Contacts of the helix formed by residues 362 - 371 (chain B) in PDB entry 2BVA
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 362 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B LEU* 1.3 61.0 + - - +
364B PHE* 3.0 17.9 + - + +
365B ASN* 3.2 22.4 + - - +
366B GLU* 3.8 2.4 + - - +
460B GLY 4.9 8.5 - - - +
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Residues in contact with LEU 363 (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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308B LEU* 4.9 6.5 - - + +
352B MET* 5.2 2.2 - - + -
362B LEU* 1.3 73.3 - - - +
364B PHE* 1.3 66.2 + - - +
365B ASN 3.2 0.7 - - - -
366B GLU* 2.8 43.7 + - + +
367B VAL* 3.7 10.6 + - + +
391B LEU* 3.4 33.2 - - + -
393B VAL* 5.1 3.1 - - + -
460B GLY 5.7 1.3 - - - -
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Residues in contact with PHE 364 (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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304B PHE 5.3 1.3 - - - +
307B ALA* 3.7 18.8 - - + -
308B LEU* 3.9 45.6 - - + +
311B VAL* 3.3 37.0 - - + +
312B VAL* 5.5 1.4 - - + +
362B LEU* 3.0 9.4 - - + +
363B LEU* 1.3 79.7 - - - +
365B ASN* 1.3 90.6 + - - +
366B GLU 3.4 0.2 + - - -
367B VAL* 3.6 10.2 + - - +
368B VAL* 3.3 20.7 + - + +
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Residues in contact with ASN 365 (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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362B LEU 3.2 15.0 + - - +
363B LEU 3.2 0.2 - - - -
364B PHE* 1.3 94.1 - - + +
366B GLU* 1.3 65.3 + - - +
368B VAL* 2.8 43.4 + - - +
369B ILE* 3.0 24.1 + - + +
472B ARG* 4.9 14.1 - - - +
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Residues in contact with GLU 366 (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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362B LEU 3.8 2.2 + - - +
363B LEU* 2.8 48.8 + - + +
365B ASN* 1.3 79.0 - - - +
367B VAL* 1.3 65.2 + - + +
369B ILE* 3.3 7.7 + - - -
370B MET* 3.4 20.4 + - + +
381B MET* 4.0 5.6 - - - +
458B ASP* 5.0 0.7 - - - -
459B PHE* 3.7 24.9 + - + +
460B GLY* 3.4 32.1 + - - +
462B CYS* 5.8 3.1 - - - -
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Residues in contact with VAL 367 (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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308B LEU* 5.7 0.7 - - + -
311B VAL 2.9 28.3 - - - +
312B VAL* 3.9 13.5 - - + -
363B LEU* 3.7 15.2 + - + +
364B PHE* 3.6 8.2 + - - +
365B ASN 3.3 0.2 - - - -
366B GLU* 1.3 75.5 - - + +
368B VAL* 1.3 64.1 + - - +
369B ILE 3.0 1.0 + - - -
371B ARG* 3.4 17.3 - - - +
381B MET* 3.0 31.8 - - + +
384B SER* 2.8 40.4 - - - +
391B LEU* 4.4 6.7 - - + -
393B VAL* 4.9 2.7 - - + -
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Residues in contact with VAL 368 (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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311B VAL* 3.8 30.7 - - + -
364B PHE* 3.3 31.9 - - + +
365B ASN* 2.8 34.3 - - - +
367B VAL* 1.3 75.5 - - - +
369B ILE* 1.3 65.6 + - + +
371B ARG* 3.6 9.2 - - - +
372B ASP* 3.2 15.6 - - - +
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Residues in contact with ILE 369 (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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365B ASN* 3.0 31.5 + - + +
366B GLU 4.4 1.3 - - - +
367B VAL 3.2 0.2 - - - -
368B VAL* 1.3 84.3 - - + +
370B MET* 1.3 83.7 + - + +
371B ARG 3.0 2.1 + - - -
372B ASP* 2.3 34.7 + - - +
373B TYR* 4.9 0.3 - - - +
436B VAL* 4.4 8.5 - - + -
462B CYS* 4.4 17.0 - - - +
463B ALA* 4.5 3.4 - - - -
464B GLN* 4.0 44.2 - - + +
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Residues in contact with MET 370 (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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366B GLU* 3.4 13.0 + - + +
369B ILE* 1.3 101.4 - - + +
371B ARG* 1.3 62.1 + - - +
372B ASP 3.3 0.7 - - - -
373B TYR* 4.4 23.5 + - + +
378B VAL* 5.4 4.7 - - + -
381B MET* 3.4 40.1 + - + +
395B MET* 5.8 3.4 - - + -
431B LEU* 4.1 10.5 - - + -
436B VAL* 3.8 15.5 - - + -
459B PHE* 3.4 42.8 - - + +
462B CYS* 3.3 28.7 - - - -
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Residues in contact with ARG 371 (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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311B VAL* 4.4 20.0 + - - +
312B VAL* 4.7 2.2 - - - +
313B ASP* 3.3 29.7 + - - +
367B VAL* 3.4 19.2 + - - +
368B VAL* 3.6 8.4 - - - +
369B ILE 3.0 0.6 - - - -
370B MET* 1.3 80.7 - - - +
372B ASP* 1.3 74.8 + - - +
373B TYR 3.5 6.9 + - - +
381B MET* 3.1 25.5 - - + +
384B SER* 5.1 0.6 + - - +
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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