Contacts of the helix formed by residues 5 - 36 (chain B) in PDB entry 1NNQ
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 ARG 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 5.3 1.2 + - - -
98A GLN* 3.3 71.9 + - + +
100A GLU* 2.9 24.0 + - + +
3B VAL* 4.2 0.2 - - - +
4B LYS* 1.3 77.4 - - - +
6B THR* 1.3 67.0 + - - +
7B MET 3.3 0.4 + - - -
8B THR* 3.5 0.9 + - - -
9B LYS* 3.1 23.9 + - - +
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Residues in contact with THR 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 5.1 0.8 - - - +
4B LYS 3.2 6.1 + - - -
5B ARG* 1.3 72.7 - - - +
7B MET* 1.3 70.8 + - - +
9B LYS* 3.6 8.0 - - + +
10B LYS* 3.1 31.9 + - + +
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Residues in contact with MET 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 5.8 1.3 - - + -
98A GLN* 3.6 23.3 + - - +
5B ARG 3.3 1.0 - - - -
6B THR* 1.3 84.7 - - - +
8B THR* 1.3 57.0 + - - +
10B LYS* 3.2 32.5 + - - +
11B PHE* 2.9 64.2 + - + -
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Residues in contact with THR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR 5.6 1.1 - - - +
94A ALA* 3.8 2.3 + - - +
95A ALA* 3.6 24.2 + - + -
98A GLN* 2.7 27.4 + - - +
100A GLU* 3.9 12.8 - - + -
103A ALA* 3.4 33.0 - - + -
3B VAL* 3.7 15.9 - - + -
5B ARG 3.5 2.4 + - - -
7B MET* 1.3 74.6 - - - +
9B LYS* 1.3 53.0 + - - +
11B PHE* 3.2 11.7 + - + +
12B LEU* 2.8 34.5 + - + +
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Residues in contact with LYS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 3.7 26.2 - - + +
4B LYS* 4.6 9.0 - - - +
5B ARG 3.1 17.9 + - - +
6B THR* 3.6 7.4 - - + +
8B THR* 1.3 74.0 - - - +
10B LYS* 1.3 59.8 + - - +
12B LEU* 3.2 3.3 + - - +
13B GLU* 2.9 50.3 + - - +
63B LEU* 3.7 21.9 - - + +
65B LYS* 6.2 0.9 - - - +
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Residues in contact with LYS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 3.1 22.7 + - + +
7B MET* 3.6 38.9 - - - +
9B LYS* 1.3 79.5 - - - +
11B PHE* 1.3 66.2 + - + +
13B GLU* 3.3 15.4 + - - +
14B GLU* 3.0 27.9 + - + +
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 5.1 7.2 - - + -
91A TYR* 3.2 62.1 - + + +
94A ALA* 3.7 31.2 - - + -
7B MET* 2.9 50.6 + - + -
8B THR* 3.2 10.7 + - + +
10B LYS* 1.3 84.5 - - + +
12B LEU* 1.3 61.5 + - + +
14B GLU* 3.1 2.4 + - + +
15B ALA* 2.8 24.4 + - - +
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR* 6.0 0.4 - - + -
103A ALA* 4.2 13.0 - - + -
106A THR* 3.8 9.2 - - - +
107A THR* 4.2 15.0 - - + -
3B VAL* 3.7 28.3 - - + -
8B THR* 2.8 21.8 + - + +
9B LYS* 3.2 4.9 + - - +
11B PHE* 1.3 73.1 - - + +
13B GLU* 1.3 52.6 + - - +
15B ALA* 3.2 4.3 + - + +
16B PHE* 2.7 35.9 + - - +
