Contacts of the helix formed by residues 3 - 26 (chain N) in PDB entry 6PSU
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 ASP 3 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678I ARG* 3.6 9.8 + - - +
681I MET* 3.1 19.7 - - - +
814I ASP* 5.1 1.3 - - - +
1073I LYS* 3.0 30.8 + - - -
1106I ARG* 4.7 6.5 + - - +
460J ASP* 3.5 12.1 + - - +
462J ASP* 3.4 19.8 - - - +
2N SER* 1.3 83.3 + - - +
4N GLU* 1.3 64.5 + - - +
5N ALA 3.2 0.2 - - - -
6N ASP* 2.5 45.7 + - - +
7N GLU 3.1 4.2 + - - -
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Residues in contact with GLU 4 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565I GLU* 6.0 4.7 - - + -
566I GLY* 6.3 2.2 - - - -
681I MET* 4.1 10.8 - - + -
783J LEU* 4.9 9.6 - - + -
786J THR* 3.0 37.7 + - + +
787J ALA* 5.4 3.9 - - + -
790J THR* 3.8 15.6 + - - -
2N SER 4.6 5.4 - - - +
3N ASP* 1.3 81.2 - - - +
5N ALA* 1.3 52.7 + - - +
7N GLU* 3.1 15.1 + - - +
8N ALA* 2.6 40.2 + - - +
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Residues in contact with ALA 5 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677I ASN* 3.7 27.3 + - + +
678I ARG* 3.1 33.3 + - - +
681I MET* 3.2 23.9 - - + +
783J LEU* 5.5 0.4 - - - -
3N ASP 3.2 0.4 - - - -
4N GLU* 1.3 78.2 - - - +
6N ASP* 1.3 58.9 + - - +
8N ALA* 4.2 6.7 - - - -
9N TYR* 3.2 24.1 + - - +
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Residues in contact with ASP 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678I ARG* 2.2 35.2 + - - -
1105I SER* 4.5 7.8 + - - +
1106I ARG* 3.0 34.8 + - - +
731J ARG* 3.8 10.0 + - - +
2N SER* 2.8 27.5 + - - +
3N ASP* 2.5 23.3 + - - +
5N ALA* 1.3 73.8 - - - +
7N GLU* 1.3 58.5 + - - +
9N TYR* 4.5 8.6 + - - +
10N SER* 4.6 5.9 + - - -
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Residues in contact with GLU 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458J ASN* 5.4 5.4 + - - -
786J THR* 3.4 15.0 + - - +
789J LYS* 4.7 22.2 + - - +
928J THR* 5.4 1.9 - - - +
2N SER 4.3 24.3 + - - +
3N ASP 3.1 6.5 + - - +
4N GLU* 3.1 23.1 + - - +
6N ASP* 1.3 77.5 - - - +
8N ALA* 1.3 56.0 + - - +
9N TYR 3.1 2.0 - - - -
10N SER* 2.6 37.7 + - - -
11N VAL* 3.3 6.6 + - + +
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Residues in contact with ALA 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677I ASN* 4.2 12.3 - - - +
782J GLY* 3.4 17.6 - - - +
783J LEU* 3.4 10.1 - - + +
786J THR* 3.2 25.5 - - + +
4N GLU 2.6 23.7 + - - +
5N ALA* 4.2 0.4 - - - -
7N GLU* 1.3 73.2 - - - +
9N TYR* 1.3 62.4 + - - +
11N VAL* 3.3 5.7 + - - +
12N THR* 2.9 27.5 + - - -
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Residues in contact with TYR 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675I ASP* 5.3 6.1 - - - +
677I ASN* 4.5 7.5 - - - +
1105I SER 5.8 3.4 - - - +
1107I MET* 4.2 22.7 - - + -
735J ALA* 4.4 5.5 - - - +
736J GLN* 3.2 45.1 + - + +
739J GLN* 5.5 6.5 - - + +
5N ALA 3.2 18.1 + - - +
6N ASP* 4.6 8.1 - - - +
7N GLU 3.0 0.8 + - - -
8N ALA* 1.3 77.5 - - - +
10N SER* 1.3 61.4 + - - +
12N THR* 3.3 8.8 + - + -
13N GLU* 2.1 70.9 + - + +
102N 1N7 5.9 2.0 - - + -
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Residues in contact with SER 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N ASP 4.6 2.9 + - - -
7N GLU* 2.6 23.9 + - - -
9N TYR* 1.3 83.2 - - - +
