Contacts of the helix formed by residues 2 - 26 (chain A) in PDB entry 1V9P
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 THR 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 70.6 - - - +
3A ARG* 1.3 56.0 + - - +
4A GLU* 2.6 15.8 + - + +
5A GLU* 2.5 53.1 + - + +
6A ALA 3.1 8.0 + - - -
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Residues in contact with ARG 3 (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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1A MET 3.3 5.5 + - - -
2A THR* 1.3 71.8 + - - +
4A GLU* 1.3 63.8 + - - +
6A ALA* 3.6 1.4 + - - -
7A ARG 3.4 2.3 + - - -
51A PHE* 4.4 19.4 - - + -
53A GLU* 3.4 38.2 + - - +
54A PHE* 3.3 31.3 - - + -
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Residues in contact with GLU 4 (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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2A THR* 2.6 18.3 + - + +
3A ARG* 1.3 72.4 - - - +
5A GLU* 1.3 66.9 + - - +
7A ARG* 2.9 57.9 + - - +
8A ARG* 3.3 24.9 + - - +
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 2.8 47.4 - - + +
2A THR* 2.5 29.7 + - + +
4A GLU* 1.3 75.2 - - - +
6A ALA* 1.3 61.6 + - - +
8A ARG* 3.0 25.2 + - + +
9A ARG* 3.0 14.0 + - + +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.8 20.3 - - + +
2A THR 3.1 3.4 + - - +
3A ARG 3.8 8.7 - - - +
5A GLU* 1.3 78.3 - - - +
7A ARG* 1.3 62.3 + - - +
9A ARG 3.6 0.5 + - - -
10A ILE* 2.9 31.1 + - + +
47A LEU* 4.0 3.9 - - + +
51A PHE* 3.7 44.9 - - + -
54A PHE* 3.8 6.3 - - + -
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Residues in contact with ARG 7 (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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3A ARG 3.9 0.2 - - - +
4A GLU* 2.9 51.8 + - - +
6A ALA* 1.3 78.8 - - - +
8A ARG* 1.3 55.9 + - - +
10A ILE* 2.9 7.3 + - + +
11A ASN* 2.6 49.9 + - - +
54A PHE* 3.2 40.3 - - + -
129A GLU* 2.5 40.6 + - - +
130A GLU* 2.8 36.5 + - - +
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Residues in contact with ARG 8 (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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4A GLU* 3.8 26.9 + - - +
5A GLU* 3.0 15.1 + - + +
7A ARG* 1.3 83.2 - - - +
9A ARG* 1.3 52.7 + - - +
11A ASN* 2.8 12.6 + - - +
12A GLU* 2.7 54.1 + - - +
130A GLU* 3.8 43.2 + - + +
132A VAL* 6.5 0.2 - - - -
167A ASP* 5.7 0.6 + - - -
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Residues in contact with ARG 9 (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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1A MET* 4.6 7.2 - - + -
5A GLU* 3.0 11.9 + - + +
6A ALA 4.0 3.4 - - - +
8A ARG* 1.3 78.1 - - - +
10A ILE* 1.3 56.2 + - - +
12A GLU* 4.1 15.5 + - - +
13A LEU* 2.5 71.9 + - + +
16A LEU* 5.9 5.1 - - - +
40A LEU* 4.9 7.5 - - - +
43A GLU* 2.6 47.8 + - - +
47A LEU* 4.0 13.7 - - + -
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Residues in contact with ILE 10 (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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6A ALA* 2.9 20.1 + - + +
7A ARG* 2.9 9.9 + - + +
9A ARG* 1.3 78.6 - - - +
11A ASN* 1.3 63.8 + - - +
13A LEU* 4.2 6.0 - - + +
14A ARG* 2.6 60.1 + - - +
44A LEU* 4.7 5.6 - - + -
47A LEU* 4.0 37.5 - - + +
48A GLU* 4.2 8.3 - - + +
54A PHE* 3.4 44.4 - - + +
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Residues in contact with ASN 11 (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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7A ARG* 2.6 37.8 + - - +
8A ARG* 3.2 9.4 - - - +
10A ILE* 1.3 79.2 - - - +
12A GLU* 1.3 62.1 + - + +
14A ARG* 3.9 5.2 - - - +
15A ASP* 3.2 20.3 + - - +
18A ARG* 5.6 0.2 + - - -
129A GLU* 3.2 32.6 + - - +
130A GLU* 4.9 2.4 - - - +
132A VAL* 3.8 22.0 - - + +
