Contacts of the helix formed by residues 5 - 36 (chain D) in PDB entry 1VLG
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 SER 5 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D MET* 3.9 0.7 - - - -
3D VAL 3.8 1.2 + - - -
4D ILE* 1.3 77.5 - - - +
6D GLU* 1.3 52.7 + - - +
7D LYS* 3.5 4.5 + - - -
8D VAL* 3.0 20.5 + - - +
9D ARG* 2.7 33.4 + - - +
113D GLU* 2.7 32.4 + - - -
115D ASP* 5.2 0.8 + - - -
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Residues in contact with GLU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D MET* 3.6 18.8 - - + +
5D SER* 1.3 72.5 - - - +
7D LYS* 1.3 58.4 + - - +
9D ARG* 3.2 41.4 + - - -
10D LYS* 2.8 34.6 + - + +
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Residues in contact with LYS 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D SER* 3.1 3.6 + - - +
6D GLU* 1.3 78.4 - - - +
8D VAL* 1.3 56.8 + - - +
10D LYS* 3.6 9.6 - - + +
11D ALA* 3.0 27.5 + - - +
109D LEU* 3.8 32.5 - - + +
113D GLU* 3.8 18.5 + - - +
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Residues in contact with VAL 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 4.1 5.6 - - + -
5D SER* 3.0 26.5 + - - +
7D LYS* 1.3 71.8 - - - +
9D ARG* 1.3 67.6 + - - +
11D ALA* 3.3 6.9 + - - +
12D LEU* 3.0 41.4 + - + +
106D ILE* 5.3 3.8 - - + -
109D LEU* 4.3 13.9 - - + -
110D ALA* 4.4 13.2 - - + +
113D GLU* 3.5 17.9 - - - +
115D ASP* 3.7 25.8 - - + +
118D THR* 3.9 11.9 - - + +
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Residues in contact with ARG 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D MET* 3.8 21.8 - - + -
4D ILE* 3.6 23.1 - - + +
5D SER 2.7 20.2 + - - +
6D GLU* 3.2 34.8 + - - +
8D VAL* 1.3 74.9 - - - +
10D LYS* 1.3 75.3 + - - +
12D LEU* 3.3 3.7 + - - +
13D ASN* 2.9 57.4 + - - +
63D ILE* 4.8 5.1 - - + +
68D GLY* 4.7 3.8 - - - -
69D ARG* 3.0 34.9 + - - +
70D VAL 4.2 0.2 - - - -
71D GLU* 3.7 16.6 + - - +
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Residues in contact with LYS 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLU* 2.8 28.7 + - + +
7D LYS* 3.6 10.3 - - + +
9D ARG* 1.3 86.6 - - - +
11D ALA* 1.3 57.5 + - - +
13D ASN* 3.7 1.2 - - - +
14D ASP* 2.6 70.1 + - - +
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Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LYS 3.0 17.3 + - - +
8D VAL 3.3 5.1 + - - +
10D LYS* 1.3 75.5 - - - +
12D LEU* 1.3 58.4 + - - +
14D ASP* 3.7 7.4 - - - +
15D GLN* 3.0 27.4 + - - +
18D ARG* 4.5 1.9 + - - -
106D ILE* 3.7 29.1 - - + +
109D LEU* 4.1 18.2 - - + -
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 4.0 16.2 - - + -
8D VAL* 3.0 38.9 + - + +
9D ARG 3.7 2.7 - - - +
11D ALA* 1.3 73.2 - - - +
13D ASN* 1.3 60.1 + - - +
15D GLN* 3.2 6.0 + - - +
16D LEU* 2.9 27.7 + - - +
59D PHE* 3.9 30.9 - - + -
62D TYR* 3.9 26.0 - - + -
63D ILE* 4.0 18.0 - - + +
106D ILE* 4.0 17.9 - - + -
118D THR* 4.0 11.2 - - + -
121D PHE* 4.5 6.3 - - + -
122D LEU* 4.5 4.3 - - + -
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Residues in contact with ASN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ARG* 2.9 45.4 + - - +
10D LYS* 3.8 3.6 - - - +
12D LEU* 1.3 73.7 - - - +
14D ASP* 1.3 70.3 + - - +
