Contacts of the strand formed by residues 233 - 237 (chain V) in PDB entry 3EXG
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 CYS 233 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202V ARG* 2.9 24.7 + - - +
203V GLN 3.2 12.0 - - - +
204V GLY* 3.2 1.2 - - - -
207V ILE* 3.6 26.0 - - + +
209V VAL* 4.4 8.5 - - + -
223V ALA* 4.0 30.5 - - + -
226V LEU* 4.1 24.9 - - - -
231V VAL* 3.6 8.2 + - - -
232V GLU* 1.3 74.1 - - - +
234V GLU* 1.3 59.5 + - - +
235V VAL* 3.7 4.5 - - + -
323V ILE* 4.1 9.9 - - - -
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Residues in contact with GLU 234 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200V ILE* 3.5 30.0 - - + +
202V ARG 3.3 10.8 - - - +
203V GLN* 3.3 7.1 - - - +
204V GLY 2.8 39.3 + - - +
207V ILE 2.8 16.8 + - - +
208V THR* 4.0 1.0 - - - -
209V VAL 3.3 18.1 + - - +
232V GLU 4.0 0.2 + - - -
233V CYS* 1.3 71.7 - - - +
235V VAL* 1.3 65.1 + - - +
236V ILE* 3.3 7.9 + - + +
252V SER* 3.1 33.6 + - - +
255V LYS* 2.8 23.8 + - - -
256V THR* 4.6 2.2 - - + -
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Residues in contact with VAL 235 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200V ILE* 3.7 1.4 - - - -
201V GLU* 2.9 27.0 + - + -
202V ARG* 3.4 33.7 + - + +
209V VAL* 3.4 12.8 - - + +
211V SER* 5.8 0.7 - - - -
216V VAL* 4.6 8.5 - - + +
219V CYS* 3.6 28.5 - - + -
220V LEU* 3.8 30.3 - - + +
223V ALA* 4.0 14.1 - - + -
233V CYS* 3.7 5.8 - - + -
234V GLU* 1.3 71.6 - - - +
236V ILE* 1.3 68.4 + - - +
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Residues in contact with ILE 236 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198V ALA* 4.2 21.8 - - + -
199V LYS 3.8 4.5 - - - +
200V ILE* 4.1 16.2 - - + -
208V THR* 3.6 17.7 - - + -
209V VAL 2.7 14.2 + - - +
210V VAL* 3.8 10.3 - - + -
211V SER* 3.2 24.6 + - - +
216V VAL* 4.7 0.5 - - - +
234V GLU* 3.7 7.0 - - + +
235V VAL* 1.3 83.1 - - - +
237V ASN* 1.3 65.3 + - - +
238V MET* 4.5 1.6 - - - +
248V THR* 4.3 17.7 - - + -
249V ILE* 4.4 17.3 - - + -
252V SER* 3.6 31.9 - - - +
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Residues in contact with ASN 237 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146V SER 5.0 1.6 + - - -
148V TRP* 4.0 9.0 + - - +
152V ASP* 3.0 28.9 - - - +
198V ALA* 3.4 2.5 - - - +
199V LYS* 2.8 34.3 + - + +
201V GLU* 3.2 32.0 - - + +
211V SER 3.6 8.3 + - - -
212V HIS* 4.3 4.6 - - - +
213V SER 4.9 0.8 - - - +
216V VAL* 3.8 20.3 - - + +
235V VAL 4.3 0.4 + - - -
236V ILE* 1.3 71.7 - - - +
238V MET* 1.3 65.9 + - - +
239V ARG* 3.5 21.6 + - - +
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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
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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