Contacts of the helix formed by residues 2 - 26 (chain Q) in PDB entry 2JA7
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 2 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q GLN* 1.3 78.7 + - + +
4Q GLU 2.8 5.5 + - - -
5Q ASN* 3.0 23.0 + - - +
6Q GLU* 3.0 34.5 + - - +
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Residues in contact with GLN 3 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q ASP* 1.3 83.7 - - + +
4Q GLU* 1.3 66.5 + - + +
6Q GLU* 3.4 12.1 + - - +
7Q ARG* 3.4 33.0 + - - +
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Residues in contact with GLU 4 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1218M GLN* 3.9 21.2 + - - +
2Q ASP 2.8 5.2 + - - +
3Q GLN* 1.3 81.4 - - + +
5Q ASN* 1.3 68.3 + - - +
6Q GLU 3.2 0.6 + - - -
7Q ARG* 3.4 6.4 + - - +
8Q ASN* 3.2 22.5 + - - +
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Residues in contact with ASN 5 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q ASP 3.0 15.4 + - - +
4Q GLU* 1.3 80.7 + - - +
6Q GLU* 1.3 61.0 + - - +
7Q ARG 3.3 0.7 - - - -
8Q ASN* 3.6 19.4 + - + +
9Q ILE* 3.0 34.8 + - + +
52Q ARG* 4.4 29.4 - - + +
53Q PRO* 6.3 0.9 - - + -
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Residues in contact with GLU 6 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q ASP* 3.0 52.9 + - - +
3Q GLN* 3.4 11.1 + - - +
4Q GLU 3.2 0.2 - - - -
5Q ASN* 1.3 78.9 - - - +
7Q ARG* 1.3 60.4 + - + +
9Q ILE* 3.5 7.5 + - - +
10Q SER* 3.1 25.1 + - - -
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Residues in contact with ARG 7 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137M ALA* 6.2 1.8 - - - +
1320M PRO* 5.6 14.7 - - + +
3Q GLN* 3.4 19.5 + - - +
4Q GLU* 3.4 8.2 + - - +
5Q ASN 3.3 0.2 - - - -
6Q GLU* 1.3 77.0 - - + +
8Q ASN* 1.3 58.4 + - - +
9Q ILE 3.0 6.5 + - - -
10Q SER* 3.9 8.4 - - - -
11Q ARG* 3.1 34.2 + - + +
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Residues in contact with ASN 8 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4Q GLU 3.2 15.9 + - - +
5Q ASN* 3.8 20.9 + - + +
6Q GLU 3.4 0.6 - - - -
7Q ARG* 1.3 76.4 - - - +
9Q ILE* 1.3 61.8 + - + +
11Q ARG* 4.2 7.8 - - - +
12Q LEU* 3.7 16.4 + - - +
53Q PRO* 5.5 1.4 - - - +
55Q ARG* 4.1 15.8 + - - -
113Q GLN* 5.4 0.7 - - - +
137Q GLU* 5.3 2.6 - - - +
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Residues in contact with ILE 9 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q ASN* 3.0 21.5 + - + +
6Q GLU* 3.7 6.5 - - - +
7Q ARG 3.0 0.4 - - - -
8Q ASN* 1.3 79.8 - - + +
10Q SER* 1.3 55.9 + - - +
11Q ARG 2.8 4.7 - - - -
12Q LEU* 2.8 6.8 + - + +
13Q TRP* 2.7 33.6 + - - +
39Q LEU* 5.1 6.3 - - + -
42Q PHE* 4.4 20.9 - - + -
43Q LYS* 5.7 6.7 - - + -
47Q CYS* 5.1 8.3 - - - -
51Q GLY 3.7 16.8 - - - +
52Q ARG* 4.6 0.7 - - + -
53Q PRO* 3.3 43.1 - - + -
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Residues in contact with SER 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q GLU 3.1 15.3 + - - -
7Q ARG* 3.5 10.5 + - - -
9Q ILE* 1.3 79.5 - - - +
11Q ARG* 1.3 58.6 + - - +
13Q TRP* 3.5 20.8 - - - +
14Q ARG* 3.1 30.4 + - - +
39Q LEU* 4.6 15.4 - - - +
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Residues in contact with ARG 11 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1318M THR* 3.6 31.0 + - - +
1320M PRO* 6.5 0.7 - - + -
7Q ARG* 3.1 22.1 + - + +
8Q ASN* 4.5 7.2 - - - +
9Q ILE 2.8 1.2 + - - -
10Q SER* 1.3 77.8 - - - +
12Q LEU* 1.3 57.3 + - - +
13Q TRP 2.9 4.4 + - - -
14Q ARG* 3.1 7.9 + - - +
15Q ALA* 2.7 34.0 + - - +
