Contacts of the strand formed by residues 237 - 242 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196T SER* 3.6 3.8 + - - -
210T ALA* 3.6 24.2 - - + +
211T SER 3.1 18.7 + - - +
214T LYS* 3.6 31.9 - - - +
215T THR 3.6 6.5 - - - +
216T ILE* 4.0 11.4 - - + -
233T HIS* 4.1 15.5 - - + +
235T GLU 4.0 3.6 - - - +
236T TRP* 1.3 89.5 + - - +
238T ARG* 1.3 64.1 + - - +
239T MET 4.0 6.3 - - - +
251T SER* 3.5 17.5 - - - +
252T CYS 3.4 11.0 - - - +
253T SER* 3.9 0.7 - - - -
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Residues in contact with ARG 238 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R GLU* 2.5 36.6 + - - -
113T ARG* 5.8 1.2 + - - -
196T SER* 2.7 35.5 + - - +
197T SER* 3.7 1.5 - - - -
236T TRP* 3.2 29.7 - - + -
237T VAL* 1.3 69.5 - - - +
239T MET* 1.3 59.5 + - + +
252T CYS* 2.4 28.5 + - + +
253T SER* 4.3 4.5 - - - -
254T ASN* 3.6 19.2 + - - +
278T VAL* 4.1 7.1 - - - +
279T VAL 3.7 18.8 - - - +
280T GLU* 2.9 49.8 + - + +
316T ARG* 3.7 6.1 - - - +
342T ARG* 4.8 6.3 - - - +
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Residues in contact with MET 239 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T ARG* 5.3 11.4 - - - +
197T SER* 3.3 18.8 - - - +
210T ALA* 4.3 1.5 - - - +
237T VAL* 3.7 4.2 - - - +
238T ARG* 1.3 80.1 - - - +
240T VAL* 1.3 65.4 + - - +
241T ARG* 3.5 34.8 - - - +
250T ALA 4.1 0.9 - - - -
251T SER* 3.3 6.1 - - - -
252T CYS* 3.3 35.1 + - + -
280T GLU 3.7 17.3 - - - +
281T CYS* 3.8 3.1 - - + -
282T ILE* 3.6 39.9 - - + +
283T SER* 5.6 0.7 - - - +
342T ARG 6.1 0.9 - - - +
343T GLY* 6.6 0.7 - - - -
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Residues in contact with VAL 240 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197T SER* 3.3 15.2 + - - +
198T VAL* 4.6 0.9 - - - +
199T SER* 4.1 3.3 - - - +
208T VAL* 3.8 21.8 - - + +
209T SER* 3.8 15.0 - - - -
210T ALA* 3.8 16.4 - - + -
216T ILE* 3.7 40.8 - - + -
239T MET* 1.3 80.0 - - - +
241T ARG* 1.3 88.6 + - - +
242T PRO* 4.6 0.2 - - - -
249T ILE* 5.1 5.4 - - + -
250T ALA 3.1 8.5 - - - +
251T SER* 4.5 4.3 - - - -
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Residues in contact with ARG 241 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T ARG* 4.4 4.6 - - - +
115T ILE* 6.0 2.6 - - - +
155T ASP* 3.3 26.3 + - - -
156T ILE 5.0 2.2 + - - -
157T SER* 5.3 1.8 - - - -
197T SER* 3.9 6.1 + - - -
198T VAL 3.0 24.8 + - - -
199T SER* 3.6 8.6 - - - -
239T MET* 3.5 29.4 - - + +
240T VAL* 1.3 90.2 + - - +
242T PRO* 1.3 72.0 - - + +
249T ILE* 3.4 7.1 - - - +
250T ALA 2.8 39.1 + - - +
282T ILE* 3.7 28.5 - - + +
283T SER* 5.3 0.7 - - - -
284T TRP* 3.2 26.5 + - + +
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Residues in contact with PRO 242 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199T SER* 3.8 25.4 - - - +
200T ILE 4.2 13.0 - - - +
201T MET* 4.0 25.6 - - + -
202T PRO* 4.2 12.6 - - + -
241T ARG* 1.3 96.6 - - + +
243T ASN* 1.3 59.0 + - - +
244T GLN 4.1 0.7 + - - -
248T LEU 3.4 8.1 - - - +
249T ILE* 3.8 4.9 - - + -
284T TRP* 2.7 26.5 + - - -
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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