Contacts of the helix formed by residues 2 - 33 (chain A) in PDB entry 2QQY
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 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 1.3 82.4 - - - +
3A HIS* 1.3 64.3 + - - +
4A ASP* 3.4 10.7 + - - +
5A VAL* 2.9 33.2 + - - +
6A LYS* 3.1 18.7 + - - +
111A LEU* 4.6 2.8 - - - +
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Residues in contact with HIS 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 1.3 74.4 - - - +
4A ASP* 1.3 65.4 + - - +
6A LYS* 3.4 19.0 + - + +
7A GLU* 3.0 50.1 + - + +
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Residues in contact with ASP 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.2 9.1 + - - +
3A HIS* 1.3 88.2 - - - +
5A VAL* 1.3 55.0 + - - +
7A GLU* 3.0 27.1 - - + +
8A LEU* 3.0 28.4 + - - +
107A GLN* 5.9 0.3 - - - +
110A ASN* 6.1 0.9 - - - +
111A LEU* 3.8 28.1 - - + +
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Residues in contact with VAL 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.9 14.8 - - + -
2A SER* 2.9 30.2 + - - +
4A ASP* 1.3 74.0 - - - +
6A LYS* 1.3 62.9 + - - +
8A LEU* 3.2 6.8 + - - +
9A ILE* 2.9 49.5 + - + +
66A LEU* 4.1 19.1 - - + +
111A LEU* 4.3 10.5 - - + -
113A MSE 4.3 22.4 - - + -
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Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.5 32.5 - - + +
2A SER 3.1 14.9 + - - +
3A HIS* 3.4 22.2 - - + +
5A VAL* 1.3 78.6 - - - +
7A GLU* 1.3 58.0 + - + +
9A ILE* 3.5 3.3 + - - +
10A GLU* 2.7 56.5 + - - +
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 3.0 34.0 + - + +
4A ASP* 3.0 43.9 - - - +
6A LYS* 1.3 74.0 - - + +
8A LEU* 1.3 59.7 + - + +
10A GLU* 3.7 15.4 + - - +
11A GLY* 3.1 21.5 + - - -
103A LYS* 4.9 0.9 + - - -
107A GLN* 3.4 35.5 + - + +
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP 3.0 17.9 + - - +
5A VAL* 3.6 7.2 - - - +
7A GLU* 1.3 77.0 - - - +
9A ILE* 1.3 55.8 + - - +
11A GLY* 3.1 4.0 + - - -
12A LEU* 2.8 37.4 + - + +
66A LEU* 3.8 19.7 - - + -
104A ARG* 3.9 26.0 - - + +
107A GLN* 4.0 24.5 - - + -
108A ALA* 4.2 5.6 - - - +
111A LEU* 3.9 13.7 - - + -
113A MSE 3.5 33.9 - - + -
116A LEU* 4.0 14.4 - - + -
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Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 3.7 24.9 - - + -
5A VAL* 2.9 23.6 + - + +
6A LYS* 3.7 4.7 - - - +
8A LEU* 1.3 73.0 - - - +
10A GLU* 1.3 65.7 + - + +
12A LEU* 3.3 9.2 + - + +
13A ASN* 2.9 39.0 + - - +
63A ILE* 4.1 9.0 - - + +
66A LEU* 3.5 49.6 - - + +
68A GLY* 3.8 25.4 - - - +
69A THR 4.9 0.4 - - - +
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 2.7 59.3 + - + +
7A GLU* 3.8 12.1 - - - +
9A ILE* 1.3 76.6 - - + +
11A GLY* 1.3 57.6 + - - +
13A ASN* 3.4 8.0 + - - +
14A GLU* 3.0 37.4 + - - +
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Residues in contact with GLY 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU 3.1 9.7 + - - -
8A LEU 3.1 7.2 + - - -
10A GLU* 1.3 73.0 - - - +
12A LEU* 1.3 59.1 + - - +
14A GLU* 3.0 13.7 + - - +
15A ASP 2.9 23.4 + - - -
104A ARG* 3.1 39.3 + - - -
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 2.8 29.1 + - + +
9A ILE* 3.3 8.3 + - - +
11A GLY* 1.3 70.8 - - - +
13A ASN* 1.3 52.3 + - - +
15A ASP* 3.2 11.4 + - - +
16A LEU* 2.7 35.0 + - - +
59A LEU* 3.8 20.7 - - + +
62A LYS* 3.9 16.2 - - + -
63A ILE* 3.6 27.5 - - + +
66A LEU* 3.8 28.3 - - + -
104A ARG* 3.4 26.3 - - + +
116A LEU* 4.8 13.5 - - + -
120A LEU* 5.1 1.8 - - + -
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Residues in contact with ASN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 2.9 32.5 + - - +