11N VAL* 1.3 60.3 + - - -
13N GLU* 3.9 3.4 - - - +
14N GLN* 2.9 26.3 + - - +
102N 1N7 3.5 35.1 - - - +
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Residues in contact with VAL 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781J LYS* 4.9 1.3 - - + +
782J GLY* 3.9 27.8 - - - +
785J ASP* 4.4 18.6 - - + +
786J THR* 4.5 12.3 - - - +
789J LYS* 5.6 9.2 - - - +
931J THR* 6.0 9.6 - - + -
932J MET* 5.6 9.6 - - + +
933J ARG* 6.0 3.1 - - + -
7N GLU* 3.3 10.2 + - + +
8N ALA* 3.6 7.9 - - - +
10N SER* 1.3 80.1 - - - +
12N THR* 1.3 63.4 + - - +
14N GLN* 3.4 4.6 + - - +
15N LEU* 3.0 28.0 + - + +
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Residues in contact with THR 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677I ASN* 5.5 0.9 + - - -
747J MET* 4.9 18.8 - - + -
778J GLY* 2.6 42.6 + - - +
779J ALA* 4.1 4.9 + - - +
782J GLY* 3.4 7.1 - - - -
8N ALA 2.9 18.1 + - - -
9N TYR* 3.8 9.4 - - + -
11N VAL* 1.3 78.4 - - - +
13N GLU* 1.3 58.4 + - - +
15N LEU* 3.3 10.7 + - + +
16N THR* 2.9 29.7 + - + +
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Residues in contact with GLU 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735J ALA* 4.2 14.7 - - - +
9N TYR* 2.1 57.6 + - + +
10N SER 4.1 2.2 - - - +
12N THR* 1.3 76.1 - - - +
14N GLN* 1.3 61.6 + - - +
16N THR* 3.2 10.0 - - + +
17N MET* 2.8 56.5 + - + +
102N 1N7 2.9 30.7 + - + +
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Residues in contact with GLN 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931J THR* 4.0 24.2 - - + +
935J PHE* 3.1 47.5 - - - +
10N SER* 2.9 18.8 + - - +
11N VAL* 3.7 6.6 - - - +
13N GLU* 1.3 77.8 - - - +
15N LEU* 1.3 68.6 + - - +
17N MET* 3.8 0.2 - - - +
18N THR* 2.9 43.8 + - - +
102N 1N7 3.4 44.0 - - + +
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Residues in contact with LEU 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748J ALA* 4.1 12.0 - - + +
749J LYS 3.7 20.0 - - - +
750J PRO* 3.1 24.2 - - + +
751J ASP 4.5 8.7 - - - +
752J GLY* 5.0 6.3 - - - +
778J GLY* 5.7 3.8 - - - -
781J LYS* 4.5 16.2 - - + -
11N VAL* 3.0 21.7 + - + +
12N THR* 3.5 11.9 - - + +
14N GLN* 1.3 82.6 + - - +
16N THR* 1.3 66.4 + - - +
18N THR* 2.9 22.2 + - - -
19N GLY* 3.0 11.1 + - - -
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Residues in contact with THR 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746J LEU 5.2 1.0 + - - -
747J MET* 4.3 17.6 + - + +
748J ALA* 3.8 30.7 + - - +
754J ILE* 4.1 1.4 - - - +
12N THR* 2.9 22.1 + - + +
13N GLU* 3.2 21.8 - - + +
15N LEU* 1.3 80.3 - - - +
17N MET* 1.3 65.7 + - + +
19N GLY* 3.2 1.1 + - - +
20N ILE* 2.9 42.1 + - + +
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Residues in contact with MET 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N GLU* 2.8 51.0 + - + +
14N GLN 3.8 3.1 - - - +
16N THR* 1.3 76.5 - - + +
18N THR* 1.3 56.6 + - - +
20N ILE* 3.3 11.9 + - - +
21N ASN* 2.9 39.3 + - - +
102N 1N7 3.7 40.6 - - + +
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Residues in contact with THR 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935J PHE* 4.7 10.3 - - + +
936J HIS 4.9 10.1 - - - +
14N GLN* 2.9 40.7 + - - +
15N LEU* 2.9 16.6 + - - -
17N MET* 1.3 76.0 - - - +
19N GLY* 1.3 57.1 + - - +
21N ASN* 3.7 8.0 - - - +
22N ARG* 2.9 44.9 + - - +
