Contacts of the helix formed by residues 11 - 34 (chain B) in PDB entry 3ABD
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 11 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 3.1 46.7 - - + +
122A LEU* 4.7 7.6 - - + -
124A ALA* 5.2 3.6 - - + -
125A ALA* 4.3 20.6 - - + -
128A LEU* 4.9 7.6 - - + -
10B ASN* 1.3 82.7 + - - +
12B GLY* 1.3 56.7 + - - +
14B VAL* 3.2 16.2 + - + -
15B VAL* 2.9 31.2 + - + +
104B GLN* 5.5 0.4 - - - -
107B LEU* 2.6 40.1 - - + +
110B ILE* 4.2 16.4 - - + -
196B ILE* 4.2 17.9 - - + -
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Residues in contact with GLY 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 3.3 1.0 + - - -
10B ASN* 2.9 17.4 + - - -
11B PHE* 1.3 75.1 - - - +
13B GLN* 1.3 59.7 + - - +
15B VAL* 4.1 0.4 - - - +
16B ALA* 2.9 32.2 + - - +
75B LEU 4.6 0.5 - - - +
76B GLU* 3.7 25.5 - - - -
104B GLN* 4.4 13.0 - - - -
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP 5.5 0.2 - - - +
114A SER* 4.1 22.6 - - - +
117A SER* 3.4 27.5 + - - +
118A HIS* 3.9 13.5 - - - +
121A GLN* 3.0 17.0 + - - +
12B GLY* 1.3 75.2 - - - +
14B VAL* 1.3 63.7 + - - +
16B ALA* 4.6 3.0 - - - +
17B ASP* 2.9 65.4 + - - +
72B LYS* 4.5 11.3 - - - +
76B GLU* 3.8 21.4 - - + +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 3.8 37.2 - - + +
121A GLN* 3.6 18.6 - - + +
122A LEU* 4.0 17.3 - - + -
11B PHE* 3.2 16.9 + - + +
13B GLN* 1.3 77.1 - - - +
15B VAL* 1.3 64.7 + - - +
17B ASP* 3.3 2.1 + - - +
18B VAL* 2.9 28.4 + - + +
116B LEU* 3.7 29.8 - - + -
196B ILE* 4.6 13.2 - - + -
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE 2.9 23.9 + - - +
12B GLY 4.1 0.9 - - - +
14B VAL* 1.3 73.4 - - - +
16B ALA* 1.3 57.9 + - - +
18B VAL* 3.2 5.8 + - + +
19B LEU* 2.8 53.0 + - + +
104B GLN* 3.7 36.1 - - + +
196B ILE* 3.5 47.1 - - + +
197B LEU* 4.3 11.7 - - + -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 2.9 22.7 + - - +
13B GLN* 3.9 4.3 - - - +
15B VAL* 1.3 73.2 - - - +
17B ASP* 1.3 58.3 + - - +
19B LEU* 4.1 0.2 - - - +
20B CYS* 2.9 36.7 + - - -
72B LYS* 3.7 32.8 - - + +
75B LEU* 3.8 14.7 + - + +
76B GLU* 3.8 15.7 - - + +
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP 4.4 8.5 + - - -
114A SER 4.6 2.4 - - - +
115A LEU* 5.6 0.3 - - - +
118A HIS* 2.7 41.9 + - + +
13B GLN* 2.9 41.5 + - - +
14B VAL 3.7 1.3 - - - +
16B ALA* 1.3 75.2 - - - +
18B VAL* 1.3 62.3 + - - +
20B CYS* 3.5 1.4 + - - +
21B GLU* 3.1 25.8 + - - +
72B LYS* 3.0 26.5 + - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 5.0 6.3 - - + -
14B VAL* 2.9 31.2 + - + +
15B VAL* 3.7 5.8 - - + +
17B ASP* 1.3 74.5 - - - +
19B LEU* 1.3 66.3 + - + +
21B GLU* 3.3 10.2 + - - +
22B PHE* 3.0 26.5 + - - +
48B TYR* 4.2 2.1 + - - +
116B LEU* 4.5 19.3 - - + -
119B VAL* 4.0 16.6 - - + -
120B GLU* 5.4 10.1 - - + +
123B LEU* 4.0 22.9 - - + -
196B ILE* 6.1 3.8 - - + -
197B LEU* 5.4 3.1 - - + -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 2.8 30.9 + - + +
