Contacts of the helix formed by residues 32 - 71 (chain A) in PDB entry 4KJW
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 PRO 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LYS 3.4 6.9 - - - +
31A THR* 1.3 91.1 - - + +
33A LEU* 1.3 59.5 + - - +
34A ALA* 3.1 5.8 - - + +
35A ILE* 2.9 38.1 + - + +
36A LEU* 3.2 8.5 + - - +
172A GLU* 3.2 30.5 - - - +
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Residues in contact with LEU 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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31A THR 3.3 6.3 + - - -
32A PRO* 1.3 71.2 - - - +
34A ALA* 1.3 63.0 + - - +
36A LEU* 3.4 10.4 + - + +
37A PHE* 3.2 25.8 + - + +
438B PHE* 3.7 37.5 - - + -
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Residues in contact with ALA 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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32A PRO* 3.0 4.8 + - + +
33A LEU* 1.3 81.1 - - - +
35A ILE* 1.3 64.0 + - + +
37A PHE* 3.4 5.2 + - - +
38A MET* 3.0 31.3 + - + +
168A LEU* 4.0 19.7 - - + -
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Residues in contact with ILE 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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31A THR* 4.2 11.4 - - + -
32A PRO* 2.9 22.2 + - + +
34A ALA* 1.3 78.3 - - + +
36A LEU* 1.3 58.9 + - - +
38A MET* 3.4 5.5 + - - +
39A ALA* 2.9 28.8 + - - +
168A LEU* 5.2 4.3 - - + -
172A GLU* 3.6 31.4 - - + +
173A ALA* 3.7 37.9 - - + +
176A THR* 3.7 30.7 - - + +
177A LEU* 4.0 7.7 - - + +
217A ALA* 4.4 2.7 - - + -
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Residues in contact with LEU 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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31A THR* 3.6 39.5 - - + +
32A PRO 3.2 8.5 + - - +
33A LEU* 3.7 8.5 - - + +
34A ALA 3.3 0.2 - - - -
35A ILE* 1.3 78.2 - - - +
37A PHE* 1.3 61.5 + - - +
39A ALA* 3.4 17.4 - - - +
40A ALA* 3.4 8.0 + - - +
216A LYS* 4.1 14.6 - - + -
217A ALA* 3.9 18.6 - - + -
220A ILE* 4.2 21.3 - - + +
434B LEU* 3.7 14.1 - - + -
437B GLN* 4.3 5.8 - - - +
438B PHE* 3.5 32.5 - - + -
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Residues in contact with PHE 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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33A LEU* 3.2 20.7 + - + +
34A ALA* 3.8 4.5 - - - +
36A LEU* 1.3 76.4 - - - +
38A MET* 1.3 84.0 + - + +
40A ALA* 2.9 28.0 + - + +
41A VAL* 3.2 29.3 + - + +
166A PHE* 6.1 0.9 - + - -
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Residues in contact with MET 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 ALA* 3.0 21.3 + - + +
35A ILE* 4.0 3.1 - - - +
37A PHE* 1.3 106.2 - - + +
39A ALA* 1.3 56.2 + - - +
41A VAL* 3.5 10.9 - - + +
42A VAL* 2.9 33.8 + - - +
162A VAL* 4.1 13.2 - - + -
166A PHE* 3.6 48.5 - - + -
168A LEU* 3.6 21.5 - - + -
177A LEU* 3.9 21.5 - - + -
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Residues in contact with ALA 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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35A ILE 2.9 18.2 + - - +
36A LEU 3.4 8.7 - - - +
37A PHE 3.1 0.2 - - - -
38A MET* 1.3 77.6 - - - +
40A ALA* 1.3 55.3 + - - +
42A VAL* 3.6 2.2 + - - +
43A GLY 3.0 22.9 + - - -
177A LEU* 3.9 12.3 - - + -
180A THR* 4.1 9.2 + - + -
217A ALA* 3.4 35.4 - - + +
220A ILE* 4.6 1.3 - - + -
221A GLY* 3.3 13.7 - - - +
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Residues in contact with ALA 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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36A LEU 3.4 4.7 + - - +
37A PHE* 2.9 16.4 + - + +
39A ALA* 1.3 77.8 - - - +
41A VAL* 1.3 62.2 + - + +
44A THR* 2.8 31.1 + - - -
220A ILE* 4.0 21.1 - - + +
224A MET* 3.9 17.6 - - + +