102N 1N7 4.2 17.0 - - + -
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Residues in contact with GLY 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748J ALA* 5.6 0.7 - - - -
752J GLY* 4.5 14.1 - - - -
754J ILE* 3.3 16.6 - - - -
15N LEU 3.0 14.7 + - - -
16N THR* 3.2 5.3 + - - -
18N THR* 1.3 78.4 + - - +
20N ILE* 1.3 62.2 + - - +
22N ARG* 3.3 8.3 + - - +
23N ILE* 3.0 29.7 + - - +
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Residues in contact with ILE 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683J ILE* 5.0 5.2 - - + -
687J ALA* 4.0 25.1 - - + -
690J ASN* 5.7 3.6 - - - +
745J GLY* 5.7 1.8 - - - -
746J LEU* 3.6 34.1 - - + +
754J ILE* 3.3 20.2 - - + -
16N THR* 2.9 25.7 + - + +
17N MET* 3.9 11.4 - - - +
19N GLY* 1.3 75.5 - - - +
21N ASN* 1.3 59.8 + - - +
23N ILE* 3.7 2.9 - - - +
24N ARG* 2.9 37.8 + - + +
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Residues in contact with ASN 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N MET* 2.9 28.0 + - - +
18N THR* 3.7 7.6 - - - +
20N ILE* 1.3 78.3 - - - +
22N ARG* 1.3 57.7 + - - +
24N ARG* 3.7 7.7 - - - +
25N GLN* 2.8 51.3 + - + +
102N 1N7 3.3 35.0 + - + +
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Residues in contact with ARG 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752J GLY* 4.9 11.9 + - - -
936J HIS* 4.9 22.4 + - - +
18N THR* 2.9 32.8 + - - +
19N GLY* 3.8 10.0 - - - +
21N ASN* 1.3 75.7 - - - +
23N ILE* 1.3 66.2 + - + +
25N GLN* 3.2 5.4 + - - +
26N LYS* 3.0 33.9 + - + +
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Residues in contact with ILE 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679J TYR* 4.4 9.4 - - + +
680J ASN* 3.1 47.8 - - - +
683J ILE* 3.7 30.4 - - + +
684J ASP* 5.3 0.2 - - - +
752J GLY 4.3 7.9 - - - +
753J SER* 5.2 0.9 - - - -
754J ILE* 4.0 35.0 - - + +
19N GLY 3.0 18.3 + - - +
20N ILE 3.7 0.9 - - - +
22N ARG* 1.3 83.3 - - + +
24N ARG* 1.3 58.4 + - - +
26N LYS* 4.2 9.7 + - + +
27N ILE* 4.9 2.3 + - - +
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Residues in contact with ARG 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683J ILE* 5.6 1.3 - - + -
684J ASP* 3.0 37.5 + - + +
687J ALA* 3.2 34.4 + - - +
688J ALA* 3.2 23.6 - - - +
691J ASP* 5.0 7.4 + - - -
20N ILE* 2.9 24.0 + - + +
21N ASN* 4.0 8.5 - - - +
23N ILE* 1.3 78.9 - - - +
25N GLN* 1.3 64.4 + - + +
26N LYS 3.3 2.0 - - - -
27N ILE* 3.0 27.7 - - + +
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Residues in contact with GLN 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N ASN* 2.8 42.0 + - + +
22N ARG* 3.9 4.7 - - - +
24N ARG* 1.3 81.0 + - + +
26N LYS* 1.3 56.6 + - - +
27N ILE 3.1 18.7 + - - +
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Residues in contact with LYS 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676J GLY 4.8 4.2 + - - -
677J GLU* 3.9 13.4 - - - +
680J ASN* 3.8 24.3 + - - +
22N ARG* 3.0 20.2 + - + +
23N ILE* 4.6 6.7 - - + +
24N ARG 3.3 0.8 - - - -
25N GLN* 1.3 76.3 - - - +
27N ILE* 1.3 57.6 + - - +
28N ASN* 3.9 6.8 + - - +
66N GLU* 4.2 25.0 + - - -
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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) + - + + + + + -
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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