137Q GLU* 5.6 2.0 - - - +
138Q ALA* 3.7 23.2 - - - +
141Q VAL* 3.5 34.8 - - + +
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Residues in contact with LEU 12 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8Q ASN 3.7 14.5 + - - +
9Q ILE* 2.8 13.9 + - + +
11Q ARG* 1.3 75.4 - - - +
13Q TRP* 1.3 62.1 + - - +
15Q ALA* 4.1 7.0 - - + -
16Q PHE* 3.0 19.8 + - - +
42Q PHE* 4.8 4.9 - - + -
53Q PRO* 3.8 27.8 - - + -
55Q ARG* 3.8 24.9 - - + +
58Q MET* 3.7 34.3 - - + -
82Q PHE* 4.5 12.1 - - + -
137Q GLU* 3.7 29.3 + - - +
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Residues in contact with TRP 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q ILE 2.7 14.7 + - - +
10Q SER* 3.5 19.5 - - - +
11Q ARG 2.9 0.6 - - - -
12Q LEU* 1.3 74.8 - - - +
14Q ARG* 1.3 82.1 - - + +
16Q PHE* 2.7 28.1 + + + +
17Q ARG* 2.9 28.1 + - + +
35Q VAL 5.4 1.6 + - - -
36Q GLU 5.6 0.7 - - - -
37Q LEU* 3.1 25.4 + - + +
38Q PRO* 3.8 4.4 - - + -
39Q LEU* 3.5 53.2 - - + -
42Q PHE* 3.7 39.7 - + + -
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Residues in contact with ARG 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121M GLU* 5.0 9.1 + - - -
1317M MET 4.6 0.6 + - - -
1318M THR* 3.2 29.1 + - - +
1319M VAL 4.5 8.8 + - - -
1320M PRO* 5.1 6.3 - - - +
1322M ILE 5.9 0.4 + - - -
1324M PRO* 5.3 9.7 - - - +
10Q SER* 3.1 20.6 + - - +
11Q ARG* 3.1 7.5 + - - +
13Q TRP* 1.3 95.4 - - + +
15Q ALA* 1.3 66.5 + - - +
17Q ARG* 2.7 33.2 + - - +
18Q THR* 3.1 7.4 + - - -
141Q VAL* 3.2 44.3 + - + +
142Q VAL* 3.9 9.2 - - - +
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Residues in contact with ALA 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q ARG 2.7 22.2 + - - +
12Q LEU* 3.8 12.8 - - + +
14Q ARG* 1.3 72.7 - - - +
16Q PHE* 1.3 62.6 + - - +
18Q THR* 3.6 4.3 + - - -
19Q VAL* 2.9 24.4 + - - +
82Q PHE* 5.6 1.6 - - + -
111Q VAL* 6.5 0.2 - - + -
137Q GLU* 4.3 21.5 - - + +
140Q LEU* 3.5 18.5 - - + +
141Q VAL* 3.8 16.9 - - + +
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Residues in contact with PHE 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q LEU 3.0 14.4 + - - +
13Q TRP* 2.7 26.0 + + - +
15Q ALA* 1.3 70.9 - - - +
17Q ARG* 1.3 55.8 + - - +
19Q VAL* 2.6 40.8 + - + +
20Q LYS* 3.1 46.5 + - + -
34Q GLU 5.3 0.9 - - - -
37Q LEU* 4.8 14.6 - - + -
42Q PHE* 4.9 6.3 - + - -
46Q TYR* 4.4 19.5 - + - -
58Q MET* 4.0 35.7 - - + -
60Q PHE* 5.5 9.0 - + - -
82Q PHE* 3.6 34.1 - + + -
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Residues in contact with ARG 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Q TRP* 2.9 27.1 + - - +
14Q ARG* 2.7 22.8 + - - +
16Q PHE* 1.3 79.9 - - - +
18Q THR* 1.3 65.6 + - - +
20Q LYS* 3.0 19.1 + - - +
21Q GLU* 3.0 43.1 + - - +
32Q GLN* 5.6 2.8 - - - +
35Q VAL* 4.2 25.9 + - + +
36Q GLU* 4.6 26.1 - - - +
146Q HIS* 5.6 2.2 + - - -
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Residues in contact with THR 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q ARG 3.1 4.7 + - - -
15Q ALA 3.7 2.7 - - - -
16Q PHE 2.9 1.4 + - - -
17Q ARG* 1.3 76.0 - - - +
19Q VAL* 1.3 67.5 + - - +
20Q LYS 2.8 1.0 + - - -
21Q GLU* 2.8 14.1 + - - -
22Q MET* 2.7 25.4 + - + +
140Q LEU* 2.7 46.9 + - + +
141Q VAL 3.9 3.3 + - - -
142Q VAL* 3.8 1.1 - - - +
143Q ASN* 3.7 40.9 + - + +
187Q TYR* 4.5 8.5 - - + -
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Residues in contact with VAL 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Q ALA 2.9 21.5 - - - +
16Q PHE* 2.6 22.6 + - + +
18Q THR* 1.3 73.9 - - - +
20Q LYS* 1.3 53.2 + - - +
