Contacts of the helix formed by residues 3 - 25 (chain E) in PDB entry 6A5T
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 ASP 3 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1217A LYS* 5.7 3.1 + - - -
2E GLU* 1.3 77.3 - - + +
4E ASN* 1.3 61.4 + - - +
6E ARG* 3.1 50.1 + - - +
7E ILE* 3.2 28.0 + - - +
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Residues in contact with ASN 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E GLU* 3.0 26.3 - - + +
3E ASP* 1.3 78.4 - - - +
5E ASN* 1.3 59.6 + - - +
7E ILE* 3.3 8.8 + - - +
8E ILE* 2.9 39.0 + - - +
42E ARG* 5.4 5.9 + - - -
49E MET 3.9 9.0 - - - +
50E GLY* 2.8 34.2 + - - +
51E ASN* 4.0 12.1 + - - +
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Residues in contact with ASN 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E GLU* 2.8 42.1 + - - +
4E ASN* 1.3 76.9 - - - +
6E ARG* 1.3 58.5 + - - +
8E ILE* 3.8 4.9 - - - +
9E SER* 2.8 31.2 + - - -
38E LEU* 5.8 3.8 - - - +
39E GLU* 5.6 0.2 - - - +
42E ARG* 3.2 32.4 + - - +
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Residues in contact with ARG 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1323A PRO* 6.3 2.9 - - + -
2E GLU 3.2 5.7 + - - +
3E ASP* 3.1 49.8 + - - +
5E ASN* 1.3 78.1 - - - +
7E ILE* 1.3 70.9 + - - +
9E SER* 3.2 7.5 + - - -
10E ARG* 2.9 66.8 + - + +
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Residues in contact with ILE 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ASP* 3.2 34.6 + - - +
4E ASN* 3.8 7.9 - - - +
6E ARG* 1.3 93.8 - - - +
8E ILE* 1.3 65.8 + - + +
10E ARG* 3.1 11.9 + - + +
11E LEU* 2.9 29.3 + - + +
52E PRO* 5.7 6.7 - - + -
54E ARG* 5.5 9.2 - - - +
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Residues in contact with ILE 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ASN* 2.9 35.7 + - - +
5E ASN* 3.9 5.8 - - - +
7E ILE* 1.3 82.1 - - + +
9E SER* 1.3 57.5 + - - +
11E LEU* 3.2 5.8 + - + +
12E TRP* 2.8 27.5 + - - +
38E LEU* 5.2 4.9 - - + -
41E PHE* 3.7 29.1 - - + -
42E ARG* 3.8 25.4 - - + +
46E CYS* 4.4 8.3 - - - -
50E GLY 3.9 11.2 - - - +
52E PRO* 4.2 28.5 - - + -
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Residues in contact with SER 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ASN 2.8 19.0 + - - -
6E ARG* 3.5 7.2 - - - -
8E ILE* 1.3 78.5 - - - +
10E ARG* 1.3 59.1 + - - +
12E TRP* 3.1 12.9 + - - +
13E ARG* 2.9 44.1 + - - +
38E LEU* 4.4 16.8 - - - +
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Residues in contact with ARG 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1318A GLU* 5.1 11.8 + - - -
1321A ALA* 4.2 23.6 + - - +
1322A VAL* 5.4 3.0 - - - +
6E ARG* 2.9 50.6 + - + +
7E ILE* 3.1 11.9 + - + +
9E SER* 1.3 76.8 - - - +
11E LEU* 1.3 53.5 + - - +
13E ARG* 3.2 11.4 + - - +
14E SER* 2.6 38.1 + - - +
136E GLU* 5.3 5.1 + - - +
137E SER* 4.2 17.6 + - - -
140E VAL* 3.4 35.4 - - + +
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Residues in contact with LEU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 2.9 15.3 + - + +
8E ILE* 3.2 12.1 + - + +
10E ARG* 1.3 75.4 - - - +
12E TRP* 1.3 57.5 + - - +
14E SER* 3.1 9.6 - - - -