133A LEU 4.7 3.6 - - - +
134A VAL* 3.4 29.5 - - + +
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 2.7 42.0 + - - +
9A ARG* 3.6 15.7 + - - +
11A ASN* 1.3 69.0 - - - +
13A LEU* 1.3 67.0 + - - +
15A ASP* 2.8 11.6 + - - +
16A LEU* 2.9 25.3 - - + +
132A VAL* 3.7 30.3 - - + +
161A ARG* 4.1 14.4 + - - +
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Residues in contact with LEU 13 (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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9A ARG* 2.5 67.1 + - + +
10A ILE* 4.2 3.8 - - + +
12A GLU* 1.3 71.9 - - - +
14A ARG* 1.3 57.8 + - - +
15A ASP 3.0 0.3 + - - -
16A LEU* 3.3 7.7 + - + +
17A ILE* 2.8 36.1 + - + +
40A LEU* 3.6 38.8 - - + +
43A GLU* 3.6 23.6 - - + +
44A LEU* 3.7 28.9 - - + -
47A LEU* 4.6 3.6 - - + -
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Residues in contact with ARG 14 (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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10A ILE* 2.6 44.3 + - - +
11A ASN* 3.9 4.7 - - - +
13A LEU* 1.3 78.3 - - - +
15A ASP* 1.3 56.4 + - - +
17A ILE 3.8 0.4 - - - -
18A ARG* 2.9 54.8 + - - +
44A LEU* 3.0 17.3 - - + +
48A GLU* 3.1 21.8 + - - +
54A PHE 3.4 20.2 + - - -
56A SER* 4.0 9.4 + - - +
58A ASP* 5.4 1.1 - - - -
59A SER* 2.8 46.2 + - - +
60A PRO* 3.2 24.0 - - + +
134A VAL 5.8 1.8 - - - -
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Residues in contact with ASP 15 (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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11A ASN 3.2 10.7 + - - +
12A GLU 2.8 11.0 + - - +
14A ARG* 1.3 76.2 - - - +
16A LEU* 1.3 54.1 + - - +
17A ILE 3.0 0.7 - - - -
18A ARG* 2.6 14.3 + - - +
19A TYR* 2.6 35.0 + - - +
132A VAL* 4.2 7.6 - - + -
133A LEU* 4.7 12.9 - - - +
153A LEU* 5.3 1.4 - - - +
160A ARG* 3.1 41.9 + - - +
161A ARG* 2.4 35.0 + - - +
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Residues in contact with LEU 16 (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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9A ARG* 5.9 4.9 - - - +
12A GLU* 2.9 29.5 + - + +
13A LEU* 3.8 9.4 - - + +
15A ASP* 1.3 79.4 - - - +
17A ILE* 1.3 58.6 + - - +
19A TYR* 4.0 9.4 - - + -
20A HIS* 2.7 50.6 + - + +
40A LEU* 4.4 23.6 - - + -
160A ARG* 5.8 0.9 - - - +
161A ARG* 2.9 33.2 - - - +
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Residues in contact with ILE 17 (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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13A LEU 2.8 21.3 + - - +
14A ARG 3.9 3.1 - - - +
16A LEU* 1.3 74.7 - - - +
18A ARG* 1.3 58.8 + - - +
21A ASN* 3.0 27.4 + - - +
37A TYR* 3.8 31.6 + - + +
40A LEU* 3.6 24.0 - - + +
41A LEU* 3.3 40.4 - - + +
44A LEU* 3.8 19.1 - - + -
60A PRO* 3.5 25.8 - - + -
69A LEU* 4.0 3.6 - - + -
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Residues in contact with ARG 18 (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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14A ARG* 2.9 60.3 + - - +
15A ASP* 2.6 16.4 + - - +
17A ILE* 1.3 70.7 - - - +
19A TYR* 1.3 64.5 + - - +
21A ASN* 3.4 1.4 + - - +
22A TYR* 3.0 23.6 + - - +
58A ASP* 3.2 45.2 + - - +
60A PRO* 4.6 3.1 - - + +
69A LEU* 4.2 18.2 - - + +
133A LEU 5.2 3.2 + - - -
134A VAL 4.4 15.2 + - - -
135A PHE* 6.0 0.2 - - - +
147A GLU* 5.2 1.6 + - - -
149A THR* 4.0 33.7 + - - +
150A GLN* 3.4 34.7 - - - +
153A LEU* 4.7 8.7 - - + -
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Residues in contact with TYR 19 (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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15A ASP* 2.6 19.8 + - - +
16A LEU* 3.5 9.4 - - + +
18A ARG* 1.3 72.7 - - - +
20A HIS* 1.3 76.8 + + - +
22A TYR* 3.0 25.7 - + - +
23A ARG* 2.6 70.4 + - + -
