Contacts of the helix formed by residues 3 - 34 (chain A) in PDB entry 1KRQ
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 SER 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.3 0.2 + - - -
2A LEU* 1.3 76.9 - - - +
4A LYS* 1.3 65.2 + - - +
5A GLU* 3.5 7.9 + - - +
6A VAL* 3.1 35.1 + - - +
7A VAL* 3.1 12.0 + - - +
107A HIS* 5.4 0.9 - - - -
111A HIS* 5.9 1.6 - - - +
113A ASP* 5.5 0.6 + - - -
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Residues in contact with LYS 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU 3.8 1.4 + - - -
3A SER* 1.3 72.0 - - - +
5A GLU* 1.3 61.2 + - - +
7A VAL* 3.7 8.2 + - - +
8A LYS* 3.2 22.2 + - - +
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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
----------------------------------------------------------
3A SER* 3.1 9.2 + - - +
4A LYS* 1.3 75.8 - - - +
6A VAL* 1.3 61.3 + - - +
8A LYS* 3.1 8.6 + - - +
9A LEU* 2.9 34.8 + - + +
107A HIS* 4.3 20.2 - - + +
111A HIS* 5.3 4.0 - - + -
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Residues in contact with VAL 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.0 13.9 - - + -
3A SER* 3.1 25.5 + - - +
5A GLU* 1.3 74.8 - - - +
7A VAL* 1.3 61.7 + - - +
9A LEU* 2.9 9.8 + - - +
10A LEU* 2.8 51.3 + - + +
107A HIS* 4.3 11.4 - - + -
108A MET* 3.9 28.9 - - + -
111A HIS* 5.9 1.8 - - + -
113A ASP* 3.9 21.5 - - + +
116A THR* 4.2 2.9 - - - +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.0 14.8 - - + +
3A SER 3.1 17.3 + - - +
4A LYS* 3.9 8.7 - - - +
6A VAL* 1.3 76.6 - - - +
8A LYS* 1.3 57.6 + - - +
10A LEU* 3.4 1.5 + - - +
11A ASN* 2.8 52.2 + - - +
61A LEU* 4.4 14.5 - - + +
66A SER* 3.9 24.9 - - - +
67A HIS* 3.4 18.6 - - + +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS 3.2 12.9 + - - +
5A GLU* 3.1 11.8 + - - +
6A VAL 3.1 0.4 - - - -
7A VAL* 1.3 80.0 - - - +
9A LEU* 1.3 64.4 + - + +
11A ASN* 3.4 7.4 + - - +
12A GLU* 3.1 24.4 + - - +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 2.9 18.1 + - + +
6A VAL* 2.9 8.0 + - - +
8A LYS* 1.3 79.2 - - + +
10A LEU* 1.3 56.0 + - - +
12A GLU* 3.3 22.1 + - - +
13A GLN* 3.0 25.1 + - - +
103A THR* 5.6 4.5 - - + +
104A LEU* 3.4 30.0 - - + +
107A HIS* 3.5 49.4 - - + +
108A MET* 4.1 6.5 - - + -
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Residues in contact with LEU 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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2A LEU* 4.2 1.3 - - + -
6A VAL* 2.8 41.6 + - + +
7A VAL 4.0 2.9 - - - +
9A LEU* 1.3 69.2 - - + +
11A ASN* 1.3 61.3 + - - +
12A GLU 3.0 1.3 - - - -
13A GLN* 2.9 4.9 + - + +
14A ILE* 2.8 35.7 + - + +
57A LEU* 4.0 25.9 - - + +
60A TYR* 4.0 30.7 - - + -
61A LEU* 4.1 25.1 - - + -
104A LEU* 4.3 21.5 - - + -
108A MET* 5.4 0.7 - - + -
116A THR* 4.3 9.0 - - + -
119A PHE* 5.7 0.2 - - + -
120A LEU* 4.6 10.3 - - + -
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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
