Contacts of the helix formed by residues 10 - 38 (chain A) in PDB entry 1RCE
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 GLN 10 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.8 14.2 + - - +
9A HIS* 1.3 82.7 - - + +
11A ASP* 1.3 63.0 + - - +
13A GLU* 3.3 20.6 + - - +
14A ALA* 2.8 30.1 + - - +
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Residues in contact with ASP 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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9A HIS* 3.2 26.6 + - + -
10A GLN* 1.3 78.1 - - - +
12A CYS* 1.3 61.5 + - - +
14A ALA* 3.9 5.5 - - - +
15A GLY* 2.8 25.8 + - - -
18A ARG* 4.4 8.5 + - - +
113A LEU* 4.8 0.5 - - - +
116A VAL* 3.9 23.0 - - + +
120A LYS* 3.7 13.0 + - - -
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Residues in contact with CYS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 4.1 10.1 - - + -
9A HIS* 3.1 15.9 + - - +
11A ASP* 1.3 73.4 - - - +
13A GLU* 1.3 64.9 + - - +
15A GLY 3.9 0.4 - - - +
16A LEU* 3.0 25.1 + - - +
113A LEU* 4.7 2.2 - - - -
116A VAL* 3.7 23.8 - - - -
117A ALA* 3.8 22.2 - - - -
120A LYS* 4.0 15.9 - - - -
122A ASP* 5.0 5.6 - - - +
125A MET* 3.5 32.5 - - - +
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 2.9 32.8 + - - -
8A PHE* 3.9 11.2 - - + -
9A HIS 3.0 11.1 + - - +
10A GLN* 3.5 18.8 - - - +
12A CYS* 1.3 77.7 - - - +
14A ALA* 1.3 63.3 + - - +
16A LEU 3.2 8.0 + - - -
17A ASN* 3.2 6.9 + - - +
69A GLN* 3.1 43.5 + - - +
74A GLY* 3.7 1.7 - - - -
75A ARG* 2.8 36.2 + - - +
77A PHE* 5.2 3.1 - - - -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN 2.8 18.1 + - - +
11A ASP* 3.9 4.7 - - - +
13A GLU* 1.3 78.7 - - - +
15A GLY* 1.3 62.0 + - - +
17A ASN* 3.1 10.5 + - - +
18A ARG* 3.1 47.7 + - - +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP 2.8 19.7 + - - -
13A GLU 3.4 0.2 - - - -
14A ALA* 1.3 74.3 - - - +
16A LEU* 1.3 60.1 + - - +
18A ARG* 3.4 24.7 + - - +
19A THR* 2.8 30.0 + - - -
113A LEU* 3.6 18.4 - - - -
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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
----------------------------------------------------------
8A PHE* 3.9 13.2 - - + -
12A CYS 3.0 14.7 + - - +
13A GLU 3.3 5.8 - - - +
14A ALA 3.1 0.2 - - - -
15A GLY* 1.3 76.9 - - - +
17A ASN* 1.3 59.7 + - - +
19A THR* 3.2 4.2 + - - -
20A VAL* 3.0 30.1 + - + +
65A LEU* 3.9 40.8 - - + +
68A TYR* 3.5 32.8 - - + -
69A GLN* 3.8 26.7 - - - +
113A LEU* 4.0 10.5 - - + +
125A MET* 4.0 16.2 - - + -
128A PHE* 5.0 2.7 - - + -
129A LEU* 5.3 0.9 - - + -
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Residues in contact with ASN 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 GLU* 3.2 8.9 + - - +
14A ALA* 3.1 11.0 + - - +
16A LEU* 1.3 75.7 - - - +
18A ARG* 1.3 64.3 + - + +
20A VAL* 3.5 14.1 + - - +
