Contacts of the helix formed by residues 1 - 28 (chain B) in PDB entry 2SPC
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 ASN 1 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASN* 3.5 36.7 + - - +
0B GLN* 1.3 91.7 + - - +
2B LEU* 1.3 67.5 + - - +
3B ASP* 3.5 2.0 - - - -
4B LEU* 2.8 15.9 + - - +
5B GLN* 2.9 22.1 + - - +
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Residues in contact with LEU 2 (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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1B ASN* 1.3 74.8 - - - +
3B ASP* 1.3 67.8 + - - +
5B GLN* 2.8 28.9 + - + +
6B LEU* 2.9 38.5 + - + +
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Residues in contact with ASP 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B GLN* 4.5 2.5 - - - +
1B ASN 3.5 0.8 - - - -
2B LEU* 1.3 78.2 - - - +
4B LEU* 1.3 63.2 + - - +
6B LEU* 3.9 12.3 - - - +
7B TYR* 3.2 24.3 + - - +
64B VAL* 5.5 0.5 - - - +
68B LEU* 3.4 23.4 - - + +
71B GLN* 2.8 31.3 + - - +
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Residues in contact with LEU 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.8 14.1 - - + +
78A LEU* 3.9 22.0 - - + -
79A VAL* 3.3 31.2 - - + -
0B GLN* 3.6 43.2 - - + +
1B ASN 2.8 12.5 + - - +
3B ASP* 1.3 84.6 - - - +
5B GLN* 1.4 60.7 + - + +
7B TYR* 3.3 2.3 + - - +
8B MET* 3.0 44.4 + - + +
68B LEU* 4.1 8.1 - - + -
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Residues in contact with GLN 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B GLN 5.2 3.0 - - - +
1B ASN* 2.9 24.6 + - - +
2B LEU* 2.8 26.3 + - + +
4B LEU* 1.4 75.9 - - + +
6B LEU* 1.3 65.9 + - + +
8B MET* 3.1 5.6 + - - +
9B ARG* 2.9 24.9 + - - +
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Residues in contact with LEU 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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2B LEU* 2.9 47.9 + - + +
3B ASP* 3.9 10.5 - - - +
5B GLN* 1.3 72.0 - - + +
7B TYR* 1.3 58.4 + - - +
9B ARG* 3.1 8.7 + - + +
10B ASP* 2.8 38.1 + - - +
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Residues in contact with TYR 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.0 39.9 + - + -
82A LYS* 4.3 1.6 - - + -
83A ARG* 3.3 24.1 + - - +
3B ASP 3.2 16.1 + - - +
4B LEU 3.6 2.7 - - - +
6B LEU* 1.3 76.4 - - - +
8B MET* 1.3 91.2 - - + +
10B ASP* 3.7 7.9 - - - +
11B CYS* 3.0 45.8 + - - -
61B LEU* 3.7 24.2 - - + +
64B VAL* 3.5 29.2 - - + -
65B ALA* 3.6 10.1 - - + +
68B LEU* 3.7 17.3 - - + -
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Residues in contact with MET 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.2 34.3 - - + +
79A VAL* 5.1 0.2 - - - -
82A LYS* 3.9 29.1 - - + +
4B LEU* 3.0 38.4 + - + +
5B GLN* 3.1 6.3 + - - +
7B TYR* 1.3 99.0 - - + +
9B ARG* 1.3 64.7 + - - +
11B CYS* 3.3 4.8 + - - +
12B GLU* 2.9 40.1 + - - +
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Residues in contact with ARG 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLN 2.9 16.5 + - - +
6B LEU* 3.5 10.1 - - + +
8B MET* 1.3 78.6 - - - +
10B ASP* 1.3 57.6 + - - +
12B GLU* 2.7 46.3 + - - +
13B LEU* 2.8 63.5 + - + +
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Residues in contact with ASP 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 2.8 28.2 + - - +
7B TYR* 3.7 8.5 - - - +
9B ARG* 1.3 73.9 - - - +