16B ALA 4.1 2.0 - - - +
18B VAL* 1.3 76.3 - - + +
20B CYS* 1.3 56.6 + - - +
22B PHE* 3.6 10.4 - - + +
23B LEU* 2.8 40.2 + - + +
75B LEU* 4.1 20.0 - - + -
102B ILE* 4.1 25.4 - - + -
104B GLN* 5.1 0.2 - - - +
123B LEU* 5.2 2.0 - - + -
197B LEU* 3.8 44.2 - - + -
199B MET* 3.9 25.1 - - + -
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Residues in contact with CYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA 2.9 22.5 + - - +
17B ASP 4.1 1.8 - - - +
19B LEU* 1.3 72.9 - - - +
21B GLU* 1.3 66.9 + - - +
23B LEU* 4.5 4.0 - - - +
24B GLU* 3.1 24.1 + - - +
68B LEU* 3.7 42.0 - - + +
71B VAL* 5.0 0.7 - - - -
72B LYS* 3.8 28.3 - - - -
75B LEU* 3.7 20.9 - - - -
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASP 3.1 19.0 + - - +
18B VAL* 3.6 9.5 - - - +
20B CYS* 1.3 81.5 - - - +
22B PHE* 1.2 63.0 + - - +
24B GLU* 3.4 10.1 + - - +
25B VAL* 3.4 25.9 + - + +
47B LYS* 5.7 5.8 + - + +
48B TYR* 3.7 15.1 - - + +
120B GLU* 4.9 8.9 - - - +
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Residues in contact with PHE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL 3.0 15.6 + - - +
19B LEU* 3.6 9.0 - - + +
21B GLU* 1.2 79.9 - - - +
23B LEU* 1.3 67.7 + - + +
25B VAL* 3.2 2.6 + - - +
26B ALA* 2.8 32.9 + - + +
48B TYR* 3.1 27.5 + + - +
100B PHE* 3.7 28.7 - + - -
123B LEU* 3.7 39.3 - - + -
126B PHE* 3.7 20.6 - + + -
127B ILE* 3.7 21.5 - - + -
130B ILE* 5.5 0.2 - - + -
199B MET* 3.6 28.3 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 2.8 35.4 + - + +
20B CYS* 4.2 0.9 - - - +
22B PHE* 1.3 81.8 - - + +
24B GLU* 1.3 57.3 + - - +
26B ALA* 3.9 2.2 - - - +
27B VAL* 2.8 40.0 + - + +
68B LEU* 4.0 27.6 - - + -
71B VAL* 5.6 0.7 - - + -
75B LEU* 5.0 7.9 - - + -
83B VAL* 4.2 30.7 - - + -
100B PHE* 3.9 47.1 - - + -
102B ILE* 5.1 6.5 - - + -
199B MET* 5.7 0.2 - - - -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B CYS 3.1 19.6 + - - +
21B GLU* 3.6 10.7 - - - +
22B PHE 3.1 0.2 - - - -
23B LEU* 1.3 77.8 - - - +
25B VAL* 1.3 65.3 + - + +
27B VAL* 3.8 1.2 - - - +
28B HIS* 3.1 47.5 + - + +
54B MET* 4.4 12.5 - - + +
61B ASN* 4.9 3.6 - - - +
64B ILE* 4.3 9.7 - - + +
65B GLN* 4.5 25.2 + - - +
68B LEU* 3.5 15.6 - - + +
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 3.5 17.3 - - + +
22B PHE 3.2 6.8 + - - +
24B GLU* 1.3 76.8 - - + +
26B ALA* 1.3 58.5 + - - +
28B HIS* 3.3 3.3 + - - +
29B LEU* 2.9 27.7 + - + +
47B LYS* 4.0 35.4 - - + -
48B TYR* 4.4 10.8 - - + +
52B VAL* 3.9 32.1 - - + -
53B GLN 4.9 0.3 - - - +
54B MET* 4.1 18.0 - - + +
127B ILE* 4.0 14.6 - - + -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 2.8 20.9 + - + +
23B LEU* 3.9 6.5 - - + +
25B VAL* 1.3 76.3 - - - +
27B VAL* 1.3 56.4 + - - +
29B LEU* 3.3 3.3 + - - +
30B ILE* 2.8 36.8 + - - +
100B PHE* 4.0 22.2 - - + -
127B ILE* 4.3 13.4 - - + +
130B ILE* 3.9 21.1 - - + -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 2.8 32.3 + - + +