59B HIS* 3.5 40.1 - - + +
62B ALA* 3.8 20.4 - - + -
63B LEU* 4.0 16.8 - - + -
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 5.1 1.2 - - - +
9B LYS* 2.9 45.6 + - - +
10B LYS* 3.5 15.6 + - - +
12B LEU* 1.3 74.2 - - - +
14B GLU* 1.3 57.5 + - - +
16B PHE* 3.5 6.1 + - - +
17B ALA* 3.0 27.2 + - - +
63B LEU* 3.8 17.5 - - + +
65B LYS* 3.8 24.0 + - - -
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A MET* 5.1 11.1 - - + +
91A TYR* 3.4 22.4 - - + +
10B LYS* 3.0 13.5 + - + +
11B PHE* 3.1 8.7 + - + +
13B GLU* 1.3 73.0 - - - +
15B ALA* 1.3 61.2 + - - +
17B ALA* 3.2 13.7 + - - +
18B GLY* 2.8 27.5 + - - -
21B MET* 5.4 4.7 - - - +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A MET* 4.7 6.7 - - - -
88A TYR* 3.8 18.8 - - + +
91A TYR* 4.1 12.5 - - + -
11B PHE 2.8 17.0 + - - +
12B LEU* 3.6 8.7 - - + +
14B GLU* 1.3 74.7 - - - +
16B PHE* 1.3 59.6 + - - +
18B GLY* 3.6 1.2 - - - +
19B GLU* 2.8 35.3 + - - +
59B HIS* 3.7 23.8 - - + +
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.8 30.3 - - + -
24A MET* 3.8 24.2 - - + -
25A ARG* 4.0 20.0 - - + -
28A ILE* 4.1 2.2 - - + -
12B LEU 2.7 20.0 + - - +
13B GLU* 3.7 8.1 - - - +
15B ALA* 1.3 70.3 - - - +
17B ALA* 1.3 60.6 + - - +
19B GLU* 3.4 3.2 + - - +
20B SER* 2.7 45.8 + - - -
56B ALA* 3.3 29.4 - - + -
59B HIS* 3.9 13.8 - - + -
60B PHE* 3.4 38.1 - + + -
63B LEU* 4.8 5.8 - - + -
65B LYS* 6.3 1.6 - - + -
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 5.7 1.1 - - + -
21A MET* 3.8 31.6 - - + +
13B GLU 3.0 14.9 + - - +
14B GLU* 3.4 18.4 - - - +
16B PHE* 1.3 77.5 - - - +
18B GLY* 1.3 62.0 + - - +
20B SER* 3.3 2.3 + - - -
21B MET* 3.0 39.3 + - + +
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 4.4 11.6 - - - +
87A MET* 5.3 8.5 - - - -
14B GLU* 2.8 19.6 + - - -
15B ALA* 3.7 3.4 - - - -
17B ALA* 1.3 71.4 - - - +
19B GLU* 1.3 57.2 + - - +
21B MET* 3.5 13.0 + - - +
22B ALA* 3.0 29.8 + - - +
25B ARG* 4.7 2.8 + - - -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 4.3 5.9 - - - +
88A TYR* 2.4 28.8 + - - +
114A GLU* 3.1 4.9 - - - +
15B ALA 2.8 28.7 + - - +
16B PHE 3.9 0.2 - - - +
18B GLY* 1.3 69.8 - - - +
20B SER* 1.3 61.2 + - - +
22B ALA* 3.4 2.8 + - - +
23B HIS* 3.0 30.0 + - - +
52B GLU* 3.1 23.2 - - - +
55B HIS* 3.5 12.7 - - + +
56B ALA* 3.6 23.1 - - + -
59B HIS* 3.8 12.6 - - + -
202B ZN 2.3 34.8 - - - -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER* 3.6 29.9 - - - +
21A MET* 3.9 6.3 - - - -
24A MET* 3.5 30.2 - - - +
16B PHE* 2.7 32.2 + - - -
17B ALA 3.5 4.9 - - - -
19B GLU* 1.3 77.1 - - - +
21B MET* 1.3 56.2 + - - +
23B HIS* 3.5 5.0 + - - +
24B MET* 3.0 28.2 + - - +
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Residues in contact with MET 21 (chain B).
