Contacts of the strand formed by residues 381 - 386 (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 MET 381 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B GLU* 4.1 8.3 - - - +
367B VAL* 3.0 43.5 - - + +
370B MET* 3.4 31.9 + - + +
371B ARG* 3.1 31.6 - - + +
373B TYR 5.7 0.7 - - - +
379B VAL 3.3 2.6 + - - -
380B GLU* 1.3 79.2 - - - +
382B TYR* 1.3 62.4 + - - +
383B ASN* 4.7 9.4 - - - +
384B SER* 5.0 6.3 - - - +
393B VAL* 5.3 7.6 - - + -
394B VAL 4.7 2.5 - - - +
395B MET* 3.4 29.6 - - + +
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Residues in contact with TYR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LYS* 6.1 0.9 - - - +
347B VAL* 3.8 21.5 - - + -
380B GLU* 3.3 45.8 + - + +
381B MET* 1.3 75.2 - - - +
383B ASN* 1.3 80.7 + - - +
394B VAL* 3.2 19.3 + - + +
395B MET* 3.7 18.8 - - - -
396B GLU* 3.5 32.4 + - + +
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Residues in contact with ASN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 5.1 6.9 - - - +
314A PRO* 4.1 26.3 - - - +
313B ASP* 2.8 24.1 + - - +
381B MET* 3.8 6.0 - - - -
382B TYR* 1.3 100.5 + - - +
384B SER* 1.3 58.3 + - - +
385B TYR* 3.7 30.0 + - + +
393B VAL* 3.4 3.8 - - - +
394B VAL* 2.8 37.0 + - + +
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL* 2.9 4.7 - - - +
313B ASP* 2.6 38.0 + - - +
367B VAL* 2.8 51.8 - - - +
371B ARG* 5.1 0.9 + - - +
381B MET* 5.0 5.8 - - - +
383B ASN* 1.3 75.3 - - - +
385B TYR* 1.3 54.9 + - - +
391B LEU* 4.1 1.6 - - - -
392B TRP 3.9 4.3 - - - -
393B VAL* 3.7 19.1 - - - -
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Residues in contact with TYR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 6.4 0.9 - - + -
314A PRO* 4.6 21.4 + - + +
315A GLY* 6.4 0.9 - - - -
312B VAL* 3.3 2.4 - - - +
313B ASP* 2.8 36.6 - - + +
314B PRO* 3.1 24.5 - - + +
315B GLY 4.0 2.2 - - - +
316B ASP 5.4 0.4 - - - -
317B PRO* 3.3 48.1 - - + +
383B ASN* 3.7 27.7 + - + +
384B SER* 1.3 74.1 - - - +
386B LEU* 1.3 58.0 + - - +
387B VAL 4.4 0.2 - - - -
391B LEU* 3.0 7.5 - - - +
392B TRP* 2.5 46.3 + - - +
394B VAL* 3.6 21.6 - - + +
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Residues in contact with LEU 386 (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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320A TYR* 4.0 17.5 - - + +
305B ARG* 5.6 7.6 - - + +
308B LEU* 5.1 10.8 - - + -
309B GLN* 4.9 23.1 - - + +
312B VAL* 3.7 24.9 - - + -
313B ASP 3.7 6.7 + - - +
314B PRO* 5.0 3.6 - - + -
315B GLY 3.1 18.1 + - - +
354B LEU* 6.0 5.8 - - + -
385B TYR* 1.3 81.8 - - - +
387B VAL* 1.3 59.5 + - - +
388B GLY 3.5 9.8 + - - +
390B GLU* 2.9 23.8 - - - +
391B LEU* 4.0 14.4 - - + +
392B TRP 4.1 0.2 - - - +
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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