Contacts of the strand formed by residues 234 - 239 (chain A) in PDB entry 3V4V
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ALA* 3.3 22.2 - - - +
225A GLY 2.9 16.1 + - - +
226A HIS* 3.4 2.6 - - - -
227A PHE* 2.8 47.8 + - + -
228A ARG* 3.1 36.3 + - - +
232A THR* 2.9 27.6 + - - +
233A THR* 1.3 82.0 - - - +
235A VAL* 1.3 64.7 + - - +
250A ILE* 4.2 4.7 - - + -
251A PHE 3.3 15.9 - - - +
253A ILE* 4.9 0.2 - - - -
261A LEU* 4.2 7.6 - - + -
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 5.7 1.8 - - + -
179A VAL* 3.7 24.5 - - + -
192A LEU* 3.7 23.8 - - + -
194A VAL* 3.8 17.9 - - + -
223A GLY 3.6 12.1 - - - +
224A ALA* 4.5 1.8 - - + -
233A THR* 5.5 2.0 - - + -
234A GLU* 1.3 76.1 - - - +
236A VAL* 1.3 72.5 + - - +
250A ILE* 3.3 6.2 - - - +
251A PHE* 2.8 42.1 + - + +
253A ILE* 3.7 26.5 - - + -
258A LEU* 4.8 5.2 - - + -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.7 10.9 - - - +
222A VAL* 3.2 7.1 - - - +
223A GLY* 3.0 37.9 + - - +
224A ALA 4.4 0.4 - - - +
227A PHE* 3.7 31.0 - - + -
235A VAL* 1.3 80.8 - - - +
237A GLY* 1.3 62.9 + - - +
248A ALA* 5.2 1.8 - - + -
249A TYR 3.3 11.2 - - - +
250A ILE* 4.5 2.5 - - + -
277A VAL* 3.6 33.9 - - + -
278A CYS 5.6 0.2 - - - +
279A ALA* 4.8 3.8 - - + +
290A LEU* 3.8 25.1 - - + -
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 4.0 12.3 - - - -
218A LEU* 3.9 16.5 - - - +
221A SER 3.4 8.7 - - - -
236A VAL* 1.3 75.9 - - - +
238A GLY* 1.3 60.5 + - - -
248A ALA* 3.3 4.9 - - - +
249A TYR* 2.9 34.0 + - - -
251A PHE* 4.0 2.7 - - - -
277A VAL* 4.4 5.2 - - - -
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Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A TYR 3.3 5.2 - - - +
218A LEU* 4.2 0.9 - - - +
219A GLY 3.0 22.2 + - - -
220A TYR 3.5 3.5 + - - -
221A SER* 3.2 16.6 + - - -
237A GLY* 1.3 73.9 - - - -
239A ALA* 1.3 59.7 + - - -
240A PRO* 3.4 8.2 - - - +
247A LYS 3.6 5.4 - - - -
274A GLY* 3.1 23.3 - - - -
277A VAL* 4.3 3.4 - - - -
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A SER* 3.1 24.7 - - - +
217A TYR 4.0 1.1 - - - -
218A LEU* 4.0 12.8 - - + -
238A GLY* 1.3 75.0 - - - +
240A PRO* 1.3 53.5 - - - +
241A GLN 2.8 17.0 + - - -
242A HIS* 2.9 16.1 + - + -
247A LYS 2.7 27.6 + - - +
249A TYR* 4.1 21.1 - - + -
274A GLY 4.0 0.4 + - - -
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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