Contacts of the helix formed by residues 20 - 50 (chain A) in PDB entry 2B6V
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 ILE 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 2.8 21.1 + - + +
19A LEU* 1.4 83.0 - - + +
21A THR* 1.4 62.2 + - - +
23A GLN* 2.9 43.7 + - + +
24A ILE* 3.1 23.9 + - + +
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN* 4.0 19.5 - - + +
18A LEU* 3.0 11.3 + - + -
20A ILE* 1.4 81.4 - - - +
22A GLN* 1.3 69.7 + - + +
24A ILE* 3.1 16.4 + - - +
25A ILE* 3.1 31.1 + - - +
168A THR* 4.7 4.7 - - - +
274A ARG* 5.8 7.4 - - - +
275A TYR* 5.6 5.0 - - - -
278A GLU* 3.8 25.0 + - - +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 5.0 2.2 + - - -
14A CYS* 3.4 31.9 + - - +
15A SER* 4.7 0.6 - - - -
17A ASN* 2.9 28.3 - - - +
19A LEU* 3.2 18.2 + - - +
21A THR* 1.3 77.5 - - + +
23A GLN* 1.4 57.0 + - - +
25A ILE* 4.4 2.0 - - + -
26A PRO* 2.9 13.9 - - - +
82A SER* 2.8 39.6 - - - +
84A LEU 5.1 4.3 + - - +
85A GLY* 5.0 8.7 - - - -
168A THR* 3.2 35.1 + - - +
170A ILE* 4.5 12.7 - - + +
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.5 3.2 + - - +
20A ILE* 2.9 36.3 + - + +
22A GLN* 1.4 78.6 - - - +
24A ILE* 1.4 58.6 + - + +
26A PRO* 3.4 10.6 - - - +
27A VAL* 3.2 25.3 - - + +
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.5 30.7 - - + +
21A THR* 3.1 17.4 + - - +
23A GLN* 1.4 78.9 - - + +
25A ILE* 1.3 61.2 + - + +
27A VAL* 3.3 8.6 + - + +
28A LEU* 2.9 46.8 + - + +
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.1 17.1 + - - +
22A GLN* 4.4 2.5 - - - -
24A ILE* 1.3 79.7 - - + +
26A PRO* 1.4 56.3 - - - +
28A LEU* 3.1 7.9 + - - +
29A TYR* 2.8 49.1 + - + +
82A SER* 3.2 30.7 - - - +
168A THR* 4.0 17.9 - - + +
170A ILE* 3.8 11.4 - - + -
278A GLU* 3.2 38.1 - - + +
282A LEU* 4.1 16.2 - - + -
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Residues in contact with PRO 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 2.9 29.6 - - - +
23A GLN* 3.4 15.9 - - + +
25A ILE* 1.4 86.5 - - - +
27A VAL* 1.4 57.0 + - + +
29A TYR* 3.8 4.0 - - + +
30A CYS* 2.9 15.1 + - - +
79A LEU* 2.8 53.5 - - + +
82A SER* 3.5 15.5 - - - +
83A GLY* 4.1 8.5 - - - +
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 3.2 20.2 - - + +
24A ILE* 3.3 10.5 + - + +
25A ILE 3.1 0.4 - - - -
26A PRO* 1.4 77.1 - - + +
28A LEU* 1.4 69.8 + - + +
29A TYR 3.1 1.3 - - - -
30A CYS* 3.1 7.9 + - + +
31A MET* 3.0 42.1 + - + +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 2.9 37.2 + - + +
25A ILE* 3.5 10.5 - - + +
27A VAL* 1.4 80.7 - - + +
29A TYR* 1.4 59.4 + - - +
31A MET* 3.4 17.9 - - - +
32A VAL* 3.0 30.2 + - + +
282A LEU* 3.9 34.8 - - + -
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Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 2.8 32.8 + - + +
26A PRO* 4.1 7.0 - - + +
28A LEU* 1.4 76.8 - - - +
30A CYS* 1.3 59.4 + - - +
32A VAL* 3.5 29.8 - - + +
33A PHE* 2.9 30.0 + - - +
74A PHE* 3.5 13.6 - + - -
75A PRO* 4.4 7.5 - - + +
78A ILE* 3.2 50.3 - - + -
79A LEU* 4.5 8.7 - - + -
171A LYS* 4.1 10.9 - - + +
282A LEU* 3.6 29.8 + - + -
285A ALA* 3.0 34.1 - - + +
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Residues in contact with CYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO 2.9 19.5 + - - +