10A GLU* 3.7 7.9 - - - +
12A LEU* 1.3 72.7 - - - +
14A GLU* 1.3 66.1 + - - +
16A LEU* 3.5 1.4 + - - +
17A ALA* 3.0 21.1 + - - +
63A ILE* 3.4 9.6 - - - +
69A THR 3.0 21.5 + - - +
70A PRO* 3.4 6.2 - - - +
71A THR* 2.8 44.7 + - + +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 3.0 26.6 + - - +
11A GLY* 3.0 18.1 + - - +
13A ASN* 1.3 74.9 - - - +
15A ASP* 1.3 63.8 + - - +
17A ALA* 3.2 9.2 + - - +
18A GLY* 3.0 20.4 + - - -
75A LEU* 4.7 5.5 - - + +
100A ARG* 4.2 25.4 + - - +
104A ARG* 4.4 5.4 + - - +
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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
----------------------------------------------------------
11A GLY 2.9 11.7 + - - +
12A LEU* 3.3 15.1 - - - +
14A GLU* 1.3 76.3 - - - +
16A LEU* 1.3 57.3 + - - +
18A GLY* 3.3 2.6 + - - -
19A GLU* 2.9 31.7 + - - +
59A LEU* 4.0 8.1 - - + -
100A ARG* 3.4 23.8 + - - +
101A TYR* 3.5 34.1 + - + -
104A ARG* 2.7 46.3 + - - +
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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
----------------------------------------------------------
12A LEU 2.7 19.3 + - - +
13A ASN* 3.7 6.3 - - - +
14A GLU 3.3 0.2 - - - -
15A ASP* 1.3 70.5 - - - +
17A ALA* 1.3 65.8 + - - +
19A GLU* 3.1 3.2 + - - +
20A TYR* 3.0 50.5 + - + +
56A ALA* 3.4 39.0 - - + +
59A LEU* 3.9 11.4 - - + +
60A ALA* 3.9 9.2 - - + -
63A ILE* 4.0 10.3 - - + -
70A PRO* 3.8 23.8 - - + -
71A THR* 3.5 26.2 - - + +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN 3.0 14.8 + - - +
14A GLU* 3.5 10.5 - - - +
16A LEU* 1.3 75.0 - - - +
18A GLY* 1.3 56.0 + - - +
20A TYR* 3.5 2.2 + - - -
21A SER 3.0 23.4 + - - -
71A THR* 4.0 7.5 - - + +
73A ILE 3.3 24.7 - - - +
74A PRO* 3.5 3.1 - - - +
75A LEU* 3.1 34.2 + - + +
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU 3.0 11.5 + - - -
15A ASP 3.6 3.4 - - - -
17A ALA* 1.3 76.0 - - - +
19A GLU* 1.3 58.8 + - - +
21A SER* 3.4 4.9 - - - -
22A ALA* 3.0 26.5 + - - +
75A LEU* 3.7 22.6 - - - +
93A SER* 5.5 0.9 + - - -
97A THR* 5.1 3.6 + - - -
100A ARG* 3.9 14.9 + - - -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP 2.9 18.1 + - - +
16A LEU 3.1 7.8 + - - +
18A GLY* 1.3 74.6 - - - +
20A TYR* 1.3 65.2 + - - +
22A ALA* 3.1 7.1 + - - +
23A ILE* 3.0 28.7 + - - +
52A GLU* 2.4 42.6 - - - +
55A HIS* 3.2 20.8 + - + +
56A ALA* 4.2 18.4 - - + -
59A LEU* 3.7 11.2 - - + -
97A THR* 4.2 8.7 - - + +
101A TYR* 2.7 31.0 + - - +
127A GLU* 4.6 0.2 - - - +
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Residues in contact with TYR 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 42.5 + - + +
17A ALA* 3.9 5.6 - - - +
19A GLU* 1.3 74.8 - - - +
21A SER* 1.3 63.2 + - - +
23A ILE* 3.4 18.4 + - + +
24A ILE* 3.0 28.9 + - + +
56A ALA* 4.0 16.7 + - + +
60A ALA* 4.6 8.1 - - - +
70A PRO* 5.9 0.2 - - - +
71A THR 3.4 26.0 + - - -
72A THR* 4.2 20.1 - - + +
73A ILE 5.0 0.4 - - - -
74A PRO* 3.8 18.8 - - + -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 3.0 17.0 + - - -
18A GLY* 3.4 6.7 - - - -
20A TYR* 1.3 78.0 - - - +
22A ALA* 1.3 57.3 + - - +
24A ILE* 3.3 4.3 + - - +
25A MSE 2.8 29.3 + - - +
74A PRO* 3.8 4.4 - - - +
75A LEU* 3.1 36.5 + - - +
76A ARG 3.2 13.7 + - - -
77A VAL* 3.7 10.5 - - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.0 14.8 + - - +
19A GLU* 3.1 11.2 + - - +
21A SER* 1.3 74.4 - - - +
23A ILE* 1.3 61.2 + - - +
25A MSE 3.6 13.8 - - + +
26A TYR* 2.8 46.6 + - + -
52A GLU* 3.9 21.5 - - + -
93A SER* 4.7 8.3 - - - +
94A GLU* 5.4 1.6 - - - +
97A THR* 5.9 2.2 - - - +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 3.0 18.2 + - - +
20A TYR* 3.6 20.6 - - + +