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Residues in contact with VAL 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 PHE* 3.2 37.3 + - + +
38A MET* 3.2 17.7 + - + +
40A ALA* 1.3 75.4 - - + +
42A VAL* 1.3 67.0 + - - +
44A THR* 3.3 6.3 + - - -
45A LEU* 3.2 41.0 + - + +
162A VAL* 4.7 13.5 - - + -
166A PHE* 5.5 8.7 - - + -
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Residues in contact with VAL 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET 2.9 21.2 + - - +
39A ALA 3.8 4.0 - - - +
41A VAL* 1.3 76.6 - - - +
43A GLY* 1.3 64.6 + - - +
45A LEU* 3.3 1.8 + - - +
46A VAL* 3.0 32.6 + - + +
158A ILE* 4.8 3.1 - - + -
159A GLY* 3.8 26.7 - - - +
162A VAL* 3.7 33.7 - - + -
177A LEU* 4.1 13.5 - - + +
180A THR* 3.6 18.6 - - - +
181A GLY* 3.8 17.0 - - - +
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Residues in contact with GLY 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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39A ALA 3.0 15.4 + - - -
40A ALA 4.0 1.1 - - - -
42A VAL* 1.3 77.7 - - - +
44A THR* 1.3 61.8 + - - +
46A VAL* 3.4 0.5 + - - +
47A GLY 3.0 18.9 + - - -
184A ALA* 4.2 9.9 - - - -
221A GLY* 3.4 25.3 - - - -
224A MET* 4.2 0.2 - - - -
225A SER* 3.2 18.0 - - - -
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Residues in contact with THR 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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40A ALA 2.8 22.5 + - - -
41A VAL* 3.7 5.8 - - - -
42A VAL 3.3 0.2 - - - -
43A GLY* 1.3 75.8 - - - +
45A LEU* 1.3 68.4 + - + +
47A GLY* 3.3 2.1 + - - -
48A LEU* 3.1 33.7 + - + +
224A MET* 3.6 22.4 - - + +
228A MET* 3.7 32.6 - - + +
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Residues in contact with LEU 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 VAL* 3.2 31.9 + - + +
42A VAL 3.8 0.4 - - - +
44A THR* 1.3 81.9 - - + +
46A VAL* 1.3 58.0 + - - +
48A LEU* 3.4 14.8 + - + +
49A ALA* 2.9 30.4 + - - +
158A ILE* 3.7 29.1 - - + +
161A MET* 4.3 16.8 - - + -
162A VAL* 4.7 5.8 - - + -
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Residues in contact with VAL 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* 3.0 25.2 + - + +
43A GLY* 3.8 3.6 - - - +
45A LEU* 1.3 75.7 - - - +
47A GLY* 1.3 58.2 + - - +
49A ALA* 3.3 7.3 + - + +
50A ALA* 2.8 30.6 + - + +
151A THR 4.4 2.2 - - - +
154A ILE* 5.9 0.7 - - + -
155A GLY* 3.5 38.6 - - - +
158A ILE* 3.7 13.0 - - + -
181A GLY* 3.7 3.8 - - - +
184A ALA* 3.8 7.2 - - + +
185A GLY* 3.6 35.7 - - - +
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Residues in contact with GLY 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 GLY 3.0 12.3 + - - -
44A THR 3.3 3.3 + - - -
46A VAL* 1.3 76.2 - - - +
48A LEU* 1.3 51.4 + - - +
50A ALA* 3.0 3.3 + - - +
51A VAL* 2.7 43.1 + - - +
188A ALA* 4.4 4.9 - - - +
225A SER* 3.7 29.8 + - - -
228A MET* 4.1 3.1 - - - -
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Residues in contact with LEU 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 THR* 3.1 29.2 + - + +
45A LEU* 3.8 13.7 - - + +
47A GLY* 1.3 73.5 - - - +
49A ALA* 1.3 56.7 + - - +
51A VAL* 3.6 5.9 - - - +
52A ALA* 2.9 31.2 + - - +
228A MET* 3.6 26.6 - - + +
232A PHE* 4.2 24.5 - - + -
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Residues in contact with ALA 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 LEU 2.9 18.8 + - - +
46A VAL* 3.5 8.5 - - - +
48A LEU* 1.3 76.8 - - - +
50A ALA* 1.3 56.8 + - - +
52A ALA* 3.2 6.2 + - - +
53A PHE* 2.8 31.5 + - - +
132A PHE* 3.7 11.2 - - + -
154A ILE* 4.4 23.1 - - + -
158A ILE* 4.7 7.2 - - + -
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Residues in contact with ALA 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 2.8 23.1 + - + +
47A GLY 3.6 3.1 - - - +
49A ALA* 1.3 73.1 - - - +
51A VAL* 1.3 57.7 + - - +
53A PHE* 3.7 5.4 - - - +
54A ASP* 3.0 27.5 + - - +
151A THR* 3.7 31.8 - - + +