27A LEU* 5.5 0.9 - - + -
31A GLU* 4.1 7.3 + - - -
153A LEU* 5.4 3.1 - - + +
160A ARG* 3.1 50.7 + - - +
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Residues in contact with HIS 20 (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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16A LEU* 2.7 45.5 + - + +
19A TYR* 1.3 97.2 - + - +
21A ASN* 1.3 58.6 + - - +
22A TYR 2.9 2.0 - - - -
23A ARG* 3.5 16.8 - - + +
24A TYR* 2.7 31.0 + - - +
30A PRO* 5.4 1.4 - - + +
31A GLU* 4.4 16.2 + - + -
32A ILE* 3.4 57.5 - - + +
37A TYR* 4.4 11.9 - - + -
40A LEU* 5.9 1.1 - - + +
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Residues in contact with ASN 21 (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 ILE 3.0 20.6 + - - +
18A ARG 3.9 3.4 - - - +
20A HIS* 1.3 76.0 - - - +
22A TYR* 1.3 57.2 + - - +
25A TYR* 3.1 50.6 + - - +
26A VAL* 4.0 2.9 - - - +
37A TYR* 3.6 20.2 + - - +
65A GLY 5.3 2.4 + - - -
67A ARG 3.2 13.7 + - - -
68A PRO* 3.8 2.8 - - - +
69A LEU* 2.8 50.9 + - + +
150A GLN* 3.9 7.4 + - - +
213A PRO* 5.4 0.7 - - - +
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Residues in contact with TYR 22 (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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18A ARG 3.0 13.9 + - - +
19A TYR* 3.0 31.6 - + - +
21A ASN* 1.3 76.0 + - - +
23A ARG* 1.3 52.1 + - - +
24A TYR 2.8 13.1 + - - -
26A VAL* 3.0 48.0 + - + +
27A LEU* 2.9 63.2 + - + +
150A GLN* 4.9 6.7 - - - +
153A LEU* 3.6 38.0 + - + -
154A THR* 4.0 20.8 + - + -
156A PRO* 4.8 11.9 - - + +
217A ALA* 5.5 1.6 - - + -
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Residues in contact with ARG 23 (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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19A TYR* 2.6 53.7 + - + +
20A HIS* 3.5 23.1 - - + +
22A TYR* 1.3 71.9 - - - +
24A TYR* 1.3 57.1 + - - +
27A LEU* 3.9 24.7 - - + +
28A ALA 3.5 1.5 + - - -
29A ASP* 3.0 51.0 + - - +
30A PRO* 3.0 30.8 - - + -
31A GLU* 2.7 32.9 + - + -
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Residues in contact with TYR 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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20A HIS 2.7 16.3 + - - +
22A TYR 2.8 1.0 - - - -
23A ARG* 1.3 77.3 - - - +
25A TYR* 1.3 110.3 + + + +
26A VAL 2.5 17.4 + - - -
28A ALA* 2.8 26.6 + - - +
30A PRO* 3.6 31.9 - - + -
34A ASP* 4.1 34.6 + - + +
37A TYR* 6.4 1.3 - + + -
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Residues in contact with TYR 25 (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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21A ASN* 3.1 40.6 + - - +
24A TYR* 1.3 109.3 - + + +
26A VAL* 1.3 60.9 + - + +
28A ALA* 6.0 0.2 - - - -
34A ASP* 4.4 11.3 + - - -
37A TYR* 4.7 12.9 - + - -
65A GLY 4.4 1.9 + - - -
66A ALA* 3.2 46.3 - - + +
67A ARG* 4.1 11.2 - - - -
68A PRO* 4.2 21.9 - - + +
214A ARG* 3.5 26.3 + - - +
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Residues in contact with VAL 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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21A ASN* 4.0 5.6 - - - +
22A TYR* 3.0 55.0 - - + +
24A TYR 2.5 7.3 + - - -
25A TYR* 1.3 81.3 - - + +
27A LEU* 1.3 67.1 + - + +
28A ALA* 3.4 3.7 + - - +
68A PRO* 6.4 0.4 - - + -
150A GLN* 5.3 1.8 - - - +
154A THR* 4.4 5.2 - - + -
213A PRO* 5.1 12.6 - - + -
214A ARG* 4.4 24.9 + - + +
217A ALA* 4.1 22.9 - - + -
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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
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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) + - + + + + + -
------------------------------------------------------------
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