15E PHE* 2.9 27.2 + - - +
41E PHE* 3.6 24.7 - - + -
45E ILE* 4.8 0.9 - - + -
52E PRO* 3.8 28.7 - - + -
54E ARG* 3.8 30.3 - - - +
57E MET* 3.9 16.4 - - + -
81E PHE* 4.7 13.7 - - + -
136E GLU* 4.1 15.8 + - - +
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Residues in contact with TRP 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE 2.8 17.0 + - - +
9E SER* 3.4 7.4 - - - +
11E LEU* 1.3 77.9 - - - +
13E ARG* 1.3 86.1 + - + +
15E PHE* 3.1 6.0 + + + +
16E ARG* 2.9 64.7 + - + +
36E GLN* 3.4 19.9 + - + +
37E SER* 2.6 32.0 + - - -
38E LEU* 3.5 28.3 - - + -
41E PHE* 4.0 34.7 - + + -
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Residues in contact with ARG 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320A MET 5.0 1.0 + - - -
1321A ALA* 3.2 27.7 + - - +
1323A PRO* 4.8 9.7 - - - +
1324A GLY 5.6 0.8 - - - +
1325A VAL 5.5 2.8 + - - -
1327A SER* 4.9 8.1 + - - -
9E SER* 2.9 28.4 + - - +
10E ARG* 3.7 8.2 - - - +
12E TRP* 1.3 96.0 - - + +
14E SER* 1.3 66.6 + - - +
16E ARG* 3.8 21.8 + - - +
17E THR* 2.8 31.2 + - - +
139E LEU 4.6 1.1 - - - -
140E VAL* 4.0 32.0 + - + +
141E VAL* 4.5 11.5 - - - +
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Residues in contact with SER 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ARG 2.6 22.6 + - - -
11E LEU* 3.1 17.5 - - - -
13E ARG* 1.3 76.0 - - - +
15E PHE* 1.3 63.8 + - - -
17E THR* 3.1 4.0 + - - -
18E VAL* 2.9 30.9 + - - +
81E PHE* 5.5 5.8 - - - -
110E ILE* 6.4 0.7 - - - -
136E GLU* 3.9 26.5 + - - +
139E LEU* 4.0 15.0 - - - -
140E VAL* 4.5 9.6 - - - +
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Residues in contact with PHE 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU 2.9 13.1 + - - +
12E TRP* 3.1 11.0 + + - +
14E SER* 1.3 75.8 - - - +
16E ARG* 1.3 64.3 + - - +
18E VAL* 3.1 8.4 + - + +
19E LYS* 2.9 62.1 + - + +
33E GLU* 3.5 11.7 - - - -
36E GLN* 3.6 17.0 - - + -
41E PHE* 4.3 9.6 - + + -
57E MET* 3.3 42.2 - - + -
59E PHE* 4.1 24.7 - + - -
81E PHE* 4.6 11.2 - + - -
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Residues in contact with ARG 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E TRP* 2.9 57.5 + - + +
13E ARG* 3.9 24.5 + - - +
15E PHE* 1.3 77.3 - - - +
17E THR* 1.3 64.9 + - - +
19E LYS* 3.3 12.5 + - + +
20E GLU* 2.9 41.9 + - + +
34E MET* 4.5 17.5 - - - +
35E ASP* 6.3 0.4 - - - +
36E GLN 5.5 2.9 - - - +
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Residues in contact with THR 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ARG 2.8 19.2 + - - -
14E SER 3.3 5.8 - - - -
16E ARG* 1.3 77.8 + - - +
18E VAL* 1.3 58.1 + - - +
20E GLU* 3.0 12.7 + - - +
21E MET* 2.8 26.3 + - + +
139E LEU* 2.8 46.7 + - + +
140E VAL 3.9 7.3 + - - -
142E ASN* 3.9 29.3 + - + +
186E TYR* 4.3 7.0 + - + -
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Residues in contact with VAL 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E SER* 2.9 20.9 + - - +
15E PHE* 3.1 8.3 + - + +
17E THR* 1.3 78.4 - - - +
19E LYS* 1.3 64.3 + - + +
21E MET* 3.0 18.0 + - + +
22E ALA* 3.0 22.0 + - + +
59E PHE* 5.1 8.1 - - + -
79E VAL* 4.0 30.7 - - + -
81E PHE* 4.6 16.8 - - + -
108E ILE* 5.5 2.5 - - + -