154A ILE* 6.6 0.2 - - - -
185A GLY 5.0 0.2 - - - +
188A ALA* 3.7 28.7 - - + +
189A ALA* 5.6 0.2 - - - -
229A TYR* 6.2 0.4 - - - -
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Residues in contact with VAL 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 GLY 2.7 26.4 + - - +
48A LEU* 3.6 8.1 - - - +
50A ALA* 1.3 72.7 - - + +
52A ALA* 1.3 59.8 + - - +
54A ASP* 3.2 6.0 + - - +
55A LYS* 2.9 42.8 + - + +
188A ALA* 5.8 0.2 - - + -
228A MET* 4.0 7.4 - - + +
229A TYR* 3.7 35.9 - - + -
232A PHE* 3.7 38.1 - - + -
233A ASN* 4.5 9.2 - - - +
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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 LEU 2.9 19.2 + - - +
49A ALA* 3.6 5.8 - - - +
51A VAL* 1.3 74.4 - - - +
53A PHE* 1.3 60.6 + - - +
55A LYS* 3.8 7.3 - - - +
56A GLY* 2.9 26.2 + - - -
132A PHE* 4.2 18.6 - - + -
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Residues in contact with PHE 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 ALA 2.8 17.2 + - - +
50A ALA* 3.7 7.9 - - - +
52A ALA* 1.3 78.1 - - - +
54A ASP* 1.3 58.3 + - + +
56A GLY 3.3 0.5 + - - -
57A VAL* 3.0 43.1 + - + +
131A LYS 4.3 1.8 - - - -
132A PHE* 3.6 36.3 - + + -
135A GLY* 3.8 9.6 - - - -
136A LEU* 3.5 28.6 - - + +
139A LEU* 3.5 33.0 - - + -
147A ARG* 3.9 16.6 - - + -
150A PRO* 3.6 31.4 - - + -
151A THR* 4.6 12.1 - - + -
154A ILE* 4.7 4.5 - - + -
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Residues in contact with ASP 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 ALA 3.0 18.6 + - - +
51A VAL* 3.5 6.5 - - - +
53A PHE* 1.3 76.9 - - + +
55A LYS* 1.3 79.5 + - - +
57A VAL* 3.4 2.1 + - - +
58A ALA* 3.1 23.5 + - - +
147A ARG* 2.7 48.9 + - - +
229A TYR* 4.6 9.9 + - + -
233A ASN* 3.9 11.8 + - - +
238A LEU* 5.7 3.6 - - - +
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Residues in contact with LYS 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 VAL* 2.9 27.7 + - + +
52A ALA* 3.8 7.4 - - - +
54A ASP* 1.3 89.1 + - - +
56A GLY* 1.3 61.0 + - - +
58A ALA* 3.6 6.2 + - + +
59A TRP* 3.2 22.7 + - - +
232A PHE* 4.0 27.1 - - + -
233A ASN* 3.0 33.3 + - - +
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Residues in contact with GLY 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 2.9 17.6 + - - -
53A PHE 3.7 1.3 - - - -
54A ASP 3.2 0.2 - - - -
55A LYS* 1.3 74.9 - - - +
57A VAL* 1.3 63.3 + - - +
59A TRP* 3.3 7.7 + - - +
60A LEU* 3.2 27.9 + - - +
136A LEU* 3.6 18.2 - - - -
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Residues in contact with VAL 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.0 44.0 + - + +
54A ASP* 3.9 4.5 - - - +
56A GLY* 1.3 74.7 - - - +
58A ALA* 1.3 64.2 + - - +
60A LEU 3.6 0.5 + - - -
61A GLN* 3.2 38.0 + - - +
136A LEU* 3.4 16.8 - - + +
139A LEU* 3.7 38.4 - - + -
140A GLY* 3.9 7.1 - - - -
147A ARG* 3.7 20.4 - - - +
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Residues in contact with ALA 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP* 3.1 19.1 + - - +
55A LYS* 3.7 7.6 - - + +
57A VAL* 1.3 78.2 - - - +
59A TRP* 1.3 57.3 + - - +
61A GLN* 3.2 13.4 + - - +
62A ASN* 2.9 30.5 + - - +
147A ARG* 4.7 2.9 - - - +
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Residues in contact with TRP 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS 3.2 14.5 + - - +
56A GLY* 3.3 7.4 + - - +
58A ALA* 1.3 79.2 - - - +
60A LEU* 1.3 95.9 + - + +
62A ASN* 3.0 10.8 + - - +
63A GLN* 2.8 72.7 + - + +
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Residues in contact with LEU 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY 3.2 16.9 + - - +
59A TRP* 1.3 104.4 - - + +
61A GLN* 1.3 63.5 + - - +
63A GLN* 3.9 4.1 - - + +
64A ARG* 3.1 29.1 + - - +
89A LEU* 4.1 28.0 - - + +
136A LEU* 3.2 42.2 - - + +
140A GLY* 3.9 17.0 - - - +
