Contacts of the helix formed by residues 1 - 28 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A GLN* 1.3 80.0 - - - +
2A LEU* 1.3 68.4 + - - +
3A ASP* 2.7 23.8 - - - +
4A LEU* 3.1 10.6 + - + +
5A GLN* 3.0 16.6 + - - +
0B GLN* 5.8 2.8 - - - +
1B ASN* 3.5 36.2 + - - +
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Residues in contact with LEU 2 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLN* 4.1 8.5 - - - +
1A ASN* 1.3 74.3 + - - +
3A ASP* 1.3 51.7 + - - +
5A GLN* 3.0 20.9 + - + +
6A LEU* 2.8 33.8 + - - +
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Residues in contact with ASP 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASN* 2.7 43.8 - - - +
2A LEU* 1.3 74.6 - - - +
4A LEU* 1.3 68.2 + - - +
6A LEU* 3.2 7.6 + - - +
7A TYR* 3.2 21.7 + - - +
64A VAL* 5.6 0.9 - - - +
68A LEU* 3.1 28.1 - - + +
71A GLN* 3.3 15.6 + - - -
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Residues in contact with LEU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLN 3.6 24.0 - - - +
1A ASN* 3.1 12.1 + - + +
3A ASP* 1.3 87.1 + - - +
5A GLN* 1.3 59.6 + - + +
7A TYR* 3.4 4.8 + - + +
8A MET* 3.0 44.4 + - + +
68A LEU* 4.1 13.0 - - + -
75B ALA* 4.6 16.2 - - + +
78B LEU* 4.6 20.4 - - + -
79B VAL* 3.0 37.5 - - + -
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Residues in contact with GLN 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLN* 3.5 45.6 + - - +
1A ASN 3.0 16.3 + - - +
2A LEU* 3.0 25.2 + - + +
4A LEU* 1.3 80.2 - - + +
6A LEU* 1.3 61.7 + - - +
8A MET* 3.2 8.2 + - + +
9A ARG* 3.0 23.1 + - - +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU 2.8 16.6 + - - +
3A ASP* 3.2 9.6 + - - +
5A GLN* 1.3 71.2 - - - +
7A TYR* 1.3 57.2 + - - +
9A ARG* 3.1 50.0 - - - +
10A ASP* 2.9 38.8 + - - +
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Residues in contact with TYR 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP 3.2 5.5 + - - +
4A LEU* 3.5 10.1 - - + +
6A LEU* 1.3 77.3 - - - +
8A MET* 1.3 82.0 + - + +
10A ASP* 3.3 6.8 + - - +
11A CYS* 2.8 57.6 + - - -
61A LEU* 3.6 26.8 - - + +
64A VAL* 3.5 28.7 - - + -
65A ALA* 3.5 9.3 - - + +
68A LEU* 3.7 23.3 - - + -
79B VAL* 3.0 37.9 + - + -
82B LYS* 4.0 2.7 - - + -
83B ARG* 3.5 22.9 + - - +
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Residues in contact with MET 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.0 45.9 + - + +
5A GLN* 3.2 10.7 + - + +
7A TYR* 1.3 81.3 - - + +
9A ARG* 1.3 52.5 + - - +
11A CYS* 3.2 5.5 + - - +
12A GLU* 2.8 45.5 + - - +
78B LEU* 3.5 41.5 - - + +
79B VAL* 3.7 5.4 - - - +
82B LYS* 3.4 27.4 - - - -
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Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN 3.0 12.4 + - - +
6A LEU* 3.1 37.5 - - - +
8A MET* 1.3 75.9 - - - +
10A ASP* 1.3 82.3 + - - +
12A GLU* 3.0 12.1 + - - +
13A LEU* 2.8 51.7 + - + +
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 2.9 29.6 + - - +
7A TYR* 3.8 7.3 - - - +
9A ARG* 1.3 108.3 + - - +