21A ASN* 3.4 15.1 + - - +
69A GLN* 3.2 21.0 + - - +
75A ARG 3.2 21.6 + - - -
76A VAL* 3.9 9.2 - - - +
77A PHE* 3.6 45.1 + - + +
79A GLN* 3.8 12.3 + - - +
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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
----------------------------------------------------------
11A ASP* 4.4 9.7 + - - +
14A ALA* 3.1 28.6 + - - +
15A GLY* 3.4 28.6 - - - +
16A LEU 3.3 0.4 - - - -
17A ASN* 1.3 76.1 - - + +
19A THR* 1.3 63.8 + - - +
21A ASN* 3.3 5.5 + - - +
22A LEU* 3.1 21.7 + - - +
79A GLN* 4.1 13.2 - - - +
113A LEU* 5.7 0.2 - - - +
116A VAL* 6.1 2.2 - - - +
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Residues in contact with THR 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 GLY 2.8 21.4 + - - -
16A LEU* 3.2 4.7 + - - -
18A ARG* 1.3 76.0 - - - +
20A VAL* 1.3 59.5 + - - +
22A LEU* 3.3 17.7 + - + +
23A LYS* 3.0 30.4 + - + +
65A LEU* 4.1 14.4 - - + -
106A VAL* 5.9 0.9 - - + -
109A ALA* 5.0 9.1 + - + +
110A LEU* 3.9 29.6 - - + +
113A LEU* 3.5 20.7 - - + +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.0 21.2 + - + +
17A ASN* 3.9 15.9 - - - +
18A ARG 3.3 0.4 - - - -
19A THR* 1.3 73.0 - - - +
21A ASN* 1.3 66.3 - - + +
23A LYS* 3.1 6.2 + - - +
24A PHE* 2.9 41.4 + - + +
62A ALA* 3.9 13.8 - - + +
65A LEU* 3.8 28.3 - - + +
66A ILE* 4.3 15.7 - - + +
69A GLN* 6.5 0.2 - - + -
76A VAL* 6.0 0.4 - - + -
77A PHE 5.5 1.6 - - - +
78A LEU* 4.2 25.4 - - + -
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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
----------------------------------------------------------
17A ASN 3.4 2.5 + - - +
18A ARG* 3.3 9.6 + - - +
19A THR 3.3 0.4 - - - -
20A VAL* 1.3 86.7 - - + +
22A LEU* 1.3 56.1 + - - +
24A PHE* 3.3 7.5 + - - +
25A HIS* 2.9 30.0 + - - +
79A GLN* 3.2 47.7 + - + +
80A SER 3.0 28.7 + - - +
81A VAL* 4.2 9.8 - - - +
82A GLU* 5.3 1.7 + - - +
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Residues in contact with LEU 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 3.1 13.1 + - - +
19A THR* 3.4 16.8 - - + +
21A ASN* 1.3 74.4 - - - +
23A LYS* 1.3 64.3 + - - +
25A HIS* 3.3 15.1 + - + +
26A SER* 3.0 23.6 + - - -
102A LEU* 6.5 1.1 - - + -
105A SER* 4.7 3.4 - - - +
106A VAL* 4.2 31.0 - - + -
109A ALA* 3.4 32.8 - - + -
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Residues in contact with LYS 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 THR* 3.0 18.3 + - + +
20A VAL 3.5 7.9 - - - +
22A LEU* 1.3 78.5 - - + +
24A PHE* 1.3 60.6 + - - +
26A SER* 2.9 24.0 + - - +
27A SER* 3.0 12.1 + - - -
58A ALA* 3.7 15.4 - - - +
61A HIS* 3.1 42.4 + - + +
62A ALA* 3.6 16.6 - - + -
65A LEU* 4.1 15.7 - - + -
103A GLN* 5.4 4.2 + - - +
106A VAL* 3.8 28.0 - - + +
110A LEU* 4.8 16.0 - - - +
133A TYR* 5.2 2.9 - - - -
136A GLU* 3.8 15.0 + - - -
