4 62.7 + - + +
56A ALA* 3.3 10.1 + - + +
57A ARG* 3.2 23.6 + - - +
343A HIS* 4.9 5.6 - - + -
404A ALA* 3.9 27.6 - - + -
405A GLU* 3.9 31.2 - - + +
408A PHE* 3.5 42.2 - - + -
437A ARG* 4.9 0.9 + - - -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN* 3.1 9.9 + - - +
51A GLN* 3.1 19.1 + - - +
53A LEU* 1.4 72.0 - - + +
55A ASN* 1.3 63.9 + - - +
57A ARG* 3.1 51.4 + - - +
58A ASP* 3.3 19.0 + - - +
343A HIS* 3.6 21.3 - - + +
344A LEU* 3.6 24.0 - - + +
359A PHE* 3.4 38.6 - - + -
405A GLU* 5.4 0.2 - - - +
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Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLN* 2.8 55.8 + - - +
52A ALA* 3.7 9.0 - - - +
54A LEU* 1.3 71.2 - - - +
56A ALA* 1.3 59.1 + - - +
58A ASP* 3.2 14.1 + - - +
59A GLU* 2.8 40.4 + - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 3.0 17.1 + - - +
53A LEU* 3.6 11.2 - - + +
54A LEU 3.3 0.2 - - - -
55A ASN* 1.3 72.4 - - - +
57A ARG* 1.3 64.7 + - - +
59A GLU* 3.3 14.3 + - - +
60A LEU* 2.8 35.0 + - + +
437A ARG* 4.5 8.7 - - - +
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU 3.2 9.1 + - - +
54A LEU* 3.1 36.1 + - - +
56A ALA* 1.3 74.8 - - - +
58A ASP* 1.3 60.3 - - - +
60A LEU* 3.3 3.5 + - - +
61A GLN* 3.0 30.5 + - - +
343A HIS* 3.7 21.0 - - - +
344A LEU* 4.3 10.5 - - - +
399A LYS* 3.6 13.3 + - - +
401A HIS* 3.4 16.5 - - + -
405A GLU* 2.7 35.4 + - - -
437A ARG* 3.6 24.6 - - - +
707A ASN* 3.4 28.5 + - - +
709A TYR* 3.6 27.9 + - - -
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.6 13.1 - - - +
55A ASN* 3.2 15.2 + - - +
57A ARG* 1.3 80.9 - - - +
59A GLU* 1.3 62.5 + - - +
61A GLN* 3.3 6.7 + - - +
62A ALA* 3.0 24.8 + - - +
706A PRO* 3.9 24.8 - - - +
707A ASN* 4.8 1.0 - - - +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASN* 2.8 31.5 + - - +
56A ALA* 3.7 14.9 + - - +
58A ASP* 1.3 72.3 - - - +
60A LEU* 1.3 63.5 + - + +
62A ALA* 3.3 6.4 + - - +
63A GLN* 3.2 33.5 + - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 2.8 23.6 + - + +
57A ARG* 3.8 3.6 - - - +
59A GLU* 1.3 71.8 - - + +
61A GLN* 1.3 63.5 + - - +
63A GLN* 3.0 14.2 + - - +
64A ILE* 2.9 27.5 + - + +
88A ILE* 3.3 45.5 - - + +
89A GLY 4.5 2.2 - - - +
90A TYR* 4.2 19.5 - - + +
437A ARG* 3.2 54.1 - - - +
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG 3.0 17.8 + - - +
58A ASP* 3.9 4.9 - - - +
59A GLU 3.3 0.4 - - - -
60A LEU* 1.3 76.8 - - - +
62A ALA* 1.3 56.9 + - - +
64A ILE* 3.1 12.3 + - - +
65A ASP* 2.8 60.1 + - - +
469A HIS* 3.7 31.7 + - + +
470A THR* 2.8 50.8 + - - +
707A ASN* 4.3 13.7 + - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP 3.0 16.2 + - - +
59A GLU* 3.3 6.3 + - - +
61A GLN* 1.3 76.7 - - - +
63A GLN* 1.3 62.8 + - + +
65A ASP* 3.5 10.9 + - - +
66A LYS* 2.9 25.7 + - - +
69A ARG* 5.0 1.2 + - - -
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 3.2 23.3 + - + +