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 5.1 1.6 - - - +
16A PHE* 3.8 22.8 - - + -
17A ALA* 3.7 32.3 - - + +
20A SER* 3.8 17.9 - - - +
14B GLU* 5.4 5.2 - - - +
17B ALA* 3.0 34.7 + - + +
18B GLY* 3.9 8.7 - - - +
19B GLU 3.4 0.2 - - - -
20B SER* 1.3 74.0 - - - +
22B ALA* 1.3 60.6 + - - +
24B MET* 3.3 1.7 + - - +
25B ARG* 2.8 52.4 + - - +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLU* 5.5 0.4 - - - +
83A GLU* 5.0 9.4 - - - +
18B GLY 3.0 19.0 + - - +
19B GLU* 3.8 6.1 - - - +
21B MET* 1.3 76.2 - - - +
23B HIS* 1.3 57.8 + - - +
25B ARG* 3.4 20.2 + - - +
26B TYR* 2.9 56.5 + - + +
52B GLU* 4.3 10.3 - - + +
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Residues in contact with HIS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER 5.9 0.2 - - - -
23A HIS* 3.1 39.4 + + - -
24A MET* 3.5 19.1 - - + +
27A LEU* 3.7 15.3 - - + +
19B GLU 3.0 18.8 + - - +
20B SER 3.5 5.2 - - - +
22B ALA* 1.3 76.3 - - - +
24B MET* 1.3 59.6 + - - +
26B TYR* 3.3 3.1 + - - +
27B LEU* 3.0 49.4 + - + +
49B ALA* 2.8 33.6 + - + +
50B TYR* 4.8 1.3 - - - -
52B GLU* 4.0 14.0 - - + +
53B PHE* 4.0 8.7 - - + +
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Residues in contact with MET 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.8 10.3 - - + -
19A GLU 4.1 0.7 - - - +
20A SER* 3.3 32.8 - - - +
23A HIS* 3.4 43.5 - - + +
53A PHE* 3.6 43.1 - - - +
56A ALA* 3.7 25.1 - - + -
20B SER 3.0 13.1 + - - +
21B MET 3.5 3.4 - - - +
23B HIS* 1.3 76.5 - - - +
25B ARG* 1.3 64.6 + - - +
27B LEU* 3.1 8.0 + - - +
28B ILE* 3.0 30.0 + - + +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.9 10.5 - - + -
60A PHE* 3.4 32.5 - - + -
75A MET* 3.8 27.0 + - - +
79A GLY* 5.5 9.5 - - - -
18B GLY* 4.7 2.6 + - - -
21B MET* 2.8 42.0 + - - +
22B ALA* 3.6 28.4 - - - +
24B MET* 1.3 72.3 - - - +
26B TYR* 1.3 66.9 + - + +
28B ILE* 3.2 9.5 + - - +
29B PHE* 2.7 45.2 + - + -
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Residues in contact with TYR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLY* 3.8 18.7 + - - -
79A GLY* 5.5 1.2 - - - -
80A GLU* 2.6 27.5 + - - +
121A TYR* 3.3 36.7 - + - -
22B ALA* 2.9 31.3 + - + +
23B HIS 3.8 4.3 - - - +
25B ARG* 1.3 84.8 + - + +
27B LEU* 1.3 58.0 + - - +
29B PHE* 3.7 15.2 - + - -
30B ALA* 2.9 29.1 + - - +
45B PHE* 3.5 32.6 - + + +
48B ILE* 3.8 10.3 - - + -
49B ALA* 3.8 6.1 - - + -
52B GLU* 3.3 32.3 - - + -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A HIS* 3.7 20.0 - - + +
53A PHE* 3.9 23.8 - - + -
23B HIS* 3.0 46.3 + - + +
24B MET* 3.1 9.2 + - - +
26B TYR* 1.3 73.6 - - - +
28B ILE* 1.3 64.8 + - - +
30B ALA* 3.4 5.4 + - + +
31B GLU* 3.4 21.7 + - - +
46B ARG* 4.6 18.6 - - + +
49B ALA* 3.9 17.3 - - + -
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 4.0 13.7 - - + -
53A PHE* 3.9 20.9 - - + -
57A LYS* 3.8 34.3 - - + +
