Contacts of the strand formed by residues 277 - 284 (chain B) in PDB entry 2V3D
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 ARG 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B TRP* 2.8 26.6 + - + +
229B ALA* 3.2 10.0 - - + -
230B VAL* 2.8 29.0 + - - +
268B LEU* 5.8 0.2 - - - -
275B ASN 3.3 10.8 + - - +
276B VAL* 1.3 75.2 - - - +
278B LEU* 1.3 59.7 + - - +
279B LEU* 4.1 1.6 - - + -
306B HIS* 3.4 52.9 + - + +
1505B SO4 3.0 38.9 + - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B VAL* 3.4 18.2 - - + +
232B ALA* 3.9 16.2 - - + +
260B ILE* 3.7 38.4 - - + -
264B LEU* 3.7 32.5 - - + -
265B GLY* 4.8 4.5 - - - +
268B LEU* 4.5 11.7 - - + -
276B VAL 3.9 1.4 + - - +
277B ARG* 1.3 73.3 - - - +
279B LEU* 1.3 68.5 + - - +
304B TYR* 3.5 26.6 + - + +
305B VAL* 3.8 4.1 - - + -
306B HIS* 2.9 30.0 + - - +
307B GLY 3.5 2.8 + - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 3.8 24.2 - - + -
228B TRP* 4.1 17.9 - - + -
229B ALA* 4.2 5.8 - - + -
230B VAL 2.8 16.1 + - - +
231B THR* 3.1 11.5 - - + -
232B ALA* 2.9 27.4 + - - +
277B ARG* 4.7 2.9 - - + -
278B LEU* 1.3 78.7 - - - +
280B MET* 1.3 60.8 + - - +
306B HIS* 3.9 9.9 - - + -
307B GLY* 3.3 33.2 - - - +
309B ALA* 4.3 14.8 - - + -
335B MET* 3.9 15.3 - - + -
337B PHE* 4.1 20.4 - - + -
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Residues in contact with MET 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ALA* 4.5 5.4 - - - -
256B GLN* 3.4 12.1 - - - +
260B ILE* 4.3 12.6 - - + -
278B LEU 4.2 0.6 + - - -
279B LEU* 1.3 74.4 - - - +
281B LEU* 1.3 71.9 + - + +
282B ASP* 3.0 4.5 + - - -
288B LEU* 5.6 0.2 - - + -
291B TRP* 3.6 40.2 - - + +
292B ALA* 4.1 3.6 - - - +
295B VAL* 3.6 32.5 - - + -
296B LEU* 4.3 10.8 - - - -
305B VAL* 3.7 15.6 - - + +
307B GLY 2.9 20.0 + - - +
308B ILE* 3.7 20.0 - - + -
309B ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ALA* 5.2 0.8 - - - +
233B GLU 3.5 2.0 - - - +
236B PRO* 3.0 26.3 - - - +
256B GLN* 3.0 19.3 + - - +
280B MET* 1.3 76.0 - - + +
282B ASP* 1.3 72.2 + - - +
283B ASP* 3.6 28.0 - - + +
284B GLN 4.3 5.4 - - - +
287B LEU* 3.8 16.6 - - + -
288B LEU* 3.7 33.2 - - + -
291B TRP* 3.6 33.7 - - + -
308B ILE* 3.8 11.0 - - + -
309B ALA 3.4 12.6 - - - +
310B VAL* 4.0 7.6 - - + -
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Residues in contact with ASP 282 (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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120B ARG* 3.0 24.0 + - - -
177B SER* 3.4 0.2 + - - -
231B THR* 2.8 38.9 + - + -
232B ALA 5.5 0.2 - - - +
233B GLU 3.3 9.9 - - - +
234B ASN* 3.3 9.6 - - - -
235B GLU* 2.7 31.0 + - - -
280B MET 3.0 5.8 + - - +
281B LEU* 1.3 72.6 - - - +
283B ASP* 1.3 55.1 + - - +
309B ALA* 2.8 20.5 + - - -
311B HIS* 2.8 19.8 + - - -
339B SER* 2.6 29.8 + - - -
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU* 3.4 12.5 - - - +
236B PRO* 3.3 6.5 - - + +
237B SER* 3.0 43.2 + - - -
281B LEU* 3.2 28.6 - - + +
282B ASP* 1.3 77.7 - - - +
284B GLN* 1.3 94.0 + - - +
287B LEU* 3.5 10.2 - - - +
309B ALA 3.5 2.6 + - - +
310B VAL* 3.2 8.0 - - - +
311B HIS* 2.7 32.3 + - - -
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Residues in contact with GLN 284 (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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317A LEU* 4.9 7.2 - - + -
235B GLU* 2.9 30.9 + - - -
281B LEU* 4.3 1.9 - - - +
283B ASP* 1.3 97.4 + - - +
285B ARG* 1.3 61.3 + - - +
286B LEU* 3.1 21.8 - - + +
287B LEU* 3.0 30.3 + - + +
311B HIS* 3.5 11.3 - - - +
313B TYR* 3.1 31.0 + - - +
314B LEU* 3.6 24.2 + - + +
1504B NBV 3.7 19.6 - - + +
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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
------------------------------------------------------------
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