----------------------------------------------------------
7A VAL* 2.8 44.9 + - - +
8A LYS* 3.7 7.5 - - - +
10A LEU* 1.3 76.2 - - - +
12A GLU* 1.3 61.1 + - - +
14A ILE* 3.5 10.6 + - - +
15A ASN* 3.2 21.0 + - - +
61A LEU* 4.2 7.1 - - - +
67A HIS 3.3 10.5 + - - -
68A VAL* 3.5 8.3 - - - +
69A GLU* 2.6 52.8 + - + +
70A LEU* 5.6 0.2 - - - +
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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
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8A LYS 3.1 13.8 + - - +
9A LEU* 3.3 26.5 - - - +
10A LEU 3.0 0.2 - - - -
11A ASN* 1.3 76.2 - - - +
13A GLN* 1.3 64.7 + - - +
15A ASN* 3.3 8.0 + - + +
16A LYS* 3.2 46.1 + - + +
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Residues in contact with GLN 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 LEU 3.0 13.4 + - - +
10A LEU* 2.9 10.6 + - + +
12A GLU* 1.3 74.7 - - - +
14A ILE* 1.3 66.1 + - - +
16A LYS* 3.1 19.1 + - - +
17A GLU* 3.0 48.3 + - - +
57A LEU* 3.6 20.6 - - + -
97A ILE* 4.5 7.5 - - - +
100A SER* 3.5 27.6 - - - +
101A ILE* 3.9 20.9 - - + +
104A LEU* 3.6 26.1 - - + +
120A LEU* 6.2 0.2 - - + -
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Residues in contact with ILE 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 LEU* 2.8 17.1 + - + +
11A ASN* 3.7 15.5 - - - +
12A GLU 3.3 0.2 - - - -
13A GLN* 1.3 75.8 - - - +
15A ASN* 1.3 63.1 + - - +
17A GLU* 3.3 6.1 + - - +
18A MET* 3.0 36.0 + - + +
54A ALA* 4.2 7.6 - - + +
57A LEU* 3.6 25.6 - - + -
58A ILE* 3.7 39.9 - - + +
61A LEU* 3.5 31.9 - - + -
68A VAL* 5.0 4.0 - - + -
70A LEU* 4.3 14.1 - - + -
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Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN 3.2 10.8 + - - +
12A GLU* 3.5 11.2 - - + +
13A GLN 3.2 0.6 - - - -
14A ILE* 1.3 80.5 - - - +
16A LYS* 1.3 65.5 + - - +
18A MET* 3.2 12.1 + - + +
19A TYR* 2.9 25.0 + - - +
71A GLN* 3.5 28.1 + - + +
72A GLU 3.1 28.5 + - - +
73A VAL* 4.5 8.8 - - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.2 39.3 + - + +
13A GLN* 3.1 21.8 + - - +
15A ASN* 1.3 78.3 - - - +
17A GLU* 1.3 58.1 + - - +
19A TYR* 3.2 9.5 + - - +
20A ALA* 2.9 28.8 + - - +
93A HIS* 4.7 2.6 - - + -
96A PHE* 3.3 34.5 - - + -
97A ILE* 5.5 7.0 - - + -
100A SER* 3.3 34.9 + - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.0 35.8 + - - +
14A ILE 3.6 6.1 - - - +
16A LYS* 1.3 74.6 - - - +
18A MET* 1.3 64.7 + - - +
20A ALA* 3.3 4.6 + - - +
21A ALA* 3.0 22.9 + - - +
50A GLU* 2.5 41.9 - - - +
51A SER* 5.2 0.2 - - - -
53A HIS* 3.8 19.2 + - + +
54A ALA* 3.8 18.6 - - + +
57A LEU* 4.4 8.3 - - + -
97A ILE* 4.1 15.9 - - - +
101A ILE* 4.8 0.3 - - - +
123A TYR* 4.1 14.4 - - - -
127A GLN* 5.4 0.3 - - - +
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Residues in contact with MET 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.0 22.5 + - + +
15A ASN* 3.2 12.3 + - - +
17A GLU* 1.3 76.1 - - - +
19A TYR* 1.3 63.5 + - - +
21A ALA* 3.5 7.9 + - - +
