Contacts of the strand formed by residues 237 - 243 (chain B) in PDB entry 2VR1
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 GLN 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B GLN* 3.1 4.8 - - - -
234B ARG 2.8 38.3 + - - +
235B ARG* 2.9 12.9 + - + +
236B HIS* 1.3 80.1 - - - +
238B LYS* 1.3 64.9 + - - +
239B VAL* 4.0 3.1 - - + +
338B ARG* 5.0 9.9 - - - +
382B ASP* 5.4 5.3 + - - -
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Residues in contact with LYS 238 (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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209B HIS* 3.9 19.7 - - - -
211B GLU* 3.6 0.4 + - - -
230B CYS* 3.7 24.7 - - + +
232B MET 3.7 6.3 - - - +
233B GLN* 4.2 7.6 - - - +
236B HIS 5.2 2.7 - - - +
237B GLN* 1.3 78.7 + - - +
239B VAL* 1.3 61.8 + - - +
240B VAL 4.9 0.4 - - - +
241B GLU* 3.6 16.2 - - + +
276B GLU* 2.8 28.4 + - - -
290B ASN* 4.8 0.2 - - - +
294B GLN* 3.5 6.3 - - - +
296B GLU* 2.9 31.7 + - - +
338B ARG* 3.5 36.9 + - - +
340B ASN* 5.4 1.7 - - - +
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Residues in contact with VAL 239 (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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232B MET 2.9 12.1 + - - +
234B ARG* 4.2 11.4 - - + +
237B GLN* 4.0 9.9 - - + +
238B LYS* 1.3 77.5 - - - +
240B VAL* 1.3 61.5 + - + +
241B GLU* 4.8 0.2 - - - -
338B ARG* 3.3 22.7 + - - +
340B ASN* 5.5 5.6 - - - +
417B ASN* 4.8 7.4 - - - +
420B LEU* 5.1 8.5 - - + -
421B GLN* 3.1 38.7 + - - +
424B ILE* 4.0 23.6 - - + -
440B LEU* 3.8 21.5 - - + -
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Residues in contact with VAL 240 (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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229B ASP 4.3 0.5 - - - +
230B CYS* 3.8 14.2 - - - -
232B MET* 3.6 22.8 + - + +
238B LYS* 4.9 0.2 - - - +
239B VAL* 1.3 84.3 + - + +
241B GLU* 1.3 74.9 + - - +
242B GLU* 5.5 1.6 - - + -
335B VAL* 3.9 21.5 - - + -
336B GLU 3.3 12.8 - - - +
337B CYS* 4.4 0.4 - - - -
421B GLN* 3.3 26.7 - - - +
424B ILE* 4.1 21.3 - - + -
425B MET* 4.2 9.9 - - + -
430B PHE* 4.4 12.6 - - + -
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Residues in contact with GLU 241 (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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228B ARG* 5.3 0.4 - - + -
229B ASP 3.5 5.4 - - - -
230B CYS* 3.5 26.9 - - + -
238B LYS* 3.6 6.9 - - + +
240B VAL* 1.3 83.7 - - - +
242B GLU* 1.3 62.1 + - - +
296B GLU* 3.4 24.2 - - + +
299B VAL* 4.6 5.6 - - + -
335B VAL* 3.4 2.8 - - - +
336B GLU* 2.6 73.6 + - + +
338B ARG* 2.8 42.3 + - - +
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Residues in contact with GLU 242 (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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228B ARG* 3.1 5.6 - - - -
229B ASP* 2.8 53.8 + - + +
240B VAL* 5.5 1.8 - - + -
241B GLU* 1.3 77.4 - - - +
243B ALA* 1.3 61.5 + - - +
244B PRO 3.9 3.4 - - - +
246B PRO* 3.7 15.0 - - - +
299B VAL* 4.4 5.2 - - - -
333B HIS* 2.7 26.6 + - - +
334B ALA 3.2 13.0 - - - +
335B VAL* 4.0 12.6 - - + +
395B ARG* 2.8 35.9 + - - +
430B PHE* 4.1 11.8 - - - -
434B GLY 5.5 1.6 + - - -
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Residues in contact with ALA 243 (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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227B GLU 3.4 15.9 - - - +
228B ARG* 4.1 3.6 - - + -
242B GLU* 1.3 76.0 - - - +
244B PRO* 1.3 68.4 - - - +
299B VAL* 4.0 26.4 - - + +
300B THR* 4.4 1.6 - - - +
303B ILE* 3.6 20.6 - - + +
333B HIS* 3.3 4.6 - - - -
334B ALA 2.8 33.2 + - - -
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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