Contacts of the helix formed by residues 4 - 21 (chain A) in PDB entry 1OVI
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 4 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A TYR* 3.4 14.1 + - - -
3A LEU* 1.3 81.7 + - - +
5A GLN* 1.3 68.8 + - - +
7A LEU* 3.6 3.8 - - - +
8A MET* 3.1 24.3 + - - +
159A GLN* 3.9 13.0 + - - +
160A GLU* 5.5 3.1 + - - +
162A LEU* 4.0 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A TYR* 4.2 15.2 - - + -
4A SER* 1.3 78.4 - - - +
6A ARG* 1.4 69.0 + - - +
8A MET* 3.2 8.7 + - - +
9A LEU* 2.9 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A TYR* 3.3 27.8 + - + +
5A GLN* 1.4 79.3 + - - +
7A LEU* 1.3 58.5 + - - +
9A LEU* 2.7 36.6 + - + +
10A ASP* 2.9 44.3 + - - +
91A GLN* 4.7 13.5 + - - -
95A ASP* 3.6 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A TYR 3.2 5.2 + - - +
3A LEU* 3.7 33.7 - - + +
4A SER 3.6 7.4 - - - +
6A ARG* 1.3 74.4 - - - +
8A MET* 1.3 62.4 + - - +
11A ALA* 3.1 13.9 + - + +
54A PHE* 4.6 8.5 - - + -
57A LEU* 4.0 29.8 - - + -
92A GLN* 2.8 37.5 + - - +
96A LEU* 3.8 24.5 - - + -
159A GLN* 3.1 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 3.1 15.6 + - - +
5A GLN* 3.4 9.9 - - - +
6A ARG 3.2 0.2 - - - -
7A LEU* 1.3 75.7 - - - +
9A LEU* 1.3 67.7 + - - +
11A ALA* 3.0 7.0 + - - +
12A ARG* 2.8 26.3 + - + +
156A THR* 4.8 15.2 - - + +
159A GLN* 3.3 9.0 + - - +
160A GLU* 3.4 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 2.9 16.3 + - + +
6A ARG* 2.7 28.5 + - + +
8A MET* 1.3 72.8 - - - +
10A ASP* 1.3 75.9 + - - +
12A ARG* 3.0 58.3 + - - +
13A GLU* 3.1 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 2.9 35.3 + - - +
9A LEU* 1.3 94.5 - - - +
11A ALA* 1.3 56.0 + - - +
12A ARG 3.2 0.7 - - - -
13A GLU* 3.4 11.9 - - + +
14A ASN* 2.7 34.5 + - - +
88A GLY* 4.8 10.4 - - - +
91A GLN* 6.3 2.5 - - + -
92A GLN* 2.9 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.1 22.4 + - + +
8A MET 3.0 4.8 + - - +
10A ASP* 1.3 77.4 - - - +
12A ARG* 1.3 57.9 + - - +
14A ASN* 3.4 8.4 - - - +
15A LEU* 2.9 28.4 + - - +
92A GLN* 3.5 8.3 - - - +
152A LEU* 3.6 19.1 - - + +
156A THR* 3.6 27.4 - - + -
159A GLN* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 2.8 14.9 + - + +
9A LEU* 3.0 66.3 + - - +
11A ALA* 1.3 80.5 - - - +
13A GLU* 1.3 92.4 + - - +
15A LEU* 3.4 10.8 + - + +
16A ARG* 2.7 56.1 + - - +
156A THR* 5.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.1 11.6 + - - +
10A ASP* 3.1 15.8 + - + +
12A ARG* 1.3 109.3 + - - +
14A ASN* 1.3 67.1 + - - +
16A ARG* 3.0 24.0 + - + +
17A LEU* 3.2 17.5 + - + +
88A GLY* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP 2.7 20.6 + - - +
11A ALA* 3.4 9.2 - - - +
13A GLU* 1.3 71.8 - - - +
15A LEU* 1.3 62.0 + - - +
17A LEU* 3.0 11.8 + - - -
18A LEU* 3.4 6.5 + - - +
61A LEU* 5.4 0.6 - - - +
85A LEU* 3.3 34.6 - - - +
88A GLY* 6.0 2.2 - - - -
89A LEU* 3.3 40.2 - - - +
92A GLN* 5.2 3.6 + - - +
148A MET* 3.3 20.5 - - - +
152A LEU* 3.3 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 2.9 18.3 + - - +
12A ARG* 3.5 11.0 - - + +
14A ASN* 1.3 78.1 + - - +
16A ARG* 1.3 56.7 + - - +
18A LEU* 2.7 40.1 + - + +
19A ASP* 2.9 24.1 + - - +
149A MET* 3.9 38.1 - - + -
152A LEU* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.7 53.7 + - - +
13A GLU* 3.0 21.2 + - + +
15A LEU* 1.3 75.1 - - - +
17A LEU* 1.3 61.8 + - + +
19A ASP* 3.3 18.4 + - - +
20A ARG* 2.7 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.2 28.5 + - + +
14A ASN 3.0 10.7 + - - +
16A ARG* 1.3 79.9 - - + +
18A LEU* 1.3 64.7 + - - +
20A ARG* 4.2 5.8 - - + +
21A MET* 2.8 38.8 + - + +
22A ASN 3.6 0.7 + - - -
81A LEU* 3.3 44.4 - - + +
84A GLN* 3.2 38.6 - - + +
85A LEU* 3.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.5 17.7 - - - +
15A LEU* 2.7 29.3 + - + +
17A LEU* 1.3 74.1 - - - +
19A ASP* 1.3 55.7 + - - +
21A MET* 5.5 0.4 - - + -
22A ASN* 3.7 11.2 + - + +
23A ARG* 2.9 28.7 + - - +
68A PHE* 5.3 1.8 - - + -
85A LEU* 4.1 13.9 - - + -
145A ARG* 3.9 23.7 + - + +
148A MET* 3.7 31.9 - - + -
149A MET* 3.9 37.0 - - + +
152A LEU* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 2.9 31.1 + - - +
16A ARG* 3.5 24.2 + - - +
18A LEU* 1.3 77.8 - - - +
20A ARG* 1.3 61.3 + - + +
23A ARG* 3.1 39.0 + - - +
24A LEU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 2.7 30.1 + - + +
17A LEU* 4.7 6.1 - - + -
19A ASP* 1.3 76.3 - - + +
21A MET* 1.3 59.6 + - - +
24A LEU* 3.3 31.1 - - - +
81A LEU* 3.4 28.3 - - - +
84A GLN* 5.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 2.8 21.6 + - + +
18A LEU* 5.5 0.7 - - + -
20A ARG* 1.3 78.8 - - - +
22A ASN* 1.3 79.8 + - - +
24A LEU* 3.1 9.7 + - - +
25A SER* 3.1 23.9 + - - +
68A PHE* 5.6 0.9 - - + -
77A TRP* 3.6 24.6 - - + -
78A ASN* 3.4 18.1 + - - +
81A LEU* 4.0 13.7 - - + -
82A LEU* 3.3 59.7 - - + -
85A LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
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