Contacts of the strand formed by residues 2696 - 2701 (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 LYS2696 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2375B VAL* 3.2 30.1 - - + -
2376B LEU 3.5 22.4 - - - +
2377B LYS* 3.8 11.0 - - + +
2378B GLY 4.1 2.7 - - - +
2384B ILE* 3.4 7.5 - - - +
2663B LEU* 5.7 0.7 - - - -
2686B VAL* 2.7 40.1 + - + +
2693B GLU* 2.6 31.6 + - - -
2694B GLU* 2.9 28.5 + - - +
2695B THR* 1.3 76.4 + - - +
2697B LEU* 1.3 60.7 + - - +
2698B LEU* 3.5 24.2 - - + -
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Residues in contact with LEU2697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2374B LYS 3.4 3.6 - - - +
2376B LEU* 2.8 46.7 + - + +
2378B GLY* 5.7 0.2 - - - -
2379B HIS* 4.9 0.9 - - - +
2384B ILE* 3.3 31.4 - - + -
2387B LEU* 3.3 29.6 - - + -
2394B ILE* 4.4 3.1 - - + -
2396B SER* 3.5 20.2 - - - +
2406B TRP* 3.7 22.7 - - + +
2683B VAL* 4.1 13.7 - - + -
2684B CYS 2.8 7.4 - - - +
2685B ALA* 3.5 13.7 - - - +
2696B LYS* 1.3 75.9 - - - +
2698B LEU* 1.3 66.1 + - - +
2699B VAL 3.9 0.2 - - - -
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Residues in contact with LEU2698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2373B PRO* 3.9 22.7 - - + -
2374B LYS 3.9 2.0 - - - -
2375B VAL* 4.7 8.5 - - + -
2661B VAL* 3.3 37.0 - - + -
2663B LEU* 3.8 8.1 - - + -
2682B LEU 3.0 2.3 - - - +
2683B VAL* 3.0 5.0 - - - -
2684B CYS* 2.6 48.9 + - + +
2686B VAL* 3.5 19.7 - - + -
2696B LYS* 3.5 39.9 - - + -
2697B LEU* 1.3 75.2 - - - +
2699B VAL* 1.3 61.4 + - - +
2700B LEU* 3.8 1.3 - - + +
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Residues in contact with VAL2699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2373B PRO* 3.4 3.2 - - - +
2374B LYS* 2.8 42.9 + - + +
2376B LEU* 3.7 26.7 - - + -
2394B ILE* 3.4 26.9 - - + -
2408B ALA* 3.5 28.5 - - + +
2681B LYS* 3.8 21.3 - - + -
2682B LEU 3.1 6.1 - - - +
2683B VAL* 4.3 5.4 - - + -
2698B LEU* 1.3 77.6 - - - +
2700B LEU* 1.3 61.3 + - - +
2701B ASP* 3.8 3.3 + - + +
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Residues in contact with LEU2700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2370B LEU* 4.7 14.4 - - + -
2371B LYS 5.1 3.1 - - - +
2372B SER 5.0 1.6 - - - +
2373B PRO* 3.4 37.2 - - + -
2660B LEU* 3.4 34.3 - - + +
2661B VAL* 3.4 31.0 - - + -
2681B LYS* 2.9 7.0 - - - +
2682B LEU* 2.7 48.1 + - + +
2684B CYS* 5.3 0.2 - - - -
2698B LEU* 5.3 1.8 - - + -
2699B VAL* 1.3 73.7 - - - +
2701B ASP* 1.3 59.4 + - - +
2702B PHE* 3.5 19.7 - - + -
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Residues in contact with ASP2701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2364B ASN* 3.8 5.5 + - - -
2371B LYS* 3.9 31.3 + - + +
2373B PRO* 5.6 0.2 - - - +
2374B LYS* 6.3 1.3 - - - +
2680B THR* 3.6 10.2 - - - +
2681B LYS* 3.2 32.5 + - - -
2699B VAL* 3.8 4.0 + - + +
2700B LEU* 1.3 73.2 - - - +
2702B PHE* 1.3 66.8 + - - +
2703B ASP* 3.4 19.4 + - - +
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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