22A ASN* 3.4 24.9 + - - -
51A SER* 6.1 0.7 - - - +
54A ALA* 4.1 15.9 - - + -
58A ILE* 5.6 3.8 - - - -
70A LEU* 3.8 42.2 - - + -
71A GLN 4.7 6.3 - - - +
73A VAL* 4.0 27.6 - - + -
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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
----------------------------------------------------------
15A ASN* 2.9 17.7 + - - +
16A LYS* 3.5 11.4 - - - +
17A GLU 3.2 0.4 - - - -
18A MET* 1.3 76.2 - - - +
20A ALA* 1.3 61.9 + - - +
22A ASN* 3.2 4.0 + - + +
23A LEU* 2.9 42.6 + - + +
73A VAL* 3.8 13.4 - - + +
74A LYS* 3.4 39.3 - - + +
75A GLN 3.9 9.7 + - - -
76A PRO* 3.8 26.0 - - + +
77A GLU* 4.4 9.9 + - - +
93A HIS* 3.8 24.5 - + - -
96A PHE* 6.4 0.4 - + - -
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Residues in contact with ALA 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 LYS 2.9 13.6 + - - +
17A GLU 3.3 1.5 + - - +
19A TYR* 1.3 77.4 - - - +
21A ALA* 1.3 62.0 + - - +
23A LEU* 3.2 4.0 + - - +
24A TYR* 2.8 35.3 + - + -
50A GLU* 3.6 22.4 - - + -
93A HIS* 3.2 34.5 - - + +
97A ILE* 3.9 7.4 - - + -
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Residues in contact with ALA 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 GLU 3.0 13.2 + - - +
18A MET* 3.6 11.2 - - - +
19A TYR 3.2 0.2 - - - -
20A ALA* 1.3 77.4 - - - +
22A ASN* 1.3 61.0 + - - +
24A TYR 3.2 0.2 + - - -
25A LEU* 2.8 32.9 + - + +
47A ALA* 3.5 30.3 - - + +
50A GLU* 4.2 5.3 - - - +
51A SER* 4.2 17.3 - - - +
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Residues in contact with ASN 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 MET 3.4 6.9 + - - -
19A TYR* 3.2 7.4 + - + +
21A ALA* 1.3 74.6 - - - +
23A LEU* 1.3 61.4 + - - +
25A LEU* 3.5 19.4 - - - +
26A SER* 2.8 31.5 + - - -
73A VAL* 3.3 32.7 - - + +
76A PRO* 3.9 18.2 - - + +
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Residues in contact with LEU 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* 2.9 31.0 + - + +
20A ALA* 3.2 8.3 + - - +
22A ASN* 1.3 77.6 - - - +
24A TYR* 1.3 61.8 + - + +
26A SER* 3.1 4.7 + - - -
27A MET* 3.0 56.5 + - + +
76A PRO* 3.8 20.8 - - + +
77A GLU* 4.3 24.0 - - + +
80A PHE* 4.6 1.6 - - + -
89A LYS* 5.8 0.9 - - + +
93A HIS* 3.6 42.4 - - + +
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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
----------------------------------------------------------
20A ALA* 2.8 30.0 + - + +
21A ALA 3.7 2.9 - - - +
23A LEU* 1.3 77.1 - - + +
25A LEU* 1.3 60.5 + - - +
27A MET* 3.2 19.7 + - - +
28A SER* 2.9 29.3 + - - -
43A LEU* 3.8 16.8 - - + +
46A HIS* 3.4 26.2 - + + -
47A ALA* 4.0 13.0 - - + -
50A GLU* 3.7 18.6 - - + -
90A THR* 3.8 28.2 + - + -
93A HIS* 3.1 32.1 + - + +
94A GLU* 2.5 36.6 + - - +
97A ILE* 4.3 0.9 - - - +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 2.8 19.3 + - + +
22A ASN* 3.5 23.8 - - - +
24A TYR* 1.3 77.0 - - - +
26A SER* 1.3 61.8 + - - +
28A SER* 3.4 5.7 - - - -
29A SER* 3.3 23.9 + - - -