24B GLU 3.8 2.9 - - - +
26B ALA* 1.3 68.9 - - + +
28B HIS* 1.3 68.6 + - - +
30B ILE* 3.2 8.8 + - - +
31B LEU* 2.9 46.4 + - + +
64B ILE* 4.0 26.9 - - + -
68B LEU* 5.3 6.1 - - + -
83B VAL* 6.3 1.8 - - + -
85B VAL* 3.9 24.9 - - + -
100B PHE* 6.1 0.7 - - + -
146B PHE* 4.4 11.9 - - + -
148B VAL* 5.0 9.9 - - + -
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.1 37.9 + - + +
25B VAL 3.5 8.3 - - - +
27B VAL* 1.3 77.1 - - - +
29B LEU* 1.3 63.9 + - - +
31B LEU* 3.3 6.5 + - + +
32B TYR* 3.1 18.2 + - - +
42B PHE* 3.5 11.3 - + - -
53B GLN 3.7 12.1 - - - +
54B MET* 3.5 28.0 - - + +
55B SER* 2.8 38.2 + - - -
61B ASN* 3.2 29.5 + - + -
64B ILE* 3.7 26.1 - - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL 2.9 17.6 + - - +
26B ALA* 3.7 5.6 - - - +
27B VAL 3.2 0.2 - - - -
28B HIS* 1.3 73.6 - - - +
30B ILE* 1.3 60.2 + - - +
32B TYR* 3.4 4.7 + - + +
33B VAL* 2.8 42.8 + - + +
51B PRO 5.5 0.2 - - - +
52B VAL* 4.6 7.6 - - + -
53B GLN* 3.9 34.5 + - + +
127B ILE* 3.7 34.3 - - + +
130B ILE* 3.7 17.9 - - + -
131B SER* 3.3 25.6 - - - +
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 2.8 28.4 + - - +
27B VAL* 3.6 4.3 - - - +
29B LEU* 1.3 71.5 - - - +
31B LEU* 1.3 66.6 + - + +
33B VAL* 4.2 6.5 - - - -
34B ARG* 3.0 29.3 + - + +
85B VAL* 4.0 30.7 - - + -
87B ILE* 4.2 6.5 - - + -
98B PHE* 3.7 57.7 - - + -
100B PHE* 4.2 13.0 - - + -
130B ILE* 3.9 18.6 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 2.9 35.1 + - + +
28B HIS* 3.7 6.5 - - + +
30B ILE* 1.3 82.7 - - + +
32B TYR* 1.3 60.0 + - - +
35B GLU* 3.4 1.7 + - - -
36B VAL* 2.9 47.6 + - + +
37B TYR* 3.9 18.3 + - + -
42B PHE* 4.0 11.9 - - + -
60B LEU* 4.5 5.2 - - + -
64B ILE* 4.0 14.8 - - + -
85B VAL* 5.1 2.5 - - + -
87B ILE* 5.6 0.2 - - + -
146B PHE* 3.5 51.4 - - + -
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS 3.1 12.5 + - - +
29B LEU* 3.5 9.4 - - + +
31B LEU* 1.3 75.2 - - - +
33B VAL* 1.3 77.8 + - + +
35B GLU* 3.0 22.2 + - - +
37B TYR 5.1 1.0 - - - +
39B VAL* 4.1 29.9 - - + +
42B PHE* 3.6 41.6 - + + -
53B GLN* 3.5 44.0 + - + -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.8 36.1 + - + +
30B ILE* 4.0 3.6 - - - +
32B TYR* 1.3 93.5 - - + +
34B ARG* 1.3 89.4 + - + +
35B GLU* 3.2 1.5 + - - +
98B PHE* 5.6 0.2 - - + -
130B ILE* 3.6 26.2 - - + +
131B SER* 4.0 20.9 - - - +
133B CYS* 3.9 8.3 - - - -
134B ASP* 4.3 15.0 - - - +
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.0 21.4 + - + +
33B VAL* 1.3 103.8 + - + +
35B GLU* 1.3 67.5 + - - +
36B VAL* 3.4 5.2 + - + +
87B ILE* 3.6 23.8 - - + -
96B GLU* 2.8 39.9 + - - +
98B PHE* 3.8 19.3 - - + -
133B CYS* 4.3 1.1 - - - -
134B ASP* 3.8 23.2 - - - +
137B LEU* 3.5 18.4 + - - +
138B ASP 2.9 23.6 + - - -
139B HIS* 4.3 5.7 + - - +
140B ASN* 3.6 30.4 + - - +
144B CYS* 6.0 0.7 - - - +
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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