60A PHE* 3.8 35.4 - - + -
61A ILE* 5.3 0.4 - - + -
66A LEU* 3.8 29.2 - - + +
24B MET* 3.0 25.9 + - + +
25B ARG* 3.5 7.9 - - - +
27B LEU* 1.3 71.7 - - - +
29B PHE* 1.3 67.4 + - + +
31B GLU* 3.4 7.4 + - - +
32B LYS* 3.2 20.3 + - - +
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.8 26.5 - + - -
65A LYS 4.3 1.3 - - - -
66A LEU* 3.8 8.7 - - + -
69A THR* 4.9 0.2 + - - -
72A ASN* 3.4 57.2 + - + +
75A MET* 3.9 30.1 - - + -
76A GLY 4.7 0.7 - - - -
25B ARG* 2.7 34.4 + - + +
26B TYR* 3.8 15.5 - + - +
28B ILE* 1.3 74.0 - - - +
30B ALA* 1.3 57.8 + - - +
32B LYS* 3.3 5.8 + - - +
33B ALA* 2.9 29.8 + - - +
45B PHE* 3.7 35.8 - + + -
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR 2.9 19.2 + - - +
27B LEU* 3.5 8.1 - - - +
29B PHE* 1.3 76.5 - - - +
31B GLU* 1.3 62.8 + - - +
33B ALA 3.1 2.3 + - - -
34B GLU* 3.0 20.8 + - - +
42B ALA* 3.3 16.5 - - + +
45B PHE* 3.8 20.4 - - + -
46B ARG* 3.9 27.8 - - + -
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 5.1 4.9 + - - -
53A PHE* 3.8 15.3 - - + -
57A LYS* 2.6 43.1 + - - +
27B LEU 3.4 8.4 + - - +
28B ILE 3.7 8.2 - - - +
30B ALA* 1.3 80.4 - - - +
32B LYS* 1.3 61.1 + - - +
34B GLU* 3.5 6.0 + - - +
35B GLN* 3.2 45.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.1 29.6 - - + -
67A GLY 3.5 29.2 + - - +
68A LYS* 5.5 2.8 - - - +
72A ASN* 3.9 7.2 - - - +
28B ILE 3.2 14.0 + - - +
29B PHE 3.7 7.2 - - - +
30B ALA 3.2 0.2 - - - -
31B GLU* 1.3 74.5 - - - +
33B ALA* 1.3 63.8 + - - +
35B GLN* 3.5 20.6 + - + +
36B GLU* 3.1 44.3 + - + +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 3.3 19.9 + - - +
29B PHE 2.9 17.6 + - - +
30B ALA 3.1 5.8 + - - +
32B LYS* 1.3 75.9 - - - +
34B GLU* 1.3 60.8 + - - +
36B GLU* 3.3 7.6 + - - -
37B GLY 3.3 0.2 + - - -
38B PHE* 2.8 32.9 + - + +
41B ILE* 4.2 13.5 - - + -
42B ALA* 3.8 22.4 - - - +
45B PHE* 4.2 2.5 - - + -
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 3.0 10.8 + - - +
31B GLU* 3.8 10.1 - - - +
32B LYS 3.3 0.2 - - - -
33B ALA* 1.3 76.1 - - - +
35B GLN* 1.3 57.2 + - + +
37B GLY* 2.9 20.8 + - - -
38B PHE 4.5 5.2 - - - +
39B PRO* 4.8 6.4 - - + +
42B ALA* 4.0 12.7 - - + +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU* 3.2 38.2 + - + +
32B LYS* 3.8 24.9 + - + +
33B ALA 3.4 0.2 - - - -
34B GLU* 1.3 78.7 - - + +
36B GLU* 1.3 59.8 + - + +
37B GLY 3.5 0.9 + - - -
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 3.4 31.6 - - - +
69A THR* 2.8 38.3 + - - -
70A PRO* 5.0 0.7 - - - +
32B LYS* 3.1 35.4 + - + +
33B ALA 3.8 4.7 - - - +
34B GLU 3.1 0.4 - - - -
35B GLN* 1.3 76.5 - - + +
37B GLY* 1.3 60.4 + - - +
38B PHE* 3.6 23.2 - - + -
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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
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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