Contacts of the helix formed by residues 6 - 29 (chain A) in PDB entry 1NBP
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 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A THR* 1.3 67.0 + - - +
8A LYS* 3.3 8.2 - - - +
9A LYS* 3.6 17.3 + - - +
10A THR* 3.3 25.6 + - - -
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Residues in contact with THR 7 (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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6A SER* 1.3 77.2 - - - +
8A LYS* 1.3 60.6 + - - +
10A THR* 3.5 7.3 + - - -
11A GLN* 3.0 27.5 + - - +
132A LEU* 3.8 42.5 - - + +
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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
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6A SER 3.3 5.1 - - - +
7A THR* 1.3 78.0 - - - +
9A LYS* 1.3 60.1 + - - +
11A GLN* 3.4 13.7 + - - +
12A LEU* 3.0 28.8 + - - +
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Residues in contact with LYS 9 (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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6A SER* 3.6 18.4 + - - +
7A THR 3.4 0.6 - - - -
8A LYS* 1.3 74.9 - - - +
10A THR* 1.3 66.7 + - - +
12A LEU* 3.4 8.5 + - + +
13A GLN* 3.2 48.8 + - + +
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Residues in contact with THR 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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6A SER* 3.3 14.1 + - - -
7A THR* 3.6 10.1 - - - -
8A LYS 3.3 0.2 - - - -
9A LYS* 1.3 77.7 - - - +
11A GLN* 1.3 65.5 + - - +
13A GLN* 3.2 15.4 + - - +
14A LEU* 3.1 25.7 + - + +
53A LEU* 4.1 18.9 - - + +
96A LEU* 3.9 16.6 - - + +
128A ILE* 6.2 0.2 - - + -
132A LEU* 4.0 16.8 - - + -
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Residues in contact with GLN 11 (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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7A THR 3.0 17.3 + - - +
8A LYS* 3.6 14.8 - - - +
9A LYS 3.4 0.2 - - - -
10A THR* 1.3 75.3 - - - +
12A LEU* 1.3 63.3 + - - +
14A LEU* 3.2 5.5 + - - +
15A GLU* 3.0 47.3 + - - +
129A ILE* 3.3 35.5 + - + +
132A LEU* 3.9 23.3 - - + +
133A THR* 3.4 28.6 + - - +
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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
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8A LYS 3.0 17.6 + - - +
9A LYS* 3.6 9.9 - - + +
10A THR 3.2 0.2 - - - -
11A GLN* 1.3 74.6 - - - +
13A GLN* 1.3 58.8 + - + +
15A GLU* 3.4 19.4 + - + +
16A HIS* 3.0 60.4 + - + +
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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 LYS* 3.2 42.9 + - + +
10A THR* 3.2 10.4 + - - +
12A LEU* 1.3 74.4 - - + +
14A LEU* 1.3 58.7 + - - +
16A HIS* 3.3 7.7 + - - +
17A LEU 3.0 23.4 + - - -
92A ILE* 3.5 24.9 + - + +
95A GLU* 3.2 43.6 + - - +
96A LEU* 3.7 27.0 - - + +
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Residues in contact with LEU 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 THR* 3.1 25.5 + - + +
11A GLN* 3.2 5.6 + - - +
13A GLN* 1.3 76.2 - - - +
15A GLU* 1.3 52.6 + - - +
17A LEU* 3.3 7.0 + - + +
18A LEU* 2.8 33.1 + - - +
53A LEU* 3.8 14.6 - - + -
56A LEU* 4.8 0.4 - - + -
96A LEU* 3.7 21.5 - - + -
124A PHE* 4.6 13.7 - - + -
125A CYS* 4.1 14.5 - - - +
128A ILE* 3.8 35.2 - - + -
129A ILE* 3.8 18.2 - - + +
132A LEU* 3.8 18.4 - - + -
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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
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11A GLN* 3.0 43.9 + - - +
12A LEU* 3.6 23.3 - - + +
13A GLN 3.2 0.2 - - - -
14A LEU* 1.3 75.4 - - - +
16A HIS* 1.3 60.4 + - + +
18A LEU* 3.4 8.1 + - + +
19A LEU* 3.0 38.8 + - + +
129A ILE* 3.8 28.2 - - + +
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Residues in contact with HIS 16 (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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12A LEU* 3.0 53.9 + - + +
13A GLN* 3.3 9.6 + - - +
15A GLU* 1.3 76.3 - - + +
17A LEU* 1.3 59.4 + - - +
19A LEU* 3.5 9.1 + - + +
20A ASP* 3.0 37.3 + - - +
88A ASN* 5.5 2.9 + - - +
92A ILE* 4.0 15.3 - - + -
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Residues in contact with LEU 17 (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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13A GLN 3.0 14.7 + - - +
14A LEU* 3.5 10.3 - - + +
15A GLU 3.3 0.2 - - - -
16A HIS* 1.3 73.9 - - - +
18A LEU* 1.3 64.5 + - - +
20A ASP* 3.3 7.1 + - - +
21A LEU* 3.0 34.2 + - + +
56A LEU* 3.9 25.8 - - + -
59A LEU* 4.3 4.0 - - + -
89A ILE* 3.6 40.4 - - + +
92A ILE* 3.9 9.3 - - + +
93A VAL* 4.1 12.3 - - + -
96A LEU* 4.5 14.1 - - + -
125A CYS* 3.6 22.7 - - - -
