Contacts of the strand formed by residues 234 - 239 (chain A) in PDB entry 4G83
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 GLN 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A MET* 4.0 5.5 - - - +
179A PRO* 3.1 46.2 + - + +
190A VAL* 3.5 15.2 - - + +
191A VAL* 2.2 34.7 + - - +
192A LYS* 4.6 8.6 - - + +
212A SER 5.2 2.0 - - - +
213A HIS* 3.6 43.7 - - + +
214A LEU* 4.7 4.9 - - - +
215A ILE 5.9 0.7 - - - +
226A VAL 3.2 4.9 - - - -
227A ASP* 4.5 3.6 - - - +
232A GLY 4.6 2.9 - - - +
233A ARG* 1.3 75.0 - - - +
235A SER* 1.3 64.1 + - - +
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Residues in contact with SER 235 (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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176A ARG* 2.5 44.9 + - - -
177A ALA 3.1 16.2 - - - -
178A MET* 3.6 12.8 - - - -
179A PRO* 5.0 0.9 - - - -
213A HIS* 4.1 6.3 - - - -
215A ILE* 5.9 1.8 - - - -
225A TYR* 3.7 2.1 - - - -
226A VAL* 2.9 32.5 + - - +
228A ASP* 5.3 0.7 + - - -
233A ARG 5.2 1.1 + - - -
234A GLN* 1.3 76.4 - - - +
236A VAL* 1.3 61.6 + - - +
237A VAL 4.2 0.2 - - - -
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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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175A ILE 3.5 1.9 - - - +
176A ARG* 3.3 1.0 - - - -
177A ALA* 2.9 36.8 + - + +
215A ILE* 3.9 24.0 - - + +
216A ARG 4.9 1.1 - - - -
217A VAL* 4.6 7.2 - - + -
223A SER* 4.4 7.6 - - - -
224A GLN 3.7 8.1 - - - +
225A TYR* 3.7 40.2 - - + +
235A SER* 1.3 76.3 - - - +
237A VAL* 1.3 68.9 + - - +
238A VAL* 4.3 0.4 + - + -
254A TYR* 3.8 30.2 + - + -
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Residues in contact with VAL 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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174A ALA* 4.8 11.4 - - + -
175A ILE 3.2 9.4 - - - +
176A ARG* 3.3 43.3 - - + +
222A LEU 4.3 0.5 - - - +
223A SER* 3.5 4.9 - - - -
224A GLN* 3.0 50.3 + - + +
226A VAL* 3.8 14.6 - - + -
235A SER* 4.3 0.7 - - - +
236A VAL* 1.3 79.4 - - - +
238A VAL* 1.3 62.4 + - - +
239A PRO* 5.8 0.7 - - + -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 3.2 4.9 - - - -
175A ILE* 2.8 43.7 + - + +
217A VAL* 5.6 5.8 - - + -
220A ASN* 3.1 39.5 - - + +
223A SER* 4.9 5.2 - - - +
236A VAL* 6.3 0.2 - - + -
237A VAL* 1.3 76.1 - - - +
239A PRO* 1.3 87.7 - - + +
252A ILE* 3.9 33.2 - - + -
254A TYR* 5.1 2.7 - - - +
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Residues in contact with PRO 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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172A GLY 6.0 1.1 - - - +
173A THR 3.6 8.5 - - - +
174A ALA* 4.1 4.7 - - + -
220A ASN* 5.2 0.2 - - - +
222A LEU* 3.8 39.0 - - + +
224A GLN* 5.9 0.9 - - + -
237A VAL* 4.7 1.8 - - + +
238A VAL* 1.3 109.7 - - + +
240A TYR* 1.3 68.5 + - - +
241A GLU* 3.4 5.4 + - - +
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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