16D LEU* 3.3 3.9 + - - +
17D ASN* 3.1 33.0 + - - +
63D ILE* 3.8 10.2 - - + +
70D VAL* 3.3 18.5 - - - +
71D GLU* 3.0 42.4 + - - +
73D GLU* 5.0 4.8 + - - +
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Residues in contact with ASP 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LYS* 2.6 56.3 + - - +
11D ALA* 3.7 7.8 - - - +
13D ASN* 1.3 81.5 + - - +
15D GLN* 1.3 57.2 + - - +
17D ASN* 3.5 9.6 + - - +
18D ARG* 2.9 46.9 + - - +
73D GLU* 5.9 2.4 - - - +
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Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA 3.0 15.9 + - - +
12D LEU 3.2 7.6 + - - +
14D ASP* 1.3 73.9 - - - +
16D LEU* 1.3 66.4 + - - +
18D ARG* 2.9 41.3 + - - +
19D GLU* 2.9 52.8 + - - +
59D PHE* 3.4 28.7 - - + -
99D VAL* 3.7 16.8 + - - +
102D SER* 3.4 9.2 - - - -
103D ILE* 3.5 19.5 - - + +
106D ILE* 3.7 10.0 - - + +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 5.7 1.8 - - + -
12D LEU 2.9 13.8 + - - +
13D ASN* 3.4 9.6 - - - +
15D GLN* 1.3 75.0 - - - +
17D ASN* 1.3 66.5 + - - +
19D GLU* 3.1 10.3 + - - +
20D ILE* 3.0 36.8 + - + +
56D ALA* 3.6 16.9 - - + +
57D MET* 6.6 0.7 - - - -
59D PHE* 4.1 10.0 - - + -
60D TYR* 3.5 38.6 - - + +
63D ILE* 4.1 4.9 - - + -
70D VAL* 3.6 26.7 - - + -
72D LEU* 3.9 26.2 - - + -
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.3 13.5 + - - -
13D ASN* 3.1 27.3 + - - +
14D ASP* 3.6 10.6 + - - +
16D LEU* 1.3 85.5 - - - +
18D ARG* 1.3 61.1 + - - +
20D ILE* 3.4 6.8 + - - +
21D TYR* 3.1 20.3 + - - +
71D GLU 3.1 24.0 + - - -
72D LEU* 3.7 5.2 - - - +
73D GLU* 3.0 39.0 + - + +
74D ALA 5.3 0.3 - - - +
75D ILE* 5.9 0.7 - - - +
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Residues in contact with ARG 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA 4.5 2.6 + - - -
14D ASP* 2.9 29.3 + - - +
15D GLN* 2.9 53.8 + - - +
17D ASN* 1.3 75.1 - - + +
19D GLU* 1.3 57.1 + - - +
21D TYR* 3.2 8.9 + - + +
22D SER* 2.9 30.8 + - - -
95D HIS* 4.8 1.8 + - + -
98D PHE* 3.7 34.8 - - + -
99D VAL* 5.8 4.7 - - + -
102D SER* 3.6 21.4 + - - +
106D ILE* 5.1 2.8 - - - +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLN* 2.9 42.5 + - - +
16D LEU 3.1 6.5 + - - +
18D ARG* 1.3 73.5 - - - +
20D ILE* 1.3 60.7 + - - +
22D SER* 3.4 6.0 + - - -
23D SER* 3.0 26.5 + - - -
52D GLU* 3.0 14.5 - - - +
55D HIS* 3.4 11.9 + - - +
56D ALA* 3.8 20.2 - - + +
59D PHE* 3.8 24.3 - - + -
99D VAL* 3.8 9.1 - - - +
103D ILE* 4.4 2.3 - - - +
125D PHE* 4.8 3.3 - - - -
129D GLN* 5.4 0.2 - - - +
200D FE 2.3 31.2 - - - -
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Residues in contact with ILE 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.9 18.4 - - + +
27C LEU* 4.4 22.4 - - + -
16D LEU* 3.0 31.5 + - + +
17D ASN* 3.6 9.6 - - - +
19D GLU* 1.3 72.8 - - - +
21D TYR* 1.3 65.9 + - - +
23D SER* 3.3 8.0 + - - -
24D TYR* 3.1 20.9 + - + +
53D LEU* 4.1 17.7 - - + -
56D ALA* 3.9 17.0 - - + -
57D MET* 6.3 0.2 - - - -
72D LEU* 5.1 0.2 - - + -
75D ILE* 3.6 32.8 - - + -
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Residues in contact with TYR 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ASN 3.1 10.1 + - - +
18D ARG* 3.2 10.1 + - + +
20D ILE* 1.3 81.8 - - - +