11A CYS* 1.3 55.8 + - - +
13A LEU* 3.4 10.0 + - - +
14A ALA* 2.9 29.1 + - - +
57A LYS* 4.3 12.5 + - - +
61A LEU* 3.9 18.1 - - + +
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Residues in contact with CYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 2.8 61.8 + - - +
8A MET 3.5 7.6 - - - +
10A ASP* 1.3 72.7 - - - +
12A GLU* 1.3 57.2 + - - +
14A ALA* 3.2 2.4 + - - +
15A GLU* 2.9 34.4 + - - +
61A LEU* 3.8 18.2 - - - -
82B LYS* 3.7 24.7 - - + -
83B ARG* 5.1 0.7 - - - -
86B VAL* 3.7 16.1 - - + +
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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
----------------------------------------------------------
8A MET* 2.8 25.3 + - - +
9A ARG* 3.0 10.8 + - - +
11A CYS* 1.3 77.7 - - - +
13A LEU* 1.3 57.3 + - + +
15A GLU* 3.2 9.3 + - - +
16A SER* 3.0 29.0 + - - -
82B LYS* 3.6 25.0 + - - +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.8 51.7 + - + +
10A ASP* 3.7 13.0 - - - +
12A GLU* 1.3 70.9 - - + +
14A ALA* 1.4 58.5 + - - +
16A SER* 3.3 8.4 + - - -
17A TRP* 3.0 28.6 + - - +
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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 ASP 2.9 17.9 + - - +
11A CYS 3.7 4.0 - - - +
13A LEU* 1.4 71.1 - - - +
15A GLU* 1.4 66.5 + - - +
17A TRP* 3.4 8.7 + - - +
18A MET* 3.0 38.6 + - + +
57A LYS* 3.7 31.8 - - + +
58A ILE* 5.1 0.2 - - + -
61A LEU* 3.7 15.5 - - + -
86B VAL* 4.8 0.7 - - + -
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS 2.9 16.0 + - - +
12A GLU* 3.7 11.0 - - - +
14A ALA* 1.4 78.6 - - - +
16A SER* 1.3 57.2 + - - +
18A MET* 3.2 8.7 + - + +
19A SER* 2.8 31.3 + - - -
82B LYS* 3.0 30.0 + - - -
85B GLN* 4.0 25.1 - - - +
86B VAL* 4.1 18.8 - - + -
89B ARG* 3.0 48.2 + - - +
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU 3.0 15.8 + - - -
13A LEU* 3.5 11.9 - - - -
15A GLU* 1.3 72.8 - - - +
17A TRP* 1.3 67.0 + - - +
19A SER* 3.1 10.4 + - - -
20A ALA* 3.0 21.5 + - - +
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Residues in contact with TRP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU 3.0 15.8 + - - +
14A ALA* 3.7 8.5 - - - +
16A SER* 1.3 75.4 - - - +
18A MET* 1.3 62.1 + - - +
20A ALA* 3.2 19.8 + - + +
21A ARG* 3.2 54.8 + - - +
53A GLY 6.1 1.2 - - - -
54A HIS* 3.1 30.5 + + - -
57A LYS* 6.1 7.2 - - + -
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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 ALA 3.0 31.4 + - - +
15A GLU* 3.2 19.0 + - + +
17A TRP* 1.3 76.9 - - - +
19A SER* 1.3 57.8 + - - +
21A ARG* 3.2 5.1 + - - +
22A GLU* 2.9 32.6 + - + +
54A HIS* 4.2 13.2 - - - +
58A ILE* 4.2 13.0 - - + -
86B VAL* 3.9 31.9 - - + +
89B ARG* 4.1 12.6 - - + +
90B TRP* 3.6 42.4 - - - -
93B LEU* 3.9 21.7 - - + +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU 2.8 16.0 + - - -
16A SER* 3.3 13.3 - - - -
18A MET* 1.3 75.0 - - - +
20A ALA* 1.3 65.6 + - - +
22A GLU* 3.2 10.8 + - - +
23A ALA* 3.1 20.4 + - - +
89B ARG* 3.7 19.3 + - - +