110E ILE* 4.8 8.7 - - + -
139E LEU* 4.2 24.7 - - + -
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Residues in contact with LYS 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PHE* 2.9 49.2 + - + +
16E ARG* 3.8 10.5 - - + +
18E VAL* 1.3 77.3 - - - +
20E GLU* 1.3 62.5 + - - +
22E ALA* 3.2 7.6 + - - +
23E ALA* 2.9 23.0 + - - +
29E ILE* 4.7 14.5 - - + +
33E GLU* 2.2 69.6 + - + +
34E MET* 3.6 24.7 + - - +
36E GLN* 3.9 10.9 - - - +
59E PHE* 4.9 12.3 - - + -
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Residues in contact with GLU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ARG* 2.9 37.5 + - + +
17E THR* 3.3 9.4 - - - +
19E LYS* 1.3 75.8 - - - +
21E MET* 1.3 58.6 + - - +
23E ALA* 3.1 8.6 + - - +
24E ASP* 2.8 36.0 + - - +
34E MET* 4.5 15.2 - - - +
142E ASN* 2.4 48.1 + - - +
145E HIS* 3.0 18.3 + - - -
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Residues in contact with MET 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E THR* 2.8 10.9 + - + +
18E VAL* 3.0 18.4 + - + +
20E GLU* 1.3 75.9 - - - +
22E ALA* 1.3 58.6 + - - +
24E ASP* 2.8 18.1 + - - +
25E ARG* 2.9 38.9 + - - +
108E ILE* 4.6 9.0 - - - -
134E PHE* 3.3 39.7 - - + -
139E LEU* 3.7 27.1 - - + -
186E TYR* 3.5 47.9 + - + +
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Residues in contact with ALA 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E VAL* 3.0 13.1 + - + +
19E LYS* 3.8 9.9 - - - +
21E MET* 1.3 78.3 - - - +
23E ALA* 1.3 61.9 + - - +
25E ARG* 3.6 3.9 + - - +
27E TYR* 3.1 37.0 + - + +
29E ILE* 4.9 12.6 - - + -
59E PHE* 5.2 7.9 - - + -
61E ALA* 5.2 3.6 - - + -
77E LEU* 3.8 28.7 - - + -
79E VAL* 5.7 1.1 - - + -
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LYS 2.9 14.0 + - - +
20E GLU* 3.4 9.9 - - - +
22E ALA* 1.3 78.3 - - - +
24E ASP* 1.3 64.1 + - - +
26E GLY* 3.4 11.6 + - - -
27E TYR 4.0 12.6 - - - +
29E ILE* 4.7 8.4 - - + +
34E MET* 3.8 26.2 - - + -
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Residues in contact with ASP 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLU* 2.8 16.7 + - - +
21E MET 2.8 7.1 + - - +
23E ALA* 1.3 80.1 - - - +
25E ARG* 1.3 63.7 + - - +
26E GLY* 3.0 3.2 + - - -
142E ASN* 4.0 7.0 + - - -
144E THR* 4.4 2.1 + - - -
145E HIS* 5.9 2.1 - - - -
186E TYR* 2.5 44.5 + - + -
187E LEU* 4.5 12.2 - - + +
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Residues in contact with ARG 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E MET* 2.9 39.1 + - - +
22E ALA* 3.6 7.6 + - - +
23E ALA 3.2 0.4 - - - -
24E ASP* 1.3 78.1 - - + +
26E GLY* 1.3 56.4 + - - +
27E TYR* 3.7 18.5 - - + -
71E TYR* 4.3 3.2 - - - -
74E LEU* 4.1 9.8 - - + +
77E LEU* 5.2 3.3 - - - +
106E THR* 4.7 9.8 - - - +
108E ILE* 3.6 21.4 - - - +
132E GLU* 3.1 39.2 + - - -
134E PHE* 4.6 1.2 - - - -
154E ARG* 3.7 22.7 + - - +
185E ARG 4.6 1.2 + - - -
186E TYR 3.9 12.1 - - - +
187E LEU* 3.4 25.1 + - + +
188E GLY* 3.1 20.9 + - - +
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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
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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