22Q MET* 3.8 9.6 - - + +
23Q VAL* 2.7 38.1 + - + +
60Q PHE* 5.2 3.6 - - + -
80Q VAL* 3.7 35.9 - - + -
82Q PHE* 4.1 16.4 - - + -
109Q ILE* 5.1 5.8 - - + -
111Q VAL* 4.8 5.2 - - + -
140Q LEU* 4.0 22.4 - - + -
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Residues in contact with LYS 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q PHE* 3.1 47.9 - - + +
17Q ARG* 3.0 13.8 + - - +
18Q THR 2.8 1.4 + - - -
19Q VAL* 1.3 76.1 - - + +
21Q GLU* 1.3 60.5 + - - +
23Q VAL* 2.6 28.0 + - - +
24Q LYS 3.0 8.3 + - - -
30Q ILE* 3.4 16.8 - - + +
34Q GLU* 3.3 49.3 + - + +
35Q VAL* 4.3 16.4 - - + -
37Q LEU* 6.2 0.7 - - - -
46Q TYR* 5.5 2.0 + - - -
60Q PHE* 3.3 34.9 - - + -
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Residues in contact with GLU 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q ARG* 3.3 41.6 + - - +
18Q THR* 2.8 19.9 + - - +
20Q LYS* 1.3 73.0 - - - +
22Q MET* 1.3 65.0 + - - +
24Q LYS* 2.8 26.7 + - + +
25Q ASP* 3.0 16.8 + - - +
32Q GLN* 5.7 1.6 + - - +
35Q VAL* 3.9 19.5 - - + +
143Q ASN* 3.3 22.2 + - - +
146Q HIS* 3.5 24.2 + - + -
187Q TYR* 3.7 12.1 - - - +
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Residues in contact with MET 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q THR* 2.7 19.1 + - + +
19Q VAL* 3.8 8.3 - - + +
21Q GLU* 1.3 72.9 - - - +
23Q VAL* 1.3 65.6 + - + +
24Q LYS 3.1 0.2 + - - -
25Q ASP* 3.3 1.0 + - - +
26Q ARG* 2.8 68.1 + - + +
109Q ILE* 3.7 20.0 - - + -
135Q PHE* 3.6 28.9 - - + -
140Q LEU* 5.1 5.2 - - - -
187Q TYR* 2.9 62.4 + - + +
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Residues in contact with VAL 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q VAL* 2.7 27.9 + - + +
20Q LYS* 2.6 15.4 + - - +
22Q MET* 1.3 73.8 - - + +
24Q LYS* 1.3 57.3 + - - +
26Q ARG* 3.8 8.2 - - - +
28Q TYR* 2.9 46.2 + - + +
30Q ILE* 3.7 13.2 - - + -
60Q PHE* 4.5 4.7 - - + -
62Q ALA* 3.9 14.8 - - + -
78Q LEU* 3.7 14.8 - - + -
80Q VAL* 4.2 22.0 - - + -
109Q ILE* 4.7 6.1 - - + -
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Residues in contact with LYS 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q LYS 3.0 3.6 + - - +
21Q GLU* 2.8 25.1 + - - +
23Q VAL* 1.3 69.2 - - - +
25Q ASP* 1.3 74.7 + - - +
26Q ARG 3.0 1.1 - - - -
27Q GLY* 2.8 19.6 + - - -
28Q TYR 3.1 20.2 + - - +
30Q ILE* 3.8 45.1 + - + +
31Q THR 4.9 0.4 - - - -
32Q GLN* 3.8 28.7 + - - +
35Q VAL* 5.5 4.7 - - + -
65Q THR* 5.7 0.2 - - - +
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Residues in contact with ASP 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q GLU* 3.0 13.2 + - - +
22Q MET 3.9 2.9 - - - +
24Q LYS* 1.3 91.6 - - - +
26Q ARG* 1.3 61.9 + - - +
27Q GLY* 3.1 2.3 + - - -
143Q ASN* 4.8 0.9 + - - -
145Q THR* 5.2 0.7 + - - -
146Q HIS* 5.8 1.9 - - - -
187Q TYR* 2.9 36.5 + - + -
188Q LEU* 4.8 12.1 - - + +
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Residues in contact with ARG 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Q MET* 2.8 61.9 + - - +
23Q VAL* 3.8 9.6 - - - +
24Q LYS 3.0 0.2 - - - -
25Q ASP* 1.3 77.4 - - - +
27Q GLY* 1.3 57.3 + - - +
28Q TYR* 4.1 16.8 - - + -
72Q PHE* 5.7 2.8 - - - -
75Q MET* 3.7 17.3 - - + +
78Q LEU* 4.9 3.1 - - - -
107Q THR* 4.5 11.3 - - - +
109Q ILE* 4.1 8.1 - - - +
133Q GLU* 2.7 45.5 + - - -
135Q PHE* 3.8 2.6 - - - -
155Q ARG* 4.9 14.7 + - - +
186Q LEU 3.4 8.9 + - - -
187Q TYR 3.5 13.0 + - - +
188Q LEU* 3.7 29.7 + - - +
189Q GLY* 4.0 3.6 + - - -
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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