Contacts of the strand formed by residues 283 - 287 (chain B) in PDB entry 4OV6
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 LEU 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU* 3.7 4.5 - - + +
183B TYR* 3.6 41.5 - - + +
271B ILE* 3.8 11.0 - - + -
275B GLN* 3.8 39.5 - - + +
278B GLN* 6.2 1.8 - - + -
281B GLY 3.7 5.8 + - - +
282B PRO* 1.4 73.9 - - - +
284B VAL* 1.3 63.2 + - - +
285B VAL* 3.6 24.2 - - + -
308B GLY 4.8 3.8 + - - +
309B VAL* 3.8 17.6 - - + +
310B VAL* 3.0 30.0 + - - +
400B LEU* 4.8 1.8 - - - +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 4.1 14.4 - - + -
181B GLU 3.0 6.4 + - - +
182B VAL* 3.3 15.4 - - + -
183B TYR* 2.7 33.1 + - - +
283B LEU* 1.3 72.8 - - - +
285B VAL* 1.3 64.0 + - - +
286B LEU 4.2 0.2 - - - -
310B VAL* 3.3 11.4 - - + +
312B VAL* 4.4 9.4 - - + -
393B ALA* 4.1 33.2 - - + +
396B ALA* 4.4 5.6 - - + -
397B ALA* 4.3 12.6 - - - +
400B LEU* 3.7 28.9 - - + -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.5 7.6 - - + -
185B LEU* 3.8 25.6 - - + -
268B LEU* 4.3 3.6 - - + -
271B ILE* 3.9 18.8 - - + -
283B LEU* 3.6 27.6 - - + -
284B VAL* 1.3 75.0 - - - +
286B LEU* 1.3 56.9 + - - +
287B LEU* 4.0 10.7 + - + +
304B LEU* 5.2 1.3 - - + -
309B VAL* 3.6 12.3 - - + -
310B VAL 2.8 10.7 + - - +
311B LEU* 3.4 25.8 - - + +
312B VAL* 2.8 32.9 + - - +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 4.8 5.1 - - + +
183B TYR 2.8 15.1 + - - +
184B LEU* 3.7 24.2 - - + -
185B LEU* 3.1 29.6 + - - +
230B LEU* 4.9 2.9 - - + -
234B VAL* 3.8 18.6 - - + -
247B MET* 5.4 0.7 - - + -
284B VAL* 4.2 0.8 - - - +
285B VAL* 1.3 70.8 - - - +
287B LEU* 1.4 59.4 + - - +
288B PRO* 3.4 14.7 - - + +
312B VAL* 3.4 14.8 - - - +
389B ALA* 3.7 37.0 - - + +
390B ALA* 3.8 24.9 - - + +
393B ALA* 4.1 13.5 - - + -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.3 10.5 - - + -
264B THR* 3.7 29.8 - - + -
268B LEU* 4.2 15.3 - - + -
285B VAL* 4.1 10.5 - - + -
286B LEU* 1.4 73.1 - - - +
288B PRO* 1.4 59.6 - - - +
289B LEU* 3.0 18.6 + - + -
297B LEU* 5.4 0.2 - - + -
301B CYS* 4.5 7.0 - - - -
311B LEU* 3.8 34.8 - - + -
312B VAL 2.8 13.3 + - - +
313B THR* 2.8 34.7 + - - +
314B ALA 3.4 0.7 + - - -
327B PRO* 4.1 23.1 - - + -
333B VAL* 5.4 0.4 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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