Contacts of the strand formed by residues 234 - 239 (chain C) in PDB entry 3V4P
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 GLU 234 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C ALA* 3.4 8.1 - - - +
225C GLY 2.9 28.4 + - - +
226C HIS* 3.4 2.9 - - - -
227C PHE* 2.7 49.5 + - + -
228C ARG* 3.2 41.6 + - + +
232C THR* 3.2 26.9 + - - +
233C THR* 1.3 77.4 - - - +
235C VAL* 1.3 66.1 + - - +
250C ILE* 4.1 5.4 - - + -
251C PHE 3.3 14.8 - - - +
252C SER* 4.8 0.9 - - - +
253C ILE* 5.0 0.2 - - - -
261C LEU* 4.2 7.2 - - + -
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Residues in contact with VAL 235 (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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177C LEU* 5.0 4.5 - - + -
179C VAL* 3.7 23.1 - - + -
192C LEU* 3.6 26.9 - - + -
194C VAL* 3.7 25.4 - - + -
223C GLY 3.4 11.9 - - - +
224C ALA* 4.6 2.5 - - + -
233C THR* 5.6 1.1 - - + -
234C GLU* 1.3 79.1 - - - +
236C VAL* 1.3 68.7 + - - +
249C TYR 3.8 0.2 - - - +
250C ILE* 3.2 6.6 - - - +
251C PHE* 2.8 41.7 + - + +
253C ILE* 4.0 15.9 - - + -
258C LEU* 5.3 2.5 - - + -
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C LEU* 4.0 6.1 - - - +
222C VAL* 3.2 9.0 - - - +
223C GLY* 2.9 40.9 + - - +
224C ALA 4.7 0.4 - - - +
227C PHE* 3.4 33.4 - - + -
235C VAL* 1.3 78.1 - - - +
237C GLY* 1.3 62.2 + - - +
248C ALA* 5.3 2.2 - - + -
249C TYR 3.2 11.7 - - - +
250C ILE* 4.4 3.1 - - + -
277C VAL* 3.7 33.7 - - + -
279C ALA* 4.9 3.1 - - + +
290C LEU* 3.5 28.5 - - + -
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Residues in contact with GLY 237 (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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192C LEU* 3.9 15.9 - - - -
218C LEU* 3.9 14.8 - - - +
221C SER 3.5 6.7 - - - -
236C VAL* 1.3 78.9 - - - +
238C GLY* 1.3 60.8 + - - -
248C ALA* 3.4 3.3 - - - +
249C TYR* 2.9 34.3 + - - -
251C PHE* 3.9 4.1 - - - -
277C VAL* 4.6 1.3 - - - -
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Residues in contact with GLY 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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217C TYR 3.2 5.0 - - - +
218C LEU* 4.2 1.1 - - - +
219C GLY 2.9 24.2 + - - +
220C TYR 3.4 4.0 + - - -
221C SER* 3.1 17.8 + - - -
237C GLY* 1.3 73.3 - - - -
239C ALA* 1.3 59.5 + - - -
240C PRO* 3.5 5.6 - - - -
247C LYS 3.7 4.9 - - - -
248C ALA* 4.5 0.2 - - - -
274C GLY* 3.2 22.9 - - - -
277C VAL* 4.4 3.5 - - - +
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Residues in contact with ALA 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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216C SER* 3.2 20.4 - - - +
217C TYR 3.9 0.7 - - - -
218C LEU* 4.0 12.1 - - + +
238C GLY* 1.3 74.8 - - - +
240C PRO* 1.3 57.1 - - - +
241C GLN 2.9 11.1 + - - -
242C HIS* 3.0 17.5 + - + -
247C LYS 2.7 35.5 + - - +
249C TYR* 4.3 19.3 - - + -
274C GLY 3.9 0.2 + - - -
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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