27A VAL* 3.1 10.3 + - + +
29A TYR* 1.3 76.5 - - - +
31A MET* 1.4 62.8 + - + +
33A PHE* 3.1 11.8 + - - +
34A ILE* 3.1 46.3 + - - +
79A LEU* 4.1 13.9 - - + +
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Residues in contact with MET 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.0 31.9 + - + +
28A LEU* 3.4 22.4 - - - +
30A CYS* 1.4 77.6 - - + +
32A VAL* 1.4 57.3 + - + +
34A ILE* 3.4 10.2 + - + +
35A ALA* 2.9 30.5 + - - +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.0 18.9 + - + +
29A TYR* 3.3 37.2 + - + +
31A MET* 1.4 71.5 - - - +
33A PHE* 1.3 60.1 + - - +
35A ALA* 4.4 4.5 - - - -
36A GLY* 2.8 32.1 + - - -
71A SER* 5.4 0.7 - - - -
75A PRO* 4.2 15.0 - - + -
282A LEU 6.1 0.4 - - - +
285A ALA* 4.7 5.2 - - + +
286A ALA* 5.1 9.6 - - + -
288A VAL* 3.8 29.4 - - + +
289A CYS* 5.8 2.9 - - - -
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR 2.9 19.5 + - - +
30A CYS* 3.1 11.9 + - - +
32A VAL* 1.3 75.1 - - - +
34A ILE* 1.3 65.3 + - + +
37A ILE* 3.0 61.8 + - + +
71A SER* 3.5 21.8 - - - -
72A LEU* 5.1 3.1 - - + -
75A PRO* 5.1 5.4 - - + -
76A PHE* 3.5 40.4 - + + -
79A LEU* 6.0 6.5 - - + -
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A CYS* 3.1 33.1 + - - +
31A MET* 3.7 10.1 - - + +
33A PHE* 1.3 83.3 - - + +
35A ALA* 1.4 64.4 + - - +
37A ILE* 3.5 13.7 - - + +
38A LEU* 3.4 23.1 - - + +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A MET 2.9 18.9 + - - +
32A VAL* 3.8 5.2 - - - +
34A ILE* 1.4 76.6 - - - +
36A GLY* 1.3 67.9 + - - +
38A LEU* 3.1 4.0 + - - +
39A LEU* 2.9 46.3 + - + +
289A CYS* 4.6 10.5 - - + -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL 2.8 19.8 + - - -
35A ALA* 1.3 72.6 - - - +
37A ILE* 1.4 62.0 + - - +
39A LEU* 5.0 0.7 - - - -
40A ASN* 3.0 43.2 + - - +
67A ASP 5.2 0.6 - - - +
68A PHE* 5.3 0.2 - - - -
71A SER* 4.7 5.6 - - - -
288A VAL* 3.9 15.3 - - - -
289A CYS* 4.6 8.4 - - - +
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.0 54.3 + - + +
34A ILE* 3.5 13.2 - - + +
36A GLY* 1.4 74.4 - - - +
38A LEU* 1.4 71.4 + - + +
41A GLY* 2.8 28.2 + - - -
68A PHE* 4.0 26.1 - - + -
71A SER* 3.2 26.6 - - - +
72A LEU* 4.7 1.3 - - + -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 3.4 20.4 - - + +
35A ALA* 3.1 3.8 + - - +
37A ILE* 1.4 83.4 - - + +
39A LEU* 1.3 73.2 + - + +
41A GLY* 3.3 1.0 + - - -
42A VAL* 2.9 44.1 + - + +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 2.9 28.2 + - + +
36A GLY* 4.4 0.9 - - - +
38A LEU* 1.3 84.7 - - + +
40A ASN* 1.4 62.8 + - - +
42A VAL* 3.5 6.2 + - - +
43A SER* 2.9 24.1 + - - -
289A CYS* 4.1 21.5 - - + +
292A PRO* 4.1 16.9 - - + +
293A ILE* 4.1 28.5 - - + -
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Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY* 3.0 30.6 + - - +
37A ILE 4.6 0.2 - - - +
39A LEU* 1.4 75.2 - - - +
41A GLY* 1.3 66.0 + - - +
43A SER* 2.9 10.9 + - - -
44A GLY 3.1 1.9 + - - -
63A ILE* 3.1 26.8 - - - +
64A VAL* 2.8 39.5 - - - +
67A ASP* 3.4 16.1 - - + +
68A PHE* 4.6 6.5 - - + +
288A VAL* 2.8 28.4 + - - +
289A CYS* 4.4 2.6 - - - +
292A PRO* 3.3 14.9 - - - +
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE 2.8 21.9 + - - -
