Contacts of the helix formed by residues 23 - 49 (chain A) in PDB entry 3B60
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 PHE 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR 3.7 23.1 - - - -
20A ILE* 2.7 12.6 + - - +
21A ALA 2.6 4.8 + - - -
22A PRO* 1.3 85.8 - - + +
24A LYS* 1.3 54.5 + - - -
25A ALA 3.0 11.7 + - - -
26A GLY 3.1 10.7 + - - -
91A TRP* 3.1 36.6 - + + -
92A VAL* 3.7 21.2 - - + +
95A LYS* 3.5 37.9 - - + -
96A VAL* 3.9 20.2 - - + -
99A THR* 4.0 17.3 - - + -
238B ARG* 6.1 0.9 - - - -
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Residues in contact with LYS 24 (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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17A TRP* 4.5 30.3 - - + +
20A ILE* 3.2 5.6 + - + +
21A ALA* 2.6 36.1 + - - +
22A PRO 3.6 0.8 - - - -
23A PHE* 1.3 65.0 - - - +
25A ALA* 1.3 66.2 + - + +
26A GLY 3.0 2.9 - - - -
27A LEU* 3.0 30.9 + - + +
28A ILE* 3.1 15.6 + - - +
92A VAL* 5.4 0.7 - - - -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO 5.3 1.5 + - - +
23A PHE* 3.0 3.9 + - - +
24A LYS* 1.3 81.4 - - - +
26A GLY* 1.3 59.0 + - - +
28A ILE* 3.3 8.3 - - - +
29A VAL* 3.0 35.2 + - + +
88A CYS* 4.4 1.3 - - - -
91A TRP* 5.2 7.6 - - + -
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Residues in contact with GLY 26 (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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23A PHE 3.1 9.5 + - - -
24A LYS 3.0 0.6 - - - -
25A ALA* 1.3 79.6 - - - +
27A LEU* 1.3 63.8 + - - +
29A VAL 3.4 0.2 + - - -
30A ALA* 3.0 27.6 + - - +
88A CYS* 3.2 36.3 - - - +
91A TRP* 4.0 9.8 - - - -
92A VAL* 4.6 2.7 - - - -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TRP* 5.1 12.3 - - + +
20A ILE* 5.4 7.4 - - + -
23A PHE 4.1 2.4 + - - +
24A LYS* 3.0 25.1 + - + +
26A GLY* 1.3 76.5 - - - +
28A ILE* 1.3 67.3 + - + +
30A ALA* 3.7 4.7 - - - +
31A GLY* 3.1 18.0 + - - -
92A VAL* 4.7 12.6 - - + +
143A LEU* 4.9 22.0 - - + -
144A ILE* 6.6 0.4 - - + -
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS 3.1 10.4 + - - +
25A ALA* 3.3 18.2 - - - +
27A LEU* 1.3 85.3 - - + +
29A VAL* 1.3 74.7 + - + +
31A GLY* 2.9 18.7 + - - -
32A ILE* 3.0 34.8 + - + +
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.0 21.6 + - + +
28A ILE* 1.3 87.4 - - + +
30A ALA* 1.3 58.4 + - - +
32A ILE* 3.8 8.8 + - + +
33A ALA 3.3 14.4 + - - -
84A ILE* 3.5 15.9 - - + +
87A TYR* 3.2 35.7 - - + +
88A CYS* 3.3 15.0 - - - -
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Residues in contact with ALA 30 (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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26A GLY 3.0 18.2 + - - +
27A LEU* 3.7 4.7 - - - +
29A VAL* 1.3 76.2 - - - +
31A GLY* 1.3 59.9 + - - +
32A ILE 3.3 0.2 - - - -
33A ALA* 3.3 8.5 + - - +
34A LEU* 3.1 24.4 + - - +
84A ILE 4.5 2.7 - - - -
85A SER* 4.1 19.7 + - - +
88A CYS* 4.2 10.8 - - + -
89A ILE* 4.3 11.9 - - + +
144A ILE* 5.4 9.6 - - + -
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Residues in contact with GLY 31 (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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27A LEU* 3.1 11.6 + - - -
28A ILE* 2.9 7.5 + - - -
30A ALA* 1.3 73.8 - - - +
32A ILE* 1.3 57.4 + - - +
34A LEU* 3.3 11.1 - - - +