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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
----------------------------------------------------------
16A SER 3.0 11.4 + - - +
17A TRP* 3.3 29.2 - - + +
19A SER* 1.3 76.3 - - - +
21A ARG* 1.3 62.1 + - - +
23A ALA* 3.0 19.1 + - - +
24A PHE* 3.0 14.2 + - - +
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Residues in contact with ARG 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 TRP* 3.2 49.1 + - + +
18A MET 3.5 8.1 - - - +
20A ALA* 1.3 80.3 - - - +
22A GLU* 1.4 61.4 + - - +
24A PHE* 3.3 26.4 + - + +
25A LEU* 3.0 23.6 + - - +
50A ALA* 3.7 32.5 + - - +
54A HIS* 3.0 24.6 + - - +
93B LEU* 3.8 15.5 - - + -
97B LEU* 3.9 23.1 - - + -
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 2.9 23.6 + - + +
19A SER* 3.2 10.7 + - - +
21A ARG* 1.4 75.5 - - - +
23A ALA* 1.3 63.0 + - - +
25A LEU* 3.5 12.2 + - - +
26A ASN* 3.4 17.5 + - - +
89B ARG* 4.4 4.6 - - + +
92B HIS* 2.4 43.9 + - - +
93B LEU* 3.0 34.7 + - + +
96B GLY* 5.9 1.2 - - - -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER 3.1 10.6 + - - +
20A ALA* 3.0 13.1 + - - +
22A GLU* 1.3 76.0 - - - +
24A PHE* 1.3 58.2 + - - +
26A ASN* 2.9 22.8 + - - +
27A ALA* 3.0 15.1 + - - +
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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
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20A ALA 3.0 11.4 + - - +
21A ARG* 3.3 33.6 + - - +
23A ALA* 1.3 71.2 - - - +
25A LEU* 1.3 71.2 + - + +
26A ASN 3.0 1.7 + - - -
27A ALA* 3.2 8.9 + - + +
28A ASP* 3.0 55.4 + - - +
43A LYS* 6.2 0.7 - - + -
47A PHE* 4.3 20.6 - + - -
97B LEU* 5.7 1.1 - - + -
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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 ARG 3.0 12.5 + - - +
22A GLU* 3.7 14.8 - - - +
23A ALA 3.3 0.2 - - - -
24A PHE* 1.3 79.8 - - + +
26A ASN* 1.3 63.2 + - - +
28A ASP* 4.1 0.9 - - - -
29A ASP* 3.1 9.4 + - - +
47A PHE* 3.7 16.4 - - + -
93B LEU* 3.6 21.1 - - + -
96B GLY* 3.8 23.8 - - - +
97B LEU* 3.5 34.3 - - + -
100B LYS* 2.8 56.7 - - + +
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Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU 3.4 8.4 + - - +
23A ALA* 2.9 12.8 + - - +
25A LEU* 1.3 78.9 - - - +
27A ALA* 1.3 61.9 + - - +
29A ASP* 2.7 26.5 + - - +
30A ASP* 2.5 38.0 + - - +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 3.0 11.4 + - - +
24A PHE* 3.8 12.1 - - + +
26A ASN* 1.3 76.4 - - - +
28A ASP* 1.3 55.5 + - - +
30A ASP* 2.8 39.7 + - - +
31A ALA* 3.4 6.4 + - - +
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Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.0 39.3 + - - +
25A LEU 3.4 0.7 - - - +
27A ALA* 1.3 76.3 - - - +
29A ASP* 1.3 51.3 + - - +
31A ALA 2.9 3.5 + - - -
32A ASN* 2.3 52.0 + - - +
43A LYS* 2.7 30.2 + - - +
47A PHE* 3.5 14.2 - - - -
100B LYS* 2.7 22.8 + - - +
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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