11B CYS* 1.4 56.4 + - - +
13B LEU* 3.3 12.8 + - - +
14B ALA* 2.8 29.1 + - - +
57B LYS* 4.9 2.4 + - - -
61B LEU* 3.8 20.0 - - + +
64B VAL* 5.8 4.9 - - - +
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Residues in contact with CYS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 3.7 25.4 - - + -
83A ARG* 5.5 0.2 - - - -
86A VAL* 3.8 13.5 - - + +
7B TYR* 3.0 61.0 + - - +
8B MET 3.6 4.5 - - - +
10B ASP* 1.4 76.0 - - - +
12B GLU* 1.3 58.1 + - - +
14B ALA* 3.3 7.1 + - - +
15B GLU* 2.8 34.7 + - - +
61B LEU* 4.1 17.7 - - - -
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 4.3 9.7 + - - +
8B MET* 2.9 34.3 + - - +
9B ARG* 2.7 52.6 + - - +
11B CYS* 1.3 73.0 - - - +
13B LEU* 1.3 56.3 + - - +
15B GLU* 3.1 17.1 + - - +
16B SER* 2.7 35.4 + - - -
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Residues in contact with LEU 13 (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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9B ARG* 2.8 57.8 + - + +
10B ASP* 3.8 11.4 - - - +
12B GLU* 1.3 70.7 - - - +
14B ALA* 1.3 66.1 + - - +
16B SER* 2.8 26.7 + - - +
17B TRP* 3.0 10.0 + - - +
57B LYS* 4.1 10.3 - - - +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 5.5 0.4 - - + -
10B ASP 2.8 16.9 + - - +
11B CYS 3.5 5.4 - - - +
13B LEU* 1.3 77.4 - - - +
15B GLU* 1.3 62.2 + - - +
17B TRP* 3.0 6.8 + - + +
18B MET* 2.9 34.3 + - + +
57B LYS* 3.3 32.8 - - + +
58B ILE* 5.0 1.6 - - + -
61B LEU* 3.6 22.7 - - + -
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 2.8 34.1 + - - -
86A VAL* 3.9 16.9 - - + +
89A ARG* 2.3 50.5 + - - +
11B CYS 2.8 20.3 + - - +
12B GLU* 3.1 11.4 + - - +
14B ALA* 1.3 72.3 - - - +
16B SER* 1.3 65.0 + - - +
18B MET* 3.3 19.6 + - + +
19B SER* 3.0 26.4 + - - +
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Residues in contact with SER 16 (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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12B GLU 2.7 13.3 + - - -
13B LEU* 2.8 31.9 + - - +
15B GLU* 1.3 79.0 - - - +
17B TRP* 1.3 59.7 + - - +
19B SER* 3.0 17.3 + - - -
20B ALA* 3.0 14.0 + - - +
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Residues in contact with TRP 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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13B LEU 3.0 10.9 + - - +
14B ALA* 3.0 10.5 + - + +
16B SER* 1.3 77.5 + - - +
18B MET* 1.3 61.6 + - + +
20B ALA* 3.2 8.6 + - + +
21B ARG* 3.1 41.6 + - + +
50B ALA* 5.3 0.7 - - - -
53B GLY* 3.3 25.8 - - - -
54B HIS* 2.9 43.7 + + - -
57B LYS* 3.2 60.6 - - + +
58B ILE* 5.8 1.1 - - + -
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Residues in contact with MET 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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86A VAL* 4.0 27.6 - - + +
89A ARG* 4.4 10.1 - - + +
90A TRP* 3.8 33.2 - - - -
93A LEU* 3.7 28.6 - - + +
14B ALA* 2.9 15.8 + - + +
15B GLU* 3.3 34.1 + - + +
17B TRP* 1.3 77.5 - - + +
19B SER* 1.3 59.0 + - - +
20B ALA 3.3 0.2 - - - -
21B ARG* 3.9 2.8 - - - +
22B GLU* 3.1 30.1 + - - +
54B HIS* 4.2 13.5 - - + +
58B ILE* 4.4 11.7 - - + -
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG* 6.2 0.3 - - - -
15B GLU* 3.0 14.2 + - - +
16B SER* 3.0 11.9 + - - -
18B MET* 1.3 77.7 - - - +
20B ALA* 1.3 64.7 + - - +
22B GLU* 3.9 4.1 - - - +
23B ALA* 3.0 22.5 + - - +