137A SER* 5.4 0.4 + - - -
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 2.9 34.6 + - + +
21A ASN* 3.6 8.3 - - - +
22A LEU 3.3 0.2 - - - -
23A LYS* 1.3 76.2 - - - +
25A HIS* 1.3 62.2 + - - +
27A SER* 3.4 5.1 + - - -
28A TYR* 3.1 22.7 + - - +
59A LYS* 4.3 25.1 - - + -
62A ALA* 3.6 25.4 - - + -
63A GLU* 4.9 6.1 - - + -
66A ILE* 4.3 17.0 - - + -
78A LEU* 4.4 11.0 - - + -
81A VAL* 3.9 26.1 - - + +
200A BET 3.7 24.1 - - - -
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Residues in contact with HIS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 2.9 20.5 + - - +
22A LEU* 3.6 15.0 - - + +
23A LYS 3.2 0.4 - - - -
24A PHE* 1.3 75.4 - - - +
26A SER* 1.3 61.3 + - - +
28A TYR* 3.2 4.0 + - - +
29A VAL* 2.9 44.2 + - + +
81A VAL* 3.8 10.7 - - + +
82A GLU* 2.7 41.7 + - + +
83A LYS 3.3 19.3 - - - -
84A PRO* 5.4 0.2 - - + -
85A GLU* 2.8 25.0 + - - -
102A LEU* 5.2 7.2 - - + -
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 3.0 12.6 + - - -
23A LYS* 2.9 24.4 + - - +
25A HIS* 1.3 76.2 - - - +
27A SER* 1.3 61.5 + - - +
29A VAL* 3.2 6.5 + - - +
30A TYR* 3.0 35.2 + - - -
58A ALA* 3.5 12.0 - - - +
102A LEU* 3.9 33.0 - - - -
103A GLN* 5.6 1.2 + - - -
106A VAL* 4.4 11.0 - - - +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS 3.0 14.1 + - - -
24A PHE* 3.4 11.0 - - - -
26A SER* 1.3 76.7 + - - +
28A TYR* 1.3 56.6 + - - +
30A TYR* 3.2 2.3 + - - +
31A LEU* 2.9 16.8 + - - +
55A SER* 2.8 52.3 + - - +
58A ALA* 3.9 9.9 - - - -
59A LYS* 3.6 9.0 - - - +
200A BET 3.3 24.8 + - - -
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE 3.1 9.5 + - - +
25A HIS* 3.4 11.2 - - - +
27A SER* 1.3 73.1 - - - +
29A VAL* 1.3 67.1 + - - +
31A LEU* 3.3 22.1 + - + +
32A SER* 3.1 17.8 + - - -
81A VAL* 4.1 14.8 - - + -
82A GLU 3.6 19.3 - - - +
83A LYS* 3.9 19.4 - - + +
84A PRO* 3.5 22.4 - - + +
200A BET 3.1 32.7 - - - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A HIS* 2.9 45.1 + - + +
26A SER* 3.2 10.3 + - - +
28A TYR* 1.3 75.6 - - - +
30A TYR* 1.3 58.0 + - - +
32A SER* 3.1 7.3 - - - -
33A MET* 3.1 49.2 + - + +
84A PRO* 3.7 13.2 - - + -
85A GLU* 3.9 13.2 - - - +
89A TRP* 4.1 12.3 - - + -
98A THR* 5.4 3.1 - - + -
102A LEU* 4.0 21.1 - - + -
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Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 3.0 30.0 + - - -
27A SER* 3.6 6.3 - - - +
29A VAL* 1.3 74.3 - - - +
31A LEU* 1.3 59.5 + - - +
33A MET* 3.3 9.5 + - - +
34A ALA* 2.9 30.3 + - - +
51A PHE* 3.5 39.8 - + - +
54A ARG* 3.6 41.1 - - + +
55A SER* 3.7 5.6 - - - -
58A ALA* 4.9 2.0 - - + -
99A ALA* 3.7 30.1 + - + +
102A LEU* 3.7 21.1 - - + +
103A GLN* 2.8 42.6 + - - +
144A LEU* 4.5 0.5 - - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 2.9 13.1 + - - +
28A TYR* 3.5 33.2 - - + +
29A VAL 3.3 0.2 - - - -
30A TYR* 1.3 75.8 - - - +
