Contacts of the strand formed by residues 237 - 242 (chain C) in PDB entry 1VYH
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 VAL 237 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C SER* 3.6 5.9 + - - -
210C ALA* 3.4 26.1 - - + -
211C SER 2.9 22.9 + - - +
214C LYS* 3.6 28.9 - - - +
215C THR 3.7 5.4 - - - +
216C ILE* 4.1 12.6 - - + -
233C HIS* 3.5 31.9 - - + +
235C GLU 4.0 0.9 - - - +
236C TRP* 1.3 86.6 + - - +
238C ARG* 1.3 62.5 + - - +
239C MET 4.1 9.2 - - - +
252C CYS 3.6 10.5 - - - +
253C SER* 3.9 0.2 - - - -
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Residues in contact with ARG 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU* 2.8 26.1 + - - -
113C ARG* 5.1 1.6 + - - -
196C SER* 3.5 30.4 - - - +
197C SER* 3.9 2.5 - - - -
210C ALA* 5.0 0.4 - - - -
236C TRP* 3.0 40.2 - - - -
237C VAL* 1.3 75.5 - - - +
239C MET* 1.3 60.6 + - + +
252C CYS* 2.6 26.8 + - - +
253C SER* 4.0 3.4 - - - -
254C ASN* 3.2 25.1 + - - +
278C VAL* 4.3 3.8 - - - -
279C VAL 3.6 18.8 - - - +
280C GLU* 3.4 39.5 + - - +
316C ARG* 3.4 3.6 - - - +
342C ARG* 5.8 0.8 - - - +
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Residues in contact with MET 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ARG* 4.2 13.7 - - - +
197C SER* 3.7 9.4 - - - +
210C ALA* 4.5 2.2 - - - +
237C VAL* 3.7 4.3 - - - +
238C ARG* 1.3 80.3 - - - +
240C VAL* 1.3 68.7 + - - +
241C ARG* 3.3 38.4 - - + +
250C ALA 3.5 0.8 - - - +
251C SER* 3.3 22.3 - - - -
252C CYS* 3.4 22.9 + - + +
280C GLU 3.6 19.3 - - - +
281C CYS* 3.9 6.3 - - + -
282C ILE* 3.3 39.9 - - + +
342C ARG 5.9 0.4 - - - +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C SER* 3.7 14.5 + - - +
198C VAL 4.7 0.4 - - - +
199C SER* 4.3 4.0 - - - -
208C VAL* 4.4 15.9 - - + +
209C SER* 3.8 16.8 - - - +
210C ALA* 3.6 19.5 - - + +
216C ILE* 3.7 36.1 - - + -
239C MET* 1.3 78.8 - - - +
241C ARG* 1.3 86.6 + - - +
242C PRO* 4.3 2.4 - - - +
249C ILE* 4.5 9.6 - - + -
250C ALA 3.2 9.6 - - - +
251C SER* 4.5 1.8 - - - -
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Residues in contact with ARG 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ARG* 3.8 11.1 - - - +
155C ASP* 3.3 22.3 + - - -
156C ILE 5.1 3.4 + - - -
157C SER* 5.3 1.6 - - - -
197C SER* 3.7 3.4 + - - -
198C VAL 3.3 24.4 + - - -
199C SER* 4.2 5.5 - - - +
239C MET* 3.3 31.6 - - + +
240C VAL* 1.3 90.3 + - - +
242C PRO* 1.3 80.4 - - + +
249C ILE* 3.5 5.8 - - - -
250C ALA* 2.8 40.0 + - + +
282C ILE* 3.8 22.6 + - + +
283C SER* 5.3 1.3 - - - -
284C TRP* 3.4 15.7 + - + +
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Residues in contact with PRO 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C SER* 3.7 30.7 - - - +
200C ILE 4.4 8.7 - - - +
201C MET* 3.5 30.3 - - + -
202C PRO* 4.4 10.8 - - + -
240C VAL 4.5 0.2 - - - -
241C ARG* 1.3 91.2 - - + +
243C ASN* 1.3 63.3 + - - +
244C GLN 4.1 0.7 + - - -
248C LEU 3.5 9.2 - - - +
249C ILE* 3.6 6.3 - - + -
284C TRP* 2.9 22.0 + - - -
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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