44A PHE* 4.0 35.0 - - + +
47A ALA* 3.8 19.2 - - + +
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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 ASN 2.8 18.8 + - - -
23A LEU 3.3 5.6 - - - -
25A LEU* 1.3 75.2 - - - +
27A MET* 1.3 64.8 + - - +
29A SER* 3.3 7.6 + - - -
30A TRP* 3.2 19.8 + - - +
76A PRO* 4.0 12.9 - - - +
77A GLU 2.9 26.2 + - - -
78A GLN* 3.8 13.7 - - - +
80A PHE* 4.7 1.6 - - - -
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.0 30.6 + - + +
24A TYR* 3.2 20.2 + - - +
26A SER* 1.3 75.3 - - - +
28A SER* 1.3 62.2 + - - +
30A TRP* 3.3 3.8 + - - +
31A CYS* 3.1 26.9 + - - -
43A LEU* 3.8 14.6 - - + -
77A GLU* 5.4 0.4 - - - +
80A PHE* 3.4 44.6 - - + -
86A VAL* 3.6 17.5 - - + +
89A LYS* 3.6 27.4 - - + -
90A THR* 3.2 23.6 - - - +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR 2.9 13.6 + - - -
25A LEU* 3.4 12.8 - - - -
26A SER 3.2 0.2 - - - -
27A MET* 1.3 77.0 - - - +
29A SER* 1.3 63.8 + - - +
31A CYS* 3.2 6.2 + - - +
32A TYR* 3.1 34.6 + - - -
40A GLY* 2.7 28.0 + - - -
43A LEU* 3.9 9.6 - - - +
44A PHE* 3.6 26.4 - - - +
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU 3.3 9.2 + - - -
26A SER* 3.3 10.5 + - - -
28A SER* 1.3 75.4 + - - +
30A TRP* 1.3 66.8 + - - +
32A TYR* 3.1 13.1 + - - +
33A GLU* 3.0 34.2 + - - +
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 3.2 10.9 + - - +
27A MET 3.5 7.2 - - - +
28A SER 3.3 0.2 - - - -
29A SER* 1.3 77.8 - - - +
31A CYS* 1.3 68.7 + - - +
33A GLU* 3.1 13.4 + - - -
34A ASN* 2.7 61.5 + - + +
36A LEU* 4.0 21.1 - - + -
78A GLN 4.0 15.3 - - - +
79A ASN* 4.2 10.6 - - - +
80A PHE* 3.4 56.2 + + + +
81A LYS 4.1 3.1 - - - -
82A SER* 3.5 30.7 - - - -
83A LEU 4.1 0.4 - - - -
86A VAL* 3.7 24.2 - - + -
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Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET 3.1 18.1 + - - -
28A SER 3.4 8.5 - - - +
30A TRP* 1.3 96.7 - - - +
32A TYR* 1.3 58.3 + - - +
34A ASN 3.1 6.6 + - - +
36A LEU* 2.7 55.5 + - + +
39A ALA* 3.8 21.1 - - - -
40A GLY 3.7 5.4 - - - +
43A LEU* 4.2 13.7 - - - -
83A LEU* 5.0 2.2 - - - -
86A VAL* 4.4 9.9 - - - -
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 3.1 43.2 + - - -
29A SER* 3.1 10.7 + - - +
31A CYS* 1.3 76.0 - - - +
33A GLU* 1.3 63.7 + - + +
34A ASN 3.3 0.5 + - - -
35A SER* 3.3 11.4 + - - -
36A LEU 4.7 2.7 - - - +
37A ASP* 3.7 33.8 - - + +
40A GLY* 3.5 11.4 - - - -
41A ALA* 3.2 24.9 + - - +
44A PHE* 4.8 10.9 - + + +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 3.0 26.8 + - - +
30A TRP* 3.1 16.3 + - - +
32A TYR* 1.3 76.5 - - + +
34A ASN* 1.3 66.5 + - - +
35A SER* 3.4 2.8 + - - -
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Residues in contact with ASN 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 2.7 61.0 + - + +
31A CYS 3.1 5.2 + - - +
33A GLU* 1.3 87.9 - - - +
35A SER* 1.3 72.7 + - - +
36A LEU* 3.2 24.0 + - + +
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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