22D SER* 1.3 54.2 + - - +
24D TYR* 3.1 4.0 + - + +
25D LEU* 2.8 47.4 + - + +
75D ILE* 4.0 18.1 - - + +
76D GLU* 3.5 40.2 - - + -
77D LYS 4.5 1.2 + - - -
78D PRO* 3.5 31.2 - - + +
79D PRO* 3.5 12.6 - - - +
95D HIS* 3.9 21.5 - + - -
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ARG 2.9 21.7 + - - -
19D GLU* 3.5 12.0 + - - -
20D ILE 3.3 0.2 - - - -
21D TYR* 1.3 71.5 - - - +
23D SER* 1.3 63.0 + - - +
25D LEU* 3.3 4.8 + - - +
26D TYR* 3.0 32.7 + - - -
52D GLU* 3.7 22.3 + - - -
95D HIS* 2.7 34.8 + - - -
96D GLU* 4.9 0.2 - - - -
99D VAL* 3.9 9.7 - - - +
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLU 3.0 13.9 + - - -
20D ILE 3.3 10.3 - - - -
22D SER* 1.3 74.6 - - - +
24D TYR* 1.3 58.7 + - - +
26D TYR 3.2 2.1 + - - -
27D LEU* 3.0 23.3 + - - +
49D ALA* 2.7 42.3 + - - +
52D GLU* 3.6 11.1 - - - +
53D LEU* 3.3 28.2 - - - +
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Residues in contact with TYR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN* 3.2 17.8 + - - -
20C ILE* 3.9 23.4 - - + +
72C LEU* 3.6 27.5 - - + +
73C GLU 2.6 31.7 + - - -
75C ILE* 3.3 19.9 - - + +
20D ILE* 3.1 11.7 + - + +
21D TYR* 3.5 10.3 - + + +
23D SER* 1.3 76.3 - - - +
25D LEU* 1.3 59.7 + - - +
27D LEU* 3.3 12.2 + - + +
28D SER* 2.9 29.8 + - - -
75D ILE* 3.8 20.6 - - + -
76D GLU 4.0 4.9 - - - -
78D PRO* 3.7 28.0 - - + +
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TYR* 2.8 34.4 + - + +
22D SER 3.6 4.3 - - - +
24D TYR* 1.3 73.6 - - - +
26D TYR* 1.3 63.0 + - + +
28D SER* 3.2 4.0 + - - -
29D MET* 2.9 42.7 + - + +
78D PRO* 4.1 9.9 - - + +
79D PRO* 3.8 30.5 - - + -
82D TRP* 4.1 17.3 - - + -
91D ALA* 5.3 1.1 - - + +
95D HIS* 3.7 44.0 - - + +
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Residues in contact with TYR 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D SER* 3.0 25.4 + - - -
23D SER 3.2 4.9 + - - +
25D LEU* 1.3 78.4 - - + +
27D LEU* 1.3 65.7 + - - +
29D MET* 3.2 11.7 + - + +
30D ALA 2.9 18.4 + - - -
44D TRP* 5.8 0.9 - + - -
45D MET* 3.5 47.5 - - - +
48D GLN* 3.5 19.7 - - + -
49D ALA 4.0 3.4 - - - +
52D GLU* 3.5 33.4 - - + -
92D ALA* 3.8 27.9 + - + +
95D HIS* 3.7 11.9 - + - -
96D GLU* 2.3 42.9 + - + +
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 5.6 1.8 - - + -
20C ILE* 4.4 19.1 - - + -
57C MET* 4.0 31.2 - - + -
60C TYR* 4.1 17.5 - - + -
72C LEU* 3.8 25.8 - - + -
23D SER 3.0 13.8 + - - +
24D TYR* 3.3 16.4 + - + +
26D TYR* 1.3 74.6 - - - +
28D SER* 1.3 57.8 + - - +
30D ALA* 3.1 8.0 + - + +
31D THR* 2.9 25.6 + - - +
45D MET 5.0 0.7 - - - -
46D LYS* 4.5 12.3 - - + -
49D ALA* 4.0 12.4 - - + +
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Residues in contact with SER 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 3.5 13.8 + - - +
24D TYR 2.9 13.8 + - - -
25D LEU 3.2 8.9 + - - -
27D LEU* 1.3 76.2 - - - +
29D MET* 1.3 60.4 + - - +
31D THR* 2.6 26.2 + - - -
32D TYR* 3.1 4.3 + - - +
78D PRO* 3.7 18.1 + - - +
79D PRO 2.6 28.6 + - - -
80D SER* 3.6 10.4 - - - +
82D TRP* 3.8 8.0 - - - -
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Residues in contact with MET 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 2.9 29.6 + - + +