22A ALA* 1.3 75.9 - - - +
24A ILE* 1.3 65.2 + - + +
26A TYR* 3.5 4.0 + - - +
27A ASN* 3.1 24.0 + - + +
49A ILE* 4.2 22.9 - - + +
52A GLU* 3.8 20.8 - - + +
53A GLN* 3.8 36.6 - - + +
56A ALA* 4.1 12.6 - - + -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.0 21.1 + - + +
21A SER* 3.6 7.2 - - - +
23A ILE* 1.3 78.4 - - + +
25A MSE 1.3 57.6 + - - +
27A ASN* 3.3 5.7 + - - +
28A HIS* 2.8 36.4 + - + +
74A PRO* 4.0 27.8 - - + -
77A VAL* 3.9 18.2 - - + -
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Residues in contact with MSE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 2.8 21.2 + - - +
22A ALA* 3.6 6.5 - - + +
24A ILE* 1.3 75.0 - - - +
26A TYR* 1.3 98.3 + - + +
28A HIS* 3.3 4.3 + - - +
29A ASN* 2.8 48.4 + - - +
77A VAL* 3.7 27.8 - - + +
78A LYS 5.8 0.7 - - - +
89A TYR* 4.2 6.5 - - - +
90A ALA* 3.7 30.7 - - + +
93A SER* 3.8 26.2 - - - +
94A GLU* 4.9 0.2 - - - +
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Residues in contact with TYR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 2.8 36.5 + - + +
23A ILE 4.2 0.2 - - - +
25A MSE 1.3 95.1 - - + +
27A ASN* 1.3 60.5 + - - +
29A ASN* 4.4 2.9 - - - +
30A ALA* 2.9 30.3 + - - +
44A PHE* 5.3 2.0 - + - -
45A PHE* 3.5 45.3 - + - +
48A GLU* 3.5 48.6 + - + -
49A ILE* 3.7 13.9 - - + +
52A GLU* 4.4 6.1 - - + -
90A ALA* 4.0 13.9 - - + +
94A GLU* 2.6 35.6 + - - +
134A LEU* 4.4 2.6 - - - +
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.1 16.1 + - + +
24A ILE* 3.7 8.1 - - - +
26A TYR* 1.3 72.7 - - - +
28A HIS* 1.3 70.9 + - - +
30A ALA* 3.2 5.6 + - - +
31A ALA* 3.0 27.4 + - - +
46A GLU* 5.7 1.0 + - - -
49A ILE* 3.7 19.5 - - + +
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Residues in contact with HIS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 2.8 22.6 + - + +
25A MSE 3.5 6.7 - - - +
27A ASN* 1.3 83.0 + - - +
29A ASN* 1.3 70.4 + - - +
31A ALA* 3.4 4.0 + - - +
32A THR* 2.8 59.2 + - + +
77A VAL* 5.6 8.5 - - + -
78A LYS 6.1 0.7 - - - -
79A GLN* 6.0 4.9 - - + +
80A ALA* 5.5 11.2 + - + +
86A MSE 5.5 1.9 - - + +
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Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MSE 2.8 41.3 + - - +
26A TYR* 3.8 4.7 - - - +
28A HIS* 1.3 83.3 - - - +
30A ALA* 1.3 66.3 - - - +
32A THR* 3.8 3.8 - - - -
33A VAL* 3.1 29.8 + - - +
45A PHE* 3.6 32.8 - - + -
80A ALA* 5.2 3.3 - - - +
86A MSE 3.2 40.8 + - - +
90A ALA* 4.7 2.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR 2.9 18.1 + - - +
27A ASN* 3.6 8.5 - - - +
29A ASN* 1.3 77.8 - - - +
31A ALA* 1.3 56.3 + - - +
33A VAL* 3.8 1.5 - - - +
38A ARG* 2.8 28.4 + - - -
42A LYS* 3.7 18.4 - - + +
45A PHE* 3.9 15.0 - - + -
46A GLU* 3.9 31.4 - - + -
49A ILE* 5.0 0.4 - - + -
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.0 22.2 + - - +
28A HIS* 3.6 7.4 - - - +
30A ALA* 1.3 78.9 - - - +
32A THR* 1.3 64.5 + - + +
38A ARG* 3.2 19.5 + - - +
42A LYS* 6.1 0.2 - - - +
----------------------------------------------------------
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 2.8 51.0 + - + +
31A ALA* 1.3 84.1 - - + +
33A VAL* 1.3 70.1 + - - +
34A SER* 3.4 8.1 + - - -
86A MSE 3.5 20.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN 3.1 20.2 + - - +
30A ALA 3.8 10.5 - - - +
31A ALA 3.7 0.2 - - - -
32A THR* 1.3 78.5 + - - +
34A SER* 1.3 67.0 + - - +
37A TYR* 4.7 0.2 - - + -
38A ARG* 2.8 42.5 + - + +
41A LEU* 4.0 17.0 - - + -
42A LYS 4.1 21.3 - - - +
45A PHE* 4.1 5.2 - - + -
83A VAL* 3.9 29.2 - - + -
86A MSE 3.8 18.4 - - - +
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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