Contacts of the strand formed by residues 2482 - 2487 (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 THR2482 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2459B GLY 5.3 0.2 + - - -
2460B HIS* 2.8 18.4 + - - -
2478B SER 3.5 7.6 + - - -
2480B ASP* 2.6 44.1 + - + +
2481B ALA* 1.3 87.1 - - + +
2483B LEU* 1.3 65.8 + - - +
2484B ARG* 4.3 9.5 + - - -
2496B VAL* 4.2 4.2 - - + +
2497B LEU 3.1 9.2 - - - +
2498B MET* 3.5 39.7 - - + -
2504B VAL* 4.1 1.3 - - - +
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Residues in contact with LEU2483 (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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2475B VAL* 3.8 2.7 - - + -
2476B SER 2.7 16.6 - - - +
2482B THR* 1.3 73.8 - - - +
2484B ARG* 1.3 64.6 + - - +
2496B VAL* 3.4 1.2 - - - +
2497B LEU* 2.7 53.1 + - + +
2500B HIS* 3.5 30.5 - - + -
2504B VAL* 3.8 17.3 - - + -
2507B VAL* 3.4 28.5 - - + -
2514B VAL* 3.8 8.7 - - + -
2516B SER* 3.1 25.1 - - - -
2526B TRP* 3.6 14.1 - - + +
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Residues in contact with ARG2484 (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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2458B TYR 4.6 0.4 + - - -
2459B GLY* 2.9 41.8 + - - -
2460B HIS* 3.7 12.1 + - + +
2475B VAL* 4.0 0.9 - - - -
2476B SER* 2.7 39.7 + - - +
2482B THR* 4.3 4.8 + - - +
2483B LEU* 1.3 81.0 - - - +
2485B VAL* 1.3 61.1 + - - +
2486B TRP* 2.9 48.7 - - + +
2493B CYS* 3.4 13.4 - - - +
2495B HIS 3.3 4.7 - - - +
2496B VAL* 3.0 43.8 - - + +
2497B LEU* 4.3 0.2 - - - -
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Residues in contact with VAL2485 (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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2473B ARG* 4.0 34.1 - - + -
2474B VAL 3.5 2.7 - - - +
2475B VAL* 3.9 21.1 - - + +
2484B ARG* 1.3 71.4 - - - +
2486B TRP* 1.3 61.1 + - - +
2493B CYS* 3.3 3.8 - - - -
2494B LEU* 2.8 25.8 + - + -
2495B HIS* 2.9 28.8 + - + +
2497B LEU* 3.6 21.3 - - + -
2509B TYR* 4.1 6.3 - - + +
2514B VAL* 4.4 0.2 - - + -
2528B PRO* 3.5 25.8 - - + -
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Residues in contact with TRP2486 (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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2443B LEU* 3.1 30.7 - - + +
2457B LEU* 3.1 49.6 - - + -
2458B TYR 3.0 36.6 - - - -
2460B HIS* 4.0 3.4 - + - -
2473B ARG* 3.0 8.8 - - - +
2474B VAL* 2.7 46.3 + - + +
2476B SER* 2.7 20.2 + - - -
2484B ARG* 2.9 56.7 + - + +
2485B VAL* 1.3 74.3 - - - +
2487B ASP* 1.3 61.1 + - - +
2488B ILE 3.3 1.3 + - - +
2491B GLY 4.5 2.2 - - - -
2492B GLN 3.3 8.5 - - - +
2493B CYS* 3.1 31.0 - - + -
2494B LEU* 3.7 3.1 - - - -
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Residues in contact with ASP2487 (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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2472B LYS* 3.4 16.6 + - - +
2473B ARG* 4.5 3.0 + - - +
2486B TRP* 1.3 71.3 - - - +
2488B ILE* 1.3 52.7 + - - +
2489B GLU* 2.7 32.4 + - - +
2490B THR* 2.8 50.9 + - - +
2491B GLY* 2.6 32.8 + - - -
2492B GLN 2.9 8.3 + - - +
2494B LEU* 3.1 29.0 - - + +
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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
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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