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Residues in contact with LEU 18 (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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14A LEU 2.8 19.7 + - - +
15A GLU* 3.5 10.3 - - + +
17A LEU* 1.3 74.6 - - - +
19A LEU* 1.3 60.3 + - + +
21A LEU* 3.3 4.5 + - - +
22A GLN* 3.0 51.1 + - - +
122A ILE* 3.7 30.1 - - + +
125A CYS* 4.0 12.5 - - + -
126A GLN* 3.7 38.1 - - + +
129A ILE* 3.9 15.5 - - + -
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Residues in contact with LEU 19 (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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15A GLU* 3.0 28.1 + - + +
16A HIS* 4.0 9.9 - - + +
18A LEU* 1.3 75.7 - - + +
20A ASP* 1.3 66.4 + - - +
22A GLN* 3.9 20.3 - - + +
23A MET* 3.1 23.9 + - - +
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Residues in contact with ASP 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 HIS* 3.0 27.4 + - - +
17A LEU* 3.3 3.9 + - - +
19A LEU* 1.3 76.4 - - - +
21A LEU* 1.3 63.2 + - - +
23A MET* 3.2 21.0 - - - +
24A ILE* 3.2 14.9 + - - +
85A LEU* 3.4 19.1 - - + +
88A ASN* 2.6 34.0 + - - -
89A ILE* 3.5 28.3 - - + +
92A ILE* 3.7 9.7 - - - +
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Residues in contact with LEU 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 LEU* 3.0 32.3 + - + +
18A LEU* 3.6 3.4 - - - +
20A ASP* 1.3 74.5 - - - +
22A GLN* 1.3 64.4 + - - +
24A ILE* 3.3 8.7 + - + +
25A LEU* 3.1 22.0 + - - +
59A LEU* 4.6 17.0 - - + -
66A LEU* 5.1 4.0 - - + -
89A ILE* 4.6 14.1 - - + -
117A PHE* 5.6 0.7 - - + -
118A LEU* 3.8 26.0 - - + +
121A TRP* 3.8 42.6 - - + +
122A ILE* 3.8 15.5 - - + +
125A CYS* 4.0 13.0 - - - -
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.0 42.2 + - - +
19A LEU* 3.9 28.1 - - + +
20A ASP 3.4 0.2 - - - -
21A LEU* 1.3 76.3 - - - +
23A MET* 1.3 53.7 + - - +
25A LEU* 3.4 3.0 + - + +
26A ASN* 2.8 50.4 + - - +
122A ILE* 3.8 28.1 - - + +
126A GLN* 4.4 8.3 - - - +
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Residues in contact with MET 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU 3.1 15.9 + - - +
20A ASP* 3.2 13.0 - - - +
22A GLN* 1.3 77.9 - - - +
24A ILE* 1.3 56.2 + - - +
26A ASN* 3.9 6.2 - - - +
27A GLY* 2.9 25.6 + - - -
79A HIS* 4.6 9.2 - - + +
80A LEU* 3.7 33.7 - - + -
85A LEU* 3.9 24.2 - - + -
201A MHC 4.5 4.1 - - + -
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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
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20A ASP 3.2 10.4 + - - +
21A LEU* 3.3 8.2 + - + +
23A MET* 1.3 72.9 - - - +
25A LEU* 1.3 61.0 + - - +
27A GLY* 3.2 2.3 + - - -
28A ILE* 2.8 48.7 + - + +
66A LEU* 4.1 14.1 - - + -
70A LEU* 3.9 19.5 - - + -
85A LEU* 3.6 15.9 - - + -
86A ILE* 4.0 19.7 - - + -
89A ILE* 3.7 29.2 - - + -
118A LEU* 3.8 15.0 - - + -
201A MHC 4.1 12.7 + - + -
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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
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21A LEU 3.1 13.2 + - - +
22A GLN* 3.7 7.9 - - + +
24A ILE* 1.3 76.5 - - - +
26A ASN* 1.3 61.9 + - - +
28A ILE* 3.2 4.8 + - + +
29A ASN* 2.8 52.6 + - - +
115A VAL* 3.9 44.0 - - + +
118A LEU* 3.7 17.2 - - + +
119A ASN* 3.4 25.6 - - - +
122A ILE* 3.8 16.2 - - + -
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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
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22A GLN* 2.8 36.6 + - - +
23A MET* 4.0 6.3 - - - +
25A LEU* 1.3 78.7 - - - +
27A GLY* 1.3 56.7 - - - +
29A ASN* 3.6 11.7 + - - +
30A ASN* 2.6 36.8 + - - +
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A MET 2.9 16.5 + - - -
24A ILE 3.2 4.0 + - - -
26A ASN* 1.3 76.3 - - - +
28A ILE* 1.3 60.8 + - - +
30A ASN* 3.4 13.1 + - - +
31A CYS 3.8 0.9 + - - -
78A PHE* 4.3 13.0 - - - -
201A MHC 3.6 37.8 - - - +
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Residues in contact with ILE 28 (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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24A ILE* 2.8 39.9 + - + +
25A LEU* 3.6 4.7 - - - +
27A GLY* 1.3 71.7 - - - +
29A ASN* 1.3 56.8 + - - +
30A ASN 3.0 4.9 - - - -
31A CYS* 2.9 31.4 + - - +
36A LEU* 3.7 26.8 - - + +
39A MET* 3.8 20.4 - - + -
70A LEU* 3.9 10.8 - - + -
114A ILE* 3.7 31.2 - - + -
115A VAL* 4.2 19.1 - - + -
118A LEU* 3.7 11.2 - - + -
201A MHC 4.4 3.1 - - - -
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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
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25A LEU* 2.8 46.8 + - - +
26A ASN* 3.9 14.1 + - - +
27A GLY 3.4 0.2 - - - -
28A ILE* 1.3 72.3 - - - +
30A ASN* 1.3 63.8 + - - +
31A CYS 3.4 4.7 + - - +
36A LEU* 4.6 11.3 - - - +
115A VAL* 4.3 12.3 - - - +
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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