Contacts of the helix formed by residues 15 - 26 (chain F) in PDB entry 2OV2
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 GLY 15 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F ALA 3.4 0.4 - - - -
14F VAL* 1.3 79.5 - - - +
16F LYS* 1.3 66.6 + - - +
17F THR 3.4 2.5 - - - -
18F CYS* 3.9 0.7 - - - +
19F LEU* 3.0 25.8 + - - +
115F THR* 4.9 7.0 - - - +
159F ALA* 5.0 0.2 - - - +
200F GCP 3.0 41.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F VAL* 3.9 21.0 - - + +
9F VAL* 3.4 32.8 - - - +
10F GLY* 3.0 13.8 + - - +
11F ASP 2.9 18.8 + - - -
14F VAL* 3.6 12.6 - - + -
15F GLY* 1.3 78.5 - - - +
17F THR* 1.3 62.7 + - - +
19F LEU* 3.5 8.4 - - - +
20F LEU* 3.3 26.7 + - - +
57F ASP* 3.9 9.6 - - - +
58F THR* 3.5 21.1 - - - -
59F ALA 4.7 0.2 - - - -
60F GLY* 3.8 1.3 - - - +
81F CYS* 4.1 8.1 - - + -
200F GCP 2.6 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LYS* 1.3 73.8 - - - +
18F CYS* 1.3 57.3 + - - +
20F LEU* 3.0 4.5 + - - +
21F ILE* 2.8 49.4 + - + +
29F PRO* 5.1 0.4 - - + -
35F THR* 2.9 4.3 + - - +
40F TYR* 4.1 8.3 - - + +
57F ASP* 2.5 25.0 + - - +
200F GCP 3.0 10.1 + - - -
202F MG 2.2 30.4 - - - -
1301F EDO 3.7 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F GLY 3.9 0.7 - - - +
17F THR* 1.3 76.5 - - - +
19F LEU* 1.3 55.9 + - - +
22F SER* 2.8 34.8 + - - -
28F PHE* 3.7 24.5 - - + -
29F PRO* 3.7 32.0 - - + +
31F GLU 5.6 0.4 - - - -
159F ALA* 3.5 2.5 - - - -
200F GCP 2.9 61.2 + - + +
1301F EDO 4.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F VAL* 4.4 12.1 - - + -
15F GLY 3.0 18.1 + - - +
16F LYS* 3.5 10.3 - - - +
18F CYS* 1.3 77.5 - - - +
20F LEU* 1.3 56.7 + - + +
23F TYR* 3.1 30.1 + - - +
79F LEU* 4.2 16.4 - - + -
81F CYS* 4.4 11.0 - - - -
113F VAL* 4.7 4.3 - - + -
115F THR* 5.4 5.2 - - + -
157F CYS* 3.4 25.4 - - - -
159F ALA* 3.5 12.6 - - + +
165F LEU* 3.2 31.0 - - + +
168F VAL* 4.6 6.7 - - + -
169F PHE* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F VAL* 3.8 28.9 - - + -
16F LYS 3.3 10.7 + - - +
17F THR 3.0 6.7 + - - +
19F LEU* 1.3 74.8 - - + +
21F ILE* 1.3 61.2 + - - +
23F TYR* 3.4 1.1 + - - +
24F THR* 2.9 37.1 + - - +
40F TYR* 4.4 17.7 - - + -
55F LEU* 3.9 21.8 - - + -
57F ASP* 3.4 45.1 - - + +
169F PHE* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F THR* 2.8 37.4 + - + +
20F LEU* 1.3 71.5 - - - +
22F SER* 1.3 56.0 + - - +
24F THR* 3.7 1.6 - - - -
25F THR* 2.6 51.8 + - + +
27F ALA* 3.6 12.1 - - + +
29F PRO* 3.8 23.1 - - + -
40F TYR* 3.9 34.3 - - + +
17N PHE* 4.4 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F CYS 2.8 20.7 + - - -
19F LEU 3.9 0.4 - - - -
21F ILE* 1.3 77.9 - - - +
23F TYR* 1.3 57.2 + - - +
26F ASN* 2.9 28.6 + - - +
27F ALA 3.4 17.7 + - - +
28F PHE* 5.1 3.7 + - - +
159F ALA* 2.7 30.7 + - - -
162F GLN* 3.1 23.7 + - - +
165F LEU* 3.2 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU 3.1 20.0 + - - +
20F LEU 3.8 1.1 - - - +
22F SER* 1.3 81.5 - - - +
24F THR* 1.3 74.2 + - + +
26F ASN* 4.1 4.6 - - - +
44F VAL* 3.7 23.2 - - - +
53F LEU* 3.8 14.6 - - + +
55F LEU* 4.9 1.8 - - + -
162F GLN* 5.0 0.2 - - - +
165F LEU* 3.6 12.5 - - + +
166F LYS* 4.4 26.9 - - + -
169F PHE* 3.3 61.5 - + + +
170F ASP* 4.9 3.2 + - - -
173F ILE* 4.5 4.5 - - - +
12N SER 4.9 2.3 + - - -
14N PRO* 3.4 40.1 - - + +
1206N CL 4.1 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU 2.9 25.7 + - - +
21F ILE* 3.6 3.6 + - - -
23F TYR* 1.3 89.0 - - + +
25F THR* 1.3 64.3 + - - +
40F TYR* 5.3 1.0 - - + -
42F ALA* 4.7 10.8 - - + -
55F LEU* 3.5 30.5 - - + -
14N PRO* 4.2 10.5 - - - +
15N SER* 5.9 0.7 - - - -
17N PHE* 3.3 46.0 - - + +
1206N CL 3.8 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ILE* 2.6 37.6 + - + +
24F THR* 1.3 88.1 - - - +
26F ASN* 1.3 70.6 + - - +
27F ALA* 3.2 18.0 + - - +
17N PHE* 4.1 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F SER* 2.9 18.3 + - - +
23F TYR* 4.1 5.9 - - - +
24F THR 3.8 0.2 - - - -
25F THR* 1.3 80.3 - - - +
27F ALA* 1.3 58.9 + - - +
162F GLN* 3.0 33.0 + - - +
1206N CL 3.9 18.4 - - - +
----------------------------------------------------------
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