Contacts of the strand formed by residues 2453 - 2458 (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 CYS2453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2418B VAL 5.6 0.7 - - - +
2419B GLY* 5.9 0.4 - - - -
2444B LYS* 3.3 34.1 - - - +
2445B VAL 3.5 8.1 - - - -
2446B TRP* 3.8 23.6 - - + -
2451B GLY 3.9 0.2 + - - -
2452B GLU* 1.3 73.2 - - - +
2454B ILE* 1.3 59.8 + - - +
2455B HIS 2.8 31.9 - - - -
2456B THR* 3.3 7.0 - - - -
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Residues in contact with ILE2454 (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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2433B ILE* 3.6 22.9 - - + -
2445B VAL* 3.0 37.0 + - + +
2446B TRP 4.2 3.4 - - - +
2447B ASN* 4.2 9.9 - - + +
2452B GLU* 3.3 35.0 + - + +
2453B CYS* 1.3 73.0 - - - +
2455B HIS* 1.3 90.8 + - + +
2488B ILE 4.4 2.5 - - - +
2489B GLU 5.9 0.2 - - - +
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Residues in contact with HIS2455 (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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2444B LYS* 3.2 0.9 - - - -
2445B VAL* 2.9 34.6 + - + -
2453B CYS* 2.8 17.7 + - - -
2454B ILE* 1.3 114.4 + - + +
2456B THR* 1.3 64.0 + - - +
2457B LEU* 3.7 7.6 - - + -
2488B ILE 3.6 14.1 - - - -
2489B GLU 2.6 21.4 + - - -
2490B THR 2.8 27.1 + - - -
2491B GLY* 2.9 15.1 - - - -
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Residues in contact with THR2456 (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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2442B THR* 3.7 11.9 - - - +
2443B LEU 3.4 2.9 - - - -
2444B LYS* 2.9 44.6 + - + +
2453B CYS* 3.3 3.6 - - - -
2455B HIS* 1.3 75.7 - - - +
2457B LEU* 1.3 61.7 + - - +
2458B TYR* 2.9 61.9 + - + +
2491B GLY 5.3 0.3 - - - +
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Residues in contact with LEU2457 (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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2441B ARG 4.2 0.5 - - - +
2442B THR* 3.4 6.6 - - - -
2443B LEU* 2.7 54.9 + - + +
2445B VAL* 4.0 18.4 - - + -
2455B HIS* 3.7 13.7 - - + -
2456B THR* 1.3 73.8 - - - +
2458B TYR* 1.3 59.6 - - - +
2459B GLY 4.0 0.5 + - - -
2460B HIS 4.9 0.3 + - - -
2486B TRP* 3.1 56.6 - - + -
2487B ASP 5.7 0.2 - - - +
2488B ILE* 4.5 3.6 - - + -
2491B GLY* 3.2 37.7 - - - +
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Residues in contact with TYR2458 (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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2442B THR* 3.4 28.7 - - + -
2444B LYS* 5.4 0.2 + - - -
2456B THR* 2.9 54.9 + - + +
2457B LEU* 1.3 73.0 - - - +
2459B GLY* 1.3 58.9 + - - +
2484B ARG* 4.6 1.0 + - - -
2486B TRP* 3.0 15.9 - - - -
2493B CYS* 4.9 0.9 - - - +
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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