Contacts of the strand formed by residues 235 - 239 (chain A) in PDB entry 2G5W
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 VAL 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ILE* 3.4 14.6 - - + -
185A ILE* 4.5 6.5 - - + -
223A VAL* 5.0 3.1 - - + -
226A VAL* 3.6 26.7 - - + -
227A VAL* 4.0 22.7 - - + -
230A ILE* 3.9 8.1 - - + -
231A GLY 3.4 19.1 - - - +
232A ALA 2.9 7.4 + - - +
233A SER 3.5 1.0 - - - -
234A LYS* 1.3 80.8 - - - +
236A GLY* 1.3 71.9 + - - +
237A VAL* 4.6 4.0 - - + -
275A LEU* 3.5 13.8 - - + +
276A ALA* 2.9 30.8 + - - +
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Residues in contact with GLY 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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104A PHE* 4.1 2.2 - - - -
183A ILE 2.8 11.7 + - - -
184A GLU* 3.3 5.2 - - - -
185A ILE* 2.8 23.3 + - - +
235A VAL* 1.3 78.6 - - - +
237A VAL* 1.3 68.0 + - - +
277A TYR* 3.5 32.1 - - - -
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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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184A GLU* 4.6 0.7 - - - -
185A ILE* 3.8 13.0 - - + +
219A LEU* 4.2 22.9 - - + -
223A VAL* 3.7 26.2 - - + -
235A VAL* 4.6 2.9 - - + -
236A GLY* 1.3 79.3 - - - +
238A ARG* 1.3 56.9 + - - +
239A VAL* 4.2 20.6 - - + -
264A LEU* 4.3 19.7 - - + -
275A LEU* 4.1 19.1 - - + -
277A TYR* 3.4 8.9 + - - +
278A LEU* 3.6 5.8 - - + +
279A HIS* 2.8 33.7 + - - +
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Residues in contact with ARG 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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30A ALA* 4.2 0.4 - - - +
31A PRO* 3.6 4.7 - - - +
106A GLN* 4.2 2.2 - - - +
184A GLU* 3.7 22.6 - - - +
185A ILE 2.8 16.7 + - - +
186A HIS* 4.7 0.4 - - - -
187A GLY* 2.8 34.4 + - - +
188A ALA* 4.5 8.3 - - + -
189A HIS* 3.3 9.7 - - - -
237A VAL* 1.3 73.0 - - - +
239A VAL* 1.3 63.3 - - - +
279A HIS* 3.2 44.8 + - + +
281A THR* 3.4 16.6 + - - +
320A SER* 3.0 19.6 + - - -
341A SER* 3.8 2.2 + - - -
401A FMN 2.7 82.6 + - - -
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Residues in contact with VAL 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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187A GLY* 3.8 14.4 - - - +
188A ALA* 3.8 3.6 - - - -
197A LEU* 4.5 8.3 - - + -
219A LEU* 4.2 9.4 - - + -
237A VAL* 4.1 13.2 + - + -
238A ARG* 1.3 79.2 - - - +
240A SER* 1.3 61.8 + - - +
241A PRO* 4.0 13.3 - - + +
257A GLY* 5.9 1.8 - - - +
260A VAL* 3.9 30.5 - - + -
261A VAL* 6.4 0.9 - - + -
278A LEU* 4.0 20.0 - - + -
279A HIS 2.9 9.1 + - - +
280A VAL* 3.5 13.3 - - + -
281A THR* 3.3 22.3 + - - -
309A LEU* 5.7 1.3 - - + -
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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