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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 VAL* 3.2 33.1 + - - +
58A ALA* 3.5 10.9 - - - +
60A LEU* 1.3 76.7 - - - +
62A ASN* 1.3 61.6 + - - +
64A ARG* 3.5 18.9 + - - +
65A MET* 3.3 21.8 + - - +
139A LEU 3.5 17.4 + - - +
140A GLY 3.4 17.5 - - - +
142A GLY* 4.3 9.5 - - - -
147A ARG* 4.6 6.9 + - - +
314A GLY* 5.5 6.7 - - - -
315A GLY 5.5 2.6 - - - +
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Residues in contact with ASN 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ALA 2.9 12.6 + - - +
59A TRP* 3.4 12.9 + - - +
61A GLN* 1.3 77.1 - - - +
63A GLN* 1.3 87.2 + - - +
64A ARG 3.2 0.2 - - - -
65A MET* 3.1 18.8 + - - +
66A GLY* 3.1 10.9 + - - -
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Residues in contact with GLN 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TRP* 2.8 72.5 + - + +
60A LEU* 3.4 6.0 + - + +
62A ASN* 1.3 93.5 - - - +
64A ARG* 1.3 63.6 + - + +
66A GLY* 3.2 2.8 + - - -
67A ALA* 3.0 23.4 + - - +
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Residues in contact with ARG 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU 3.1 13.1 + - - +
61A GLN* 3.5 21.5 + - - +
63A GLN* 1.3 78.9 - - + +
65A MET* 1.3 59.6 + - - +
67A ALA* 3.5 8.1 + - - +
68A LEU* 3.3 32.6 + - + +
82A ALA* 5.1 2.4 + - - +
85A CYS* 3.9 30.6 - - + -
86A SER* 3.2 24.6 + - - +
89A LEU* 4.2 10.8 - - + -
140A GLY 2.8 25.1 + - - -
141A GLY 3.0 22.6 + - - -
142A GLY* 3.3 10.3 - - - +
303A GLY* 4.2 12.1 + - - -
306A GLY* 6.1 1.6 - - - -
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Residues in contact with MET 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN 3.3 12.4 + - - +
62A ASN* 3.1 14.8 + - - +
64A ARG* 1.3 76.7 - - - +
66A GLY* 1.3 64.6 + - - +
68A LEU* 3.6 14.0 + - + +
69A VAL* 3.5 24.9 + - + +
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Residues in contact with GLY 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASN 3.1 12.0 + - - -
63A GLN* 3.2 3.6 + - - -
65A MET* 1.3 76.7 - - - +
67A ALA* 1.3 60.2 + - - +
69A VAL* 3.3 10.3 + - - +
70A HIS* 3.1 26.8 + - - +
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Residues in contact with ALA 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN 3.0 16.2 + - - +
64A ARG* 3.7 9.4 - - - +
65A MET 3.3 0.2 - - - -
66A GLY* 1.3 75.8 - - - +
68A LEU* 1.3 64.2 + - + +
70A HIS* 3.2 25.6 + - - +
71A THR* 3.4 12.3 + - - +
81A VAL* 4.2 14.3 - - + +
85A CYS* 4.6 13.2 - - - -
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Residues in contact with LEU 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.3 20.4 + - + +
65A MET* 3.8 15.0 - - + +
66A GLY 3.3 0.4 - - - -
67A ALA* 1.3 78.4 - - + +
69A VAL* 1.3 59.0 + - + +
71A THR* 3.2 7.9 + - - +
72A ALA* 3.1 24.6 + - - +
78A LEU* 3.6 29.4 - - + +
81A VAL* 3.6 24.9 - - + +
82A ALA* 3.7 15.7 - - + -
306A GLY 5.8 1.3 - - - +
307A PHE* 3.5 38.1 - - + -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 3.5 15.9 - - + +
66A GLY* 3.3 12.0 + - - +
67A ALA 3.2 0.4 - - - -
68A LEU* 1.3 75.8 - - + +
70A HIS* 1.3 64.0 + - - +
71A THR 3.0 3.1 + - - -
72A ALA* 3.2 23.0 + - + +
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Residues in contact with HIS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 3.1 13.8 + - - +
67A ALA* 3.2 17.5 + - - +
69A VAL* 1.3 76.0 - - - +
71A THR* 1.3 65.5 + - + +
72A ALA 3.6 0.6 + - - -
73A ASP* 4.6 2.1 - - - +
----------------------------------------------------------
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA 3.4 12.6 + - - +
68A LEU 3.2 6.2 + - - -
69A VAL 3.0 0.4 - - - -
70A HIS* 1.3 86.0 - - + +
72A ALA* 1.3 54.4 + - - +
73A ASP* 3.1 17.3 + - - +
74A ASN 4.0 2.9 + - - +
77A LEU* 4.0 29.6 - - + -
78A LEU* 3.1 35.9 + - - +
81A VAL* 4.3 15.9 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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