35A ILE* 2.8 40.6 + - - +
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Residues in contact with ILE 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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28A ILE* 3.0 35.2 + - + +
29A VAL* 4.0 8.5 - - + +
31A GLY* 1.3 75.6 - - - +
33A ALA* 1.3 64.8 + - - +
34A LEU 3.2 0.2 - - - -
35A ILE* 3.5 11.4 + - + +
36A LEU* 3.1 39.2 + - + +
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Residues in contact with ALA 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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29A VAL 3.3 4.4 + - - +
30A ALA 3.4 7.4 - - - +
32A ILE* 1.3 78.6 - - - +
34A LEU* 1.3 65.8 + - - +
36A LEU* 3.5 4.6 + - - -
37A ASN* 3.2 4.2 + - - +
81A THR* 2.7 31.8 - - - +
84A ILE* 3.3 38.1 - - + +
85A SER* 3.4 21.5 - - - +
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Residues in contact with LEU 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 ALA 3.1 12.7 + - - +
31A GLY* 3.3 15.7 - - - +
33A ALA* 1.3 76.9 - - - +
35A ILE* 1.3 69.8 + - + +
37A ASN* 2.9 18.3 + - + +
38A ALA* 3.1 12.4 + - + +
85A SER* 4.3 4.0 + - - +
144A ILE* 5.3 3.6 - - + +
148A ARG* 4.2 46.0 - - + +
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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 GLY* 2.8 26.4 + - - +
32A ILE* 3.6 16.4 - - + +
34A LEU* 1.3 87.1 - - + +
36A LEU* 1.3 70.3 + - + +
38A ALA* 2.7 36.3 + - + +
39A ALA* 3.1 6.6 + - + +
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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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32A ILE* 3.1 37.3 + - + +
33A ALA* 3.9 3.8 - - - +
34A LEU 3.3 0.2 - - - -
35A ILE* 1.3 92.7 - - + +
37A ASN* 1.3 62.8 + - - +
39A ALA* 3.5 9.8 + - + +
40A SER* 3.1 20.6 + - - -
77A LEU* 4.7 22.0 - - + +
81A THR* 3.7 20.4 + - - +
84A ILE* 6.5 0.4 - - + -
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Residues in contact with ASN 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 ALA 3.2 4.8 + - - +
34A LEU* 2.9 14.7 + - + +
36A LEU* 1.3 74.7 + - - +
38A ALA* 1.3 61.4 + - - +
40A SER* 3.2 3.7 + - - -
41A ASP* 2.6 36.1 + - - +
77A LEU 3.7 3.0 + - - -
78A ARG* 3.7 43.4 + - - +
81A THR* 3.0 38.0 - - + +
82A SER* 4.4 7.4 + - - -
85A SER* 5.4 1.6 + - - -
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Residues in contact with ALA 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 LEU* 3.1 11.8 + - + +
35A ILE* 2.7 21.2 + - + +
37A ASN* 1.3 79.3 - - - +
39A ALA* 1.3 58.7 + - - +
41A ASP* 3.0 26.7 + - - +
42A THR* 3.3 13.0 + - - +
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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* 3.1 7.5 + - + +
36A LEU* 3.8 11.9 - - + +
37A ASN 3.3 0.2 - - - -
38A ALA* 1.3 73.5 - - - +
40A SER* 1.3 63.6 + - - +
41A ASP 3.0 5.3 + - - -
42A THR* 2.8 27.8 + - - +
43A PHE* 3.3 18.2 - - + -
77A LEU* 5.1 6.5 - - + -
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Residues in contact with SER 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 3.1 14.8 + - - -
37A ASN* 3.4 15.0 - - - -
38A ALA 3.2 0.2 - - - -
39A ALA* 1.3 76.2 - - - +
41A ASP* 1.3 58.2 + - - +
43A PHE* 4.1 4.3 - - - +
44A MET* 2.9 40.5 + - - +
73A GLY 4.3 6.2 + - - -
74A LEU* 5.0 0.3 - - - -
77A LEU* 3.9 30.7 - - - +
