Contacts of the strand formed by residues 234 - 239 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B MET* 4.1 4.1 - - - +
179B PRO* 2.8 37.6 + - - +
190B VAL* 6.0 0.7 - - + -
191B VAL* 3.5 11.5 + - - +
192B LYS* 3.4 27.4 - - + +
213B HIS* 3.2 18.3 + - - +
214B LEU* 2.9 31.7 + - - +
215B ILE* 4.1 3.8 + - - +
226B VAL 3.1 5.2 - - - -
227B ASP* 3.2 21.5 - - - +
232B GLY 3.4 2.4 + - - +
233B ARG* 1.3 73.3 - - - +
235B SER* 1.3 61.3 + - - +
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 2.1 41.2 + - - -
177B ALA 3.0 17.3 - - - -
178B MET* 3.9 15.9 - - - -
179B PRO* 4.7 0.2 - - - -
213B HIS* 3.9 1.2 - - - -
215B ILE* 6.2 0.7 - - - -
225B TYR 3.8 0.3 - - - -
226B VAL* 2.9 34.2 + - - +
233B ARG 4.2 0.7 + - - -
234B GLN* 1.3 78.0 - - - +
236B VAL* 1.3 71.8 + - - +
237B VAL 4.2 0.2 - - - -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE 3.6 1.6 - - - +
176B ARG* 3.4 0.7 - - - -
177B ALA* 2.8 42.0 + - + +
213B HIS* 4.3 4.3 - - - +
215B ILE* 3.0 37.0 - - + +
217B VAL* 3.7 27.4 - - + -
223B SER* 4.6 3.1 - - - -
224B GLN 3.9 7.6 - - - +
225B TYR* 3.3 35.9 - - + -
235B SER* 1.3 78.3 - - - +
237B VAL* 1.3 71.3 + - - +
238B VAL* 5.6 0.2 - - - +
254B TYR* 4.6 3.3 + - - -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ALA* 4.5 11.7 - - + -
175B ILE 3.1 8.5 - - - +
176B ARG* 3.1 45.1 - - + +
223B SER* 3.6 0.5 - - - -
224B GLN* 2.7 67.4 + - + +
226B VAL* 4.1 12.8 - - + -
235B SER* 4.5 0.2 - - - +
236B VAL* 1.3 79.7 - - - +
238B VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ALA* 3.0 5.3 - - - +
175B ILE* 2.8 41.6 + - + +
217B VAL* 3.9 37.5 - - + -
220B ASN* 3.1 33.2 - - + +
223B SER* 4.3 4.9 - - - -
224B GLN* 4.3 0.4 - - - -
237B VAL* 1.3 81.0 - - - +
239B PRO* 1.4 86.3 - - + +
241B GLU* 6.2 0.9 - - + -
252B ILE* 5.0 14.4 - - + -
254B TYR* 5.8 1.8 - - - +
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Residues in contact with PRO 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY* 5.4 4.9 - - - +
173B THR 3.7 7.4 - - - +
174B ALA* 4.1 4.9 - - + -
175B ILE* 5.0 0.9 - - - +
220B ASN* 4.7 0.6 + - - +
222B LEU* 3.2 45.3 - - + +
224B GLN* 3.5 19.3 - - - +
238B VAL* 1.4 105.7 - - + +
240B TYR* 1.3 68.6 + - - +
241B GLU* 3.3 6.4 + - - +
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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
------------------------------------------------------------
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