Contacts of the strand formed by residues 235 - 239 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ILE* 3.5 15.0 - - + -
185B ILE* 4.5 7.2 - - + -
223B VAL* 5.2 2.7 - - + -
226B VAL* 3.7 26.0 - - + -
227B VAL* 4.0 15.9 - - + -
230B ILE* 3.9 8.3 - - + -
231B GLY 3.3 19.7 - - - +
232B ALA 2.7 8.9 + - - +
233B SER 3.4 0.6 - - - -
234B LYS* 1.3 80.9 - - - +
236B GLY* 1.3 69.7 + - - +
237B VAL* 4.5 4.5 - - + -
275B LEU* 3.5 20.9 - - + +
276B ALA* 2.8 31.3 + - - -
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Residues in contact with GLY 236 (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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104B PHE* 4.0 1.8 - - - -
183B ILE 2.8 12.7 + - - +
184B GLU* 3.3 7.0 - - - -
185B ILE 2.9 23.6 + - - -
235B VAL* 1.3 75.6 - - - +
237B VAL* 1.3 67.9 + - - +
277B TYR* 3.5 33.0 - - - -
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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
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184B GLU* 4.6 0.7 - - - -
185B ILE* 4.0 11.4 - - + +
187B GLY 6.0 0.2 - - - +
219B LEU* 4.4 15.7 - - + -
223B VAL* 3.9 23.3 - - + -
235B VAL* 4.5 6.1 - - + -
236B GLY* 1.3 79.1 - - - +
238B ARG* 1.3 57.1 + - - +
239B VAL* 4.3 20.0 - - + -
264B LEU* 4.1 24.0 - - + -
275B LEU* 4.1 18.6 - - + -
277B TYR* 3.2 11.8 + - - +
278B LEU* 3.6 6.1 - - + +
279B HIS* 2.7 34.9 + - - +
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Residues in contact with ARG 238 (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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31B PRO* 3.5 4.4 - - - +
106B GLN* 3.9 2.9 - - - +
184B GLU* 3.3 32.0 - - - +
185B ILE 3.1 12.0 + - - +
186B HIS* 4.8 0.4 - - - -
187B GLY* 3.0 34.3 + - - +
188B ALA* 3.7 6.0 + - + -
189B HIS* 3.4 8.3 - - - -
237B VAL* 1.3 72.4 - - - +
239B VAL* 1.3 65.2 + - - +
279B HIS* 3.0 35.7 + - + +
281B THR* 3.2 22.1 + - - +
320B SER* 3.0 24.5 + - - -
341B SER* 4.0 1.4 + - - -
403B FMN 2.7 81.5 + - - -
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Residues in contact with VAL 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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187B GLY* 3.5 16.4 - - - +
188B ALA* 3.7 4.0 - - - -
197B LEU* 4.3 15.0 - - + -
219B LEU* 4.5 4.5 - - + -
237B VAL* 4.3 11.7 - - + -
238B ARG* 1.3 79.9 - - - +
240B SER* 1.3 60.9 + - - +
241B PRO* 4.0 14.4 - - + -
257B GLY* 6.0 1.8 - - - -
260B VAL* 4.3 27.6 - - + -
278B LEU* 4.2 19.1 - - + -
279B HIS 2.9 6.5 + - - -
280B VAL* 3.4 15.1 - - + +
281B THR* 3.2 22.9 + - - -
309B LEU* 5.8 1.8 - - + -
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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