60A LEU* 3.0 22.8 + - - +
62A ALA* 1.3 76.9 - - + +
64A ILE* 1.3 59.6 + - - +
66A LYS* 3.4 10.3 + - + +
67A TRP* 3.0 28.8 + - - +
84A PHE* 3.6 18.7 - - + -
88A ILE* 3.5 35.1 + - + +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU 2.9 19.7 + - - +
61A GLN* 3.7 9.2 - - - +
63A GLN* 1.3 74.8 - - - +
65A ASP* 1.4 67.0 + - - +
67A TRP* 2.9 12.2 + - + +
68A HIS* 3.1 31.7 + - + +
81A TYR* 5.1 6.1 - - + +
84A PHE* 4.1 12.1 - - + -
85A LEU* 4.2 10.5 - - + -
88A ILE* 4.1 12.8 - - + -
90A TYR* 3.5 38.6 - - + -
436A ARG* 5.4 0.7 - - - +
470A THR* 3.4 38.1 - - + +
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Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 2.8 48.1 + - - +
62A ALA* 3.6 11.2 - - - +
64A ILE* 1.4 72.0 - - - +
66A LYS* 1.3 62.6 + - - +
68A HIS* 3.3 3.7 + - - +
69A ARG* 3.0 46.2 + - - +
469A HIS 4.8 2.6 - - - +
470A THR 4.5 1.9 - - - +
472A MET* 5.1 3.0 - - - +
473A GLU* 3.7 23.0 + - + +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 2.9 17.4 + - - +
63A GLN* 3.6 9.2 - - + +
64A ILE 3.2 0.2 - - - -
65A ASP* 1.3 76.9 - - - +
67A TRP* 1.3 62.5 + - - +
69A ARG* 3.0 29.4 + - + +
70A ARG* 3.0 50.9 + - + +
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Residues in contact with TRP 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN 3.0 13.1 + - - +
64A ILE* 2.9 8.8 + - - +
66A LYS* 1.3 76.8 - - - +
68A HIS* 1.3 88.1 + + - +
70A ARG* 3.3 1.4 + - - -
71A ARG* 3.1 84.5 + - + +
76A ILE* 4.2 15.5 - - + -
77A ASP* 4.5 4.9 - - + -
80A ALA* 4.3 7.8 + - + -
81A TYR* 3.6 49.4 - + + -
84A PHE* 3.4 52.2 - + + +
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Residues in contact with HIS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.1 42.1 + - + +
65A ASP* 3.6 7.2 - - - +
67A TRP* 1.3 102.6 - + - +
69A ARG* 1.3 62.0 + - - +
71A ARG* 3.2 23.7 + - - +
76A ILE* 4.8 5.1 - - + +
81A TYR* 4.0 10.7 + + - -
470A THR 4.6 0.2 - - - -
471A SER* 4.3 13.8 + - - -
473A GLU* 3.7 25.2 - - + +
474A ALA* 3.6 33.3 - - + +
581A ILE* 3.9 16.6 - - + -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 5.0 1.2 + - - -
65A ASP* 3.0 30.6 + - - +
66A LYS* 3.0 29.9 + - + +
68A HIS* 1.3 76.9 - - - +
70A ARG* 1.3 62.9 + - + +
71A ARG 4.8 1.2 - - - -
473A GLU* 2.7 53.0 + - + +
649A ARG* 4.0 14.1 - - - +
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 3.0 44.6 + - + +
67A TRP* 3.8 0.7 - - - +
68A HIS 3.3 0.2 - - - -
69A ARG* 1.3 77.9 - - + +
71A ARG* 1.3 88.3 + - - +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 3.1 83.2 + - + +
68A HIS* 3.2 16.1 + - - +
69A ARG 4.7 1.3 - - - -
70A ARG* 1.3 113.8 - - - +
75A PRO* 5.4 6.6 - - - +
76A ILE* 6.3 3.6 - - - -
77A ASP 6.3 0.7 - - - +
80A ALA* 5.9 3.0 - - - +
474A ALA 5.8 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il