Contacts of the strand formed by residues 2636 - 2641 (chain B) in PDB entry 2OVP
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 PHE2636 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2362B ASP* 3.1 39.0 - - + -
2365B TRP* 3.5 24.2 - + + -
2366B ARG* 3.2 39.9 - - + -
2632B PHE* 3.0 4.6 - - - +
2633B ASN* 2.4 58.6 + - - +
2635B ASN* 1.3 88.7 - - + +
2637B VAL* 1.3 66.7 + - - +
2638B ILE* 4.1 1.8 - - + -
2648B LEU* 3.2 27.4 - - + -
2649B TRP 2.9 9.0 - - - +
2651B LEU* 3.7 1.6 - - - +
2657B ILE* 3.3 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2595B VAL* 3.4 24.9 - - + -
2605B ILE* 3.5 17.5 - - + -
2617B LEU* 3.5 13.5 - - + -
2630B LEU* 4.5 1.3 - - + -
2631B GLN 3.1 9.2 - - - +
2632B PHE* 3.6 5.2 - - + -
2636B PHE* 1.3 72.5 - - - +
2638B ILE* 1.3 63.6 + - - +
2639B THR* 3.4 24.5 - - + -
2648B LEU* 3.6 0.7 - - - -
2649B TRP* 2.7 35.8 + - + -
2651B LEU* 3.3 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2638 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2365B TRP* 3.3 24.7 - - + -
2630B LEU* 2.9 5.7 - - - +
2631B GLN* 2.4 54.3 + - + +
2633B ASN* 5.0 11.4 - - - +
2636B PHE* 4.7 2.7 - - + -
2637B VAL* 1.3 73.0 - - - -
2639B THR* 1.3 58.9 + - - +
2646B VAL* 3.4 22.2 - - + -
2647B LYS 3.2 5.8 - - - +
2648B LEU* 3.7 17.7 - - + -
2660B LEU* 3.9 4.7 - - + -
2675B ILE* 3.4 21.8 - - + +
2677B ALA* 3.3 30.5 - - + -
2682B LEU* 3.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR2639 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2603B VAL* 3.2 32.8 - - + -
2623B HIS* 2.3 34.4 + - - -
2627B VAL* 4.2 0.9 - - - -
2629B CYS 3.4 6.1 - - - -
2630B LEU* 4.1 2.7 - - + -
2637B VAL* 3.4 22.0 - - + -
2638B ILE* 1.3 78.8 - - - +
2640B SER* 1.3 59.9 + - - +
2646B VAL* 3.1 2.2 - - - -
2647B LYS* 2.6 38.6 + - - +
2649B TRP* 2.6 24.0 + - + +
2675B ILE* 4.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2640 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2627B VAL* 3.4 9.2 - - - +
2628B THR* 2.5 38.8 + - - -
2629B CYS* 2.8 28.8 + - - +
2639B THR* 1.3 74.7 - - - +
2641B SER* 1.3 64.2 + - - +
2645B THR 3.5 5.4 - - - -
2646B VAL* 4.1 2.2 - - - +
2672B VAL* 3.2 31.3 + - - -
2673B TRP 3.9 0.5 + - - -
2675B ILE* 3.5 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2641 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2623B HIS* 2.8 23.8 - - - -
2625B SER 3.2 11.4 + - - -
2626B ALA 2.6 22.8 + - - -
2627B VAL* 4.0 0.2 - - - -
2628B THR* 3.6 3.4 - - - -
2640B SER* 1.3 76.2 - - - +
2642B ASP* 1.3 67.2 + - - +
2643B ASP* 2.8 30.4 + - - -
2644B GLY* 3.0 12.5 + - - -
2645B THR 3.1 5.7 + - - -
2672B VAL* 3.1 20.6 + - - +
----------------------------------------------------------
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