Contacts of the strand formed by residues 391 - 395 (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 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LEU* 5.0 9.0 - - + -
312B VAL* 3.8 27.1 - - + -
352B MET* 2.6 65.9 + - + +
353B ASP* 4.3 2.7 - - - +
354B LEU* 5.7 1.2 - - - +
363B LEU* 3.4 27.1 - - + -
367B VAL* 4.4 1.8 - - + -
384B SER* 4.1 3.4 - - - -
385B TYR 3.0 31.6 - - - +
386B LEU* 3.5 14.9 - - + +
390B GLU* 1.3 69.1 - - - +
392B TRP* 1.3 55.6 + - - +
393B VAL* 3.3 27.1 - - + -
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Residues in contact with TRP 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO* 4.5 17.5 - - + -
324B PHE* 5.5 10.8 - + - -
336B CYS* 4.3 17.0 - - - -
349B VAL* 5.1 4.7 - - + -
350B LYS 2.8 19.9 + - - +
351B LYS* 2.8 48.4 - - + +
352B MET 3.5 0.2 - - - -
385B TYR* 2.5 41.4 + - - +
387B VAL* 4.2 27.7 - - + +
390B GLU* 3.2 33.8 + - + -
391B LEU* 1.3 94.4 - - - +
393B VAL* 1.3 60.0 + - - +
394B VAL* 5.3 0.7 - - + -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ALA 3.7 1.7 - - - +
350B LYS* 2.9 54.4 + - + +
351B LYS 5.1 0.2 - - - +
363B LEU* 5.1 3.8 - - + -
367B VAL* 4.9 2.7 - - + -
381B MET* 5.3 8.1 - - + -
383B ASN 3.4 12.8 - - - +
384B SER* 3.7 17.7 - - - -
391B LEU* 3.3 34.1 - - + -
392B TRP* 1.3 73.4 - - - +
394B VAL* 1.3 69.8 + - - +
395B MET* 3.8 13.2 + - + +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO* 4.4 4.9 - - + -
321B LEU* 5.9 1.1 - - + -
347B VAL* 3.3 31.0 - - + -
348B ALA 3.4 3.8 - - - -
349B VAL* 3.8 23.1 - - + -
381B MET* 4.1 1.6 - - - -
382B TYR* 3.2 30.8 + - + -
383B ASN* 2.8 27.6 + - + +
385B TYR* 3.6 32.5 - - + +
392B TRP 5.3 0.4 - - - -
393B VAL* 1.3 78.0 - - - +
395B MET* 1.3 60.1 + - - +
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Residues in contact with MET 395 (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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334B ILE* 6.0 3.8 - - + -
347B VAL* 3.4 7.4 - - - +
348B ALA* 2.9 31.4 + - + +
350B LYS* 6.1 3.4 - - - -
370B MET* 5.8 4.5 - - + -
379B VAL* 3.1 42.0 - - + +
380B GLU 2.9 16.8 - - - +
381B MET* 3.4 31.0 - - + +
382B TYR* 3.7 9.2 - - - -
393B VAL* 3.8 11.0 + - + +
394B VAL* 1.3 73.4 - - - +
396B GLU* 1.3 69.8 + - - +
457B SER* 4.0 9.9 - - - +
459B PHE* 5.7 7.0 - - + -
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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