78A ARG* 3.2 25.0 + - - +
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Residues in contact with ASP 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 ASN* 2.6 26.6 - - - +
38A ALA* 3.2 13.6 - - - +
39A ALA 3.0 0.6 - - - -
40A SER* 1.3 76.0 - - - +
42A THR* 1.3 67.1 + - + +
43A PHE 3.1 1.8 - - - -
44A MET* 3.8 3.2 - - - +
45A LEU* 3.0 25.9 + - - +
78A ARG* 2.7 27.6 + - - +
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Residues in contact with THR 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 ALA 3.6 12.6 - - - +
39A ALA* 2.8 22.2 + - - -
41A ASP* 1.3 77.3 - - + +
43A PHE* 1.3 71.2 + - - +
45A LEU* 3.7 9.1 + - - +
46A SER* 2.9 29.8 + - - -
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Residues in contact with PHE 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* 3.3 18.9 + - + +
40A SER* 4.3 4.0 - - - +
41A ASP 3.1 0.4 - - - -
42A THR* 1.3 95.4 + - - +
44A MET* 1.3 74.9 + - + +
45A LEU 3.1 2.0 - - - -
46A SER* 3.0 31.3 + - - +
47A LEU* 3.6 5.9 + - - +
69A LEU* 6.2 3.8 - - + -
77A LEU* 6.1 4.7 - - + -
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Residues in contact with MET 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 SER* 2.9 25.9 + - - +
41A ASP* 3.2 5.6 + - - +
43A PHE* 1.3 90.8 - - + +
45A LEU* 1.3 58.5 + - - +
47A LEU* 5.8 3.6 - - + -
48A LEU* 2.8 44.8 + - + +
69A LEU 4.7 7.0 - - - +
70A VAL* 4.2 25.4 - - + +
73A GLY* 4.6 24.2 - - - -
74A LEU* 4.7 12.1 - - + +
78A ARG* 3.6 18.4 - - - +
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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 ASP 3.0 17.2 + - - +
42A THR* 3.8 8.1 - - - +
44A MET* 1.3 73.8 - - - +
46A SER* 1.3 62.4 + - - +
47A LEU 3.0 11.2 + - - -
48A LEU* 3.8 4.0 + - - +
49A LYS* 3.9 13.0 + - + +
50A PRO* 3.8 14.2 - - - +
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Residues in contact with SER 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 THR 2.9 19.9 + - - -
43A PHE* 3.0 15.4 + - - +
45A LEU* 1.3 79.1 - - - +
47A LEU* 1.3 65.4 + - - +
50A PRO* 4.6 8.6 - - - +
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Residues in contact with LEU 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 PHE 3.6 8.7 + - - +
44A MET* 5.2 3.4 - - + -
45A LEU 3.0 2.8 + - - -
46A SER* 1.3 80.9 - - - +
48A LEU* 1.3 80.9 + - + +
49A LYS 3.6 1.1 - - - -
50A PRO* 3.6 9.2 - - + +
51A LEU* 3.3 47.2 + - + +
62A SER* 4.8 6.1 - - - +
66A TRP* 3.7 44.0 - - + +
70A VAL* 5.5 9.2 - - + -
267B LEU* 4.4 10.3 - - + -
288B PHE* 5.5 0.9 - - + -
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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 MET* 2.8 47.0 + - + +
45A LEU* 4.9 1.8 - - - +
47A LEU* 1.3 87.9 - - + +
49A LYS* 1.3 64.0 + - - +
52A LEU* 3.3 21.8 + - - +
70A VAL* 4.8 8.3 - - + -
263B LEU* 5.2 4.3 - - + -
288B PHE* 3.4 41.4 - - + -
292B ILE* 3.1 42.2 - - + -
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Residues in contact with LYS 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* 3.9 17.2 + - + +
48A LEU* 1.3 74.1 - - - +
50A PRO* 1.3 81.9 - - + +
52A LEU* 2.7 39.1 - - + +
53A ASP* 3.8 26.4 + - - +
54A ASP* 5.7 1.6 - - - +
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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