32A SER* 1.3 62.4 + - - +
34A ALA* 3.2 8.5 + - + +
35A SER* 2.9 37.4 + - - +
52A ARG* 5.2 15.3 - - + +
55A SER* 3.8 10.2 + - - +
200A BET 3.5 24.9 - - - +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR 3.1 11.9 + - - -
29A VAL 3.1 11.0 - - - -
31A LEU* 1.3 77.7 - - - +
33A MET* 1.3 62.5 + - - +
35A SER* 3.2 7.3 + - - -
36A TYR* 3.0 22.2 + - - +
84A PRO* 3.8 16.8 - - - +
86A ARG 3.6 11.8 + - - -
87A ASP* 4.5 7.1 + - - +
89A TRP* 3.0 17.5 + - - -
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Residues in contact with MET 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.1 22.2 + - + +
30A TYR* 3.3 16.8 + - + +
32A SER* 1.3 73.5 - - - +
34A ALA* 1.3 63.4 + - - +
36A TYR* 3.0 11.4 + - - +
37A PHE* 3.0 23.3 + - + -
51A PHE* 3.8 41.5 - - + -
89A TRP* 3.7 44.2 - - + -
95A ALA* 3.9 15.0 - - + +
98A THR* 3.7 30.3 - - + -
99A ALA* 4.4 6.7 - - + +
102A LEU* 5.6 0.4 - - + -
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR 2.9 18.1 + - - +
31A LEU* 3.2 10.3 + - + +
33A MET* 1.3 78.0 - - - +
35A SER* 1.3 62.6 + - - +
37A PHE 3.4 3.3 + - - -
38A ASN* 3.5 8.7 + - - +
48A ALA* 3.3 50.2 - - + +
51A PHE* 4.0 2.4 - - + +
52A ARG* 4.1 20.2 - - + +
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 2.9 25.8 + - - +
32A SER* 3.6 6.9 - - - -
34A ALA* 1.3 77.2 - - - +
36A TYR* 1.3 63.1 + - - +
38A ASN* 3.1 18.9 + - - +
39A ARG* 3.6 11.6 + - - +
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Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER 3.0 13.0 + - - +
33A MET 3.0 7.4 + - - +
35A SER* 1.3 77.3 - - - +
37A PHE* 1.3 98.0 + + - +
39A ARG* 3.2 49.0 + - - +
42A VAL* 3.4 30.0 - - + +
87A ASP 4.1 4.9 - - - +
88A ASP* 3.4 28.7 + - - -
89A TRP* 3.6 40.6 - + + -
90A ALA* 3.0 27.3 + - - -
91A ASN* 4.8 0.7 - - - -
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Residues in contact with PHE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A MET* 3.0 31.1 + - + +
34A ALA 3.4 0.8 + - - -
35A SER 3.3 0.2 - - - -
36A TYR* 1.3 99.2 - + - +
38A ASN* 1.3 58.2 + - - +
39A ARG 3.3 1.3 - - - -
42A VAL* 3.5 16.6 - - + -
43A ALA* 3.4 7.5 + - - -
44A LEU* 3.0 60.9 + - + +
47A PHE* 3.8 10.3 - + + -
48A ALA* 3.8 12.6 - - + +
51A PHE* 3.7 21.5 - + - -
89A TRP* 4.7 1.1 - - + -
91A ASN* 3.8 9.4 - - - -
92A GLY* 3.9 20.2 - - - -
95A ALA* 3.6 32.3 - - + -
----------------------------------------------------------
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Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.5 7.6 + - - +
35A SER* 3.1 15.0 + - - +
37A PHE* 1.3 76.0 - - - +
39A ARG* 1.3 64.6 + - - +
40A ASP* 3.6 1.4 + - - -
43A ALA* 5.2 2.0 - - - +
45A SER* 4.2 13.7 - - - +
48A ALA* 3.7 25.2 - - - +
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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