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Residues in contact with ALA 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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16B SER 3.0 11.6 + - - +
17B TRP* 3.5 12.8 - - + +
19B SER* 1.3 79.3 - - - +
21B ARG* 1.3 57.2 + - - +
23B ALA* 2.8 21.3 + - - +
24B PHE* 2.9 14.3 + - - +
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Residues in contact with ARG 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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93A LEU* 3.7 13.0 - - + -
97A LEU* 4.0 15.5 - - + -
17B TRP* 3.1 31.7 + - + +
18B MET 4.0 3.4 - - - +
20B ALA* 1.3 73.8 - - - +
22B GLU* 1.3 53.9 + - - +
23B ALA 2.9 4.8 + - - -
24B PHE* 2.9 26.0 + - + +
25B LEU* 2.8 31.5 + - - +
50B ALA* 2.9 37.1 - - - +
54B HIS* 3.2 35.5 + - + -
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Residues in contact with GLU 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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89A ARG 4.4 2.1 - - - +
92A HIS* 2.7 36.4 + - - +
93A LEU* 2.8 46.8 + - + +
96A GLY* 6.5 1.3 - - - -
18B MET 3.1 17.2 + - - +
19B SER* 4.2 4.5 - - - +
21B ARG* 1.3 79.9 - - - +
23B ALA* 1.3 60.1 + - - +
25B LEU* 3.6 12.1 + - + +
26B ASN* 3.2 18.4 + - - +
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Residues in contact with ALA 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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19B SER 3.0 15.4 + - - +
20B ALA* 2.8 17.4 + - - +
22B GLU* 1.3 75.1 - - - +
24B PHE* 1.4 53.3 + - - +
25B LEU 3.0 1.1 - - - -
26B ASN* 2.5 35.4 + - - +
27B ALA* 3.2 4.7 + - - +
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Residues in contact with PHE 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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97A LEU* 4.7 5.4 - - + -
20B ALA 2.9 11.2 + - - +
21B ARG* 3.2 28.9 - - + +
23B ALA* 1.4 73.0 - - - +
25B LEU* 1.3 88.6 + - + +
27B ALA* 3.0 11.8 + - + +
28B ASP* 2.7 59.8 + - + -
43B LYS* 4.7 6.1 - - - -
47B PHE* 4.4 14.4 - + - -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 5.0 3.8 - - + +
96A GLY* 3.4 14.4 - - - +
97A LEU* 3.3 47.1 - - + +
100A LYS* 3.6 27.3 - - + +
21B ARG 2.8 12.5 + - - +
22B GLU* 3.6 13.2 - - + +
23B ALA 3.0 0.2 - - - -
24B PHE* 1.3 107.6 - - + +
26B ASN* 1.3 49.4 - - - +
28B ASP* 3.2 7.6 + - + +
29B ASP* 2.3 38.4 + - - +
47B PHE* 3.9 2.7 - - + -
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Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU 3.2 10.6 + - - +
23B ALA* 2.5 22.8 + - - +
25B LEU* 1.3 66.6 - - - +
27B ALA* 1.3 65.3 + - - +
29B ASP* 2.8 31.2 - - - +
30B ASP* 3.1 9.7 - - - +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA 3.2 4.0 + - - +
24B PHE* 3.0 14.8 + - + +
26B ASN* 1.3 76.5 - - - +
28B ASP* 1.3 65.3 + - - +
30B ASP* 2.5 27.8 - - - +
31B ALA* 3.0 12.4 + - + +
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Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 2.3 34.8 + - - +
24B PHE* 2.7 40.6 + - + +
25B LEU* 3.4 7.9 - - + +
27B ALA* 1.3 68.9 - - - +
29B ASP* 1.3 52.6 + - - +
30B ASP 2.4 23.0 + - - +
31B ALA* 2.7 38.8 + - - +
43B LYS* 2.9 31.9 + - - -
47B PHE* 3.7 1.7 - - - -
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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