38A LEU* 3.7 0.4 - - - -
40A ASN* 1.3 76.8 - - - +
42A VAL* 1.4 56.2 + - - +
44A GLY* 3.4 1.4 + - - -
45A TRP* 2.9 31.2 + - - +
64A VAL* 4.7 3.1 - - - -
68A PHE* 5.4 14.1 - - - -
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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
----------------------------------------------------------
38A LEU* 2.9 37.4 + - + +
39A LEU* 3.6 5.8 - - - +
41A GLY* 1.4 74.5 - - - +
43A SER* 1.4 65.7 + - - +
45A TRP* 3.0 19.6 + - + -
46A ILE* 2.9 36.3 + - + +
306A LEU* 3.4 42.0 - - + -
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 2.9 14.7 + - - -
40A ASN* 2.9 17.3 + - - -
42A VAL* 1.4 77.2 - - - +
44A GLY* 1.3 54.9 + - - +
46A ILE* 4.5 0.4 - - - -
47A PHE* 3.2 26.9 + - - +
60A LEU* 4.3 10.0 - - - +
64A VAL* 3.0 19.9 - - - +
292A PRO* 3.9 16.9 - - - +
302A PHE* 3.6 29.0 - - - -
306A LEU* 5.1 2.2 - - - -
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN 3.1 9.9 + - - -
41A GLY 3.8 1.3 - - - -
43A SER* 1.3 75.4 - - - +
45A TRP* 1.4 59.4 + - - +
47A PHE* 3.0 22.3 + - - +
48A PHE* 3.3 17.6 + - - +
61A LYS* 4.9 8.3 + - - -
64A VAL* 3.6 21.4 - - - +
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Residues in contact with TRP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 2.9 19.4 + - - +
42A VAL* 3.4 17.0 - - + +
44A GLY* 1.4 74.5 - - - +
46A ILE* 1.3 76.6 + - + +
48A PHE* 3.6 25.1 - + - -
49A TYR* 3.2 27.3 + - - +
309A LYS* 3.4 44.0 - - + +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 2.9 37.1 + - + +
43A SER 4.0 1.3 - - - +
45A TRP* 1.3 90.7 - - + +
47A PHE* 1.4 64.2 + - - +
48A PHE 3.5 0.3 + - - -
49A TYR* 3.7 12.3 + - - +
50A VAL* 4.1 10.9 + - - +
53A SER* 4.2 4.3 + - - +
302A PHE* 3.4 36.1 - - + -
305A ILE* 4.1 20.3 - - + +
306A LEU* 4.0 24.9 - - + +
309A LYS* 3.7 30.3 - - + -
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER 3.2 18.9 + - - +
44A GLY* 3.0 9.2 + - - +
46A ILE* 1.4 79.4 - - - +
48A PHE* 1.4 73.1 + - + +
50A VAL 3.2 13.7 - - - +
51A PRO* 4.5 2.8 - - - +
53A SER* 3.8 34.8 + - - -
54A LYS* 4.6 8.5 - - + -
57A ILE 3.4 25.6 - - - -
58A ILE* 4.0 20.4 - - + -
60A LEU* 5.5 0.9 - - + -
61A LYS* 3.2 51.8 - - + -
302A PHE* 4.8 8.1 - + + -
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.3 13.3 + - - -
45A TRP* 3.6 37.7 - + - -
47A PHE* 1.4 93.4 - - + +
49A TYR* 1.4 80.7 + + + +
50A VAL 3.7 5.4 - - - -
51A PRO* 3.7 10.9 - - - +
61A LYS* 5.1 3.6 - - - +
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Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.2 19.7 + - - +
46A ILE* 4.1 4.9 - - - +
47A PHE 3.4 1.6 - - - -
48A PHE* 1.4 98.6 - + + +
50A VAL* 1.4 76.7 + - + +
51A PRO* 3.4 7.6 - - - +
309A LYS* 3.2 46.1 - - + +
----------------------------------------------------------
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE 4.2 2.9 + - - +
47A PHE 3.2 16.3 - - - +
48A PHE 3.7 0.4 - - - -
49A TYR* 1.4 85.9 - - + +
51A PRO* 1.4 66.1 - - + +
52A SER* 2.9 31.3 + - - +
53A SER* 3.9 7.9 + - - +
305A ILE* 3.6 34.3 - - + -
----------------------------------------------------------
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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