26D TYR* 3.2 17.0 + - + +
28D SER* 1.3 71.5 - - - +
30D ALA* 1.3 65.1 + - - +
32D TYR* 3.1 4.6 + - - +
33D PHE* 2.9 32.2 + - + -
45D MET* 3.6 36.3 - - + +
82D TRP* 3.4 38.8 - - + -
88D ALA* 3.5 27.1 - - + +
91D ALA* 3.8 8.7 - - + -
92D ALA* 3.7 17.9 - - - +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 3.1 17.6 + - + +
26D TYR 2.9 13.0 + - - +
27D LEU* 3.1 13.0 + - + +
29D MET* 1.3 76.6 - - - +
31D THR* 1.3 57.2 + - - +
33D PHE 3.2 0.3 + - - -
34D ASP* 2.8 29.6 + - - +
42D ALA* 3.7 26.6 - - - +
45D MET* 3.8 9.9 - - + +
46D LYS* 3.9 15.0 - - + -
----------------------------------------------------------
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Residues in contact with THR 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 3.5 23.1 - - + -
64C TYR* 2.6 29.2 + - - -
69C ARG* 4.6 2.5 + - - -
70C VAL* 3.5 34.9 + - + +
71C GLU* 5.4 0.3 - - - -
72C LEU* 4.3 9.5 + - + +
27D LEU* 2.9 21.2 + - + +
28D SER* 2.6 27.9 + - - -
30D ALA* 1.3 75.8 - - - +
32D TYR* 1.3 56.6 + - - +
35D ALA* 3.1 19.4 + - - +
80D SER* 4.3 8.7 + - - -
----------------------------------------------------------
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Residues in contact with TYR 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ARG* 3.9 13.7 - - - +
28D SER 3.1 3.7 + - - +
29D MET 3.4 7.9 - - - +
30D ALA 3.1 0.4 - - - -
31D THR* 1.3 79.3 + - - +
33D PHE* 1.3 94.2 + + - +
35D ALA* 3.1 2.9 + - - +
36D GLU* 3.0 60.1 + - + +
80D SER 3.8 5.2 - - - +
81D ASN* 3.6 20.0 - - - -
82D TRP* 3.4 54.2 + + + -
83D ASN 4.1 0.2 - - - -
84D GLY* 3.2 39.4 + - - -
85D ILE* 4.1 2.0 + - + +
88D ALA* 4.5 3.1 - - + -
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Residues in contact with PHE 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D MET* 2.9 25.4 + - + +
32D TYR* 1.3 97.2 - + - +
34D ASP* 1.3 62.3 + - - +
36D GLU* 3.2 5.6 + - + +
37D GLY 3.0 4.9 + - - -
38D PHE* 2.9 46.4 + + + +
41D PHE* 3.6 34.3 - + + -
42D ALA* 3.7 7.6 - - - +
45D MET* 3.7 29.8 - - + -
85D ILE* 4.1 26.5 - - + -
88D ALA* 3.8 20.0 - - + -
89D PHE* 3.8 20.4 - + - -
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Residues in contact with ASP 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TYR* 2.5 26.7 + - - -
61C GLU* 4.9 3.0 - - - +
64C TYR* 3.6 35.2 - - + +
30D ALA 2.8 15.9 + - - +
33D PHE* 1.3 74.4 - - - +
35D ALA* 1.3 61.4 + - - +
37D GLY* 3.2 12.4 + - - +
38D PHE 4.8 1.3 - - - +
39D LYS* 4.0 22.6 - - - +
42D ALA* 3.4 14.6 - - - +
46D LYS* 2.9 25.3 + - - -
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C TYR* 3.6 10.1 - - + -
69C ARG* 3.5 42.4 - - + +
31D THR 3.1 19.6 + - - +
32D TYR 3.1 4.4 + - - +
34D ASP* 1.3 76.6 - - - +
36D GLU* 1.3 65.7 + - + +
37D GLY 3.6 0.5 + - - -
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 4.1 2.7 - - - +
145A LYS* 2.6 35.5 + - - -
69C ARG* 5.0 8.1 + - - -
32D TYR* 3.0 55.6 + - + +
33D PHE* 3.2 6.9 + - + +
35D ALA* 1.3 79.2 - - + +
37D GLY* 1.3 52.0 + - - +
38D PHE* 3.4 17.9 - - + -
81D ASN* 5.3 0.9 - - - +
----------------------------------------------------------
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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