Contacts of the strand formed by residues 277 - 281 (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 TYR 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.7 14.4 - - - -
59B PHE* 3.7 23.8 - + - -
61B ILE* 3.5 11.6 - - - +
104B PHE* 4.0 15.0 - + - -
184B GLU* 2.6 42.8 + - - +
235B VAL 3.9 0.8 + - - -
236B GLY* 3.5 15.4 - - - -
237B VAL* 3.2 25.5 + - - +
275B LEU* 3.2 7.6 - - - +
276B ALA* 1.3 86.2 - - + +
278B LEU* 1.3 61.7 + - - +
279B HIS* 3.4 25.4 - - + -
313B TYR* 3.9 10.5 - - - -
316B THR* 3.3 26.0 - - + +
318B MET* 3.7 21.5 - - + -
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Residues in contact with LEU 278 (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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237B VAL* 3.6 18.6 - - + +
239B VAL* 4.2 22.9 - - + -
260B VAL* 4.9 3.4 - - + -
261B VAL* 3.8 29.8 - - + -
264B LEU* 3.9 22.4 - - + -
277B TYR* 1.3 73.6 - - - +
279B HIS* 1.3 61.6 + - - +
280B VAL* 4.0 9.8 + - + -
309B LEU* 5.5 0.7 - - + -
313B TYR* 3.8 38.0 - - + -
316B THR 2.8 8.3 + - - +
317B PHE* 3.5 17.8 - - + -
318B MET* 2.8 27.0 + - - +
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Residues in contact with HIS 279 (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* 4.1 2.9 - - + -
61B ILE* 3.6 12.8 - - + -
184B GLU* 2.8 20.3 + - - +
237B VAL 2.7 12.6 + - - +
238B ARG* 3.0 35.9 + - - +
239B VAL 2.9 26.3 + - - -
277B TYR* 3.4 19.1 - - + -
278B LEU* 1.3 72.7 - - - +
280B VAL* 1.3 60.8 + - - +
318B MET* 3.2 44.4 - - + -
320B SER* 3.7 7.8 - - - -
341B SER* 3.0 26.2 + - - -
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Residues in contact with VAL 280 (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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239B VAL* 3.4 19.1 - - + +
241B PRO* 4.0 17.5 - - + -
278B LEU* 4.0 14.8 - - + -
279B HIS* 1.3 77.0 - - - +
281B THR* 1.3 68.2 + - - +
306B MET* 3.6 26.4 - - - +
309B LEU* 4.3 12.8 - - + -
317B PHE* 3.6 35.9 - - + -
318B MET 3.0 9.0 + - - +
319B SER 3.8 0.2 - - - -
320B SER* 3.1 24.3 + - - -
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Residues in contact with THR 281 (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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189B HIS* 3.4 12.6 + - - +
238B ARG* 3.2 29.7 + - - +
239B VAL 3.2 7.3 + - - -
240B SER* 3.9 14.8 - - - -
241B PRO* 5.0 0.5 - - - +
242B ALA* 5.4 1.0 + - - +
243B ILE* 3.5 29.8 + - + +
280B VAL* 1.3 78.1 - - - +
282B GLN* 1.3 63.0 + - - +
283B PRO* 4.4 1.0 - - - +
306B MET* 5.0 0.2 - - - +
320B SER* 3.3 17.7 - - - +
321B GLY* 4.0 7.2 - - - -
403B FMN 3.2 23.8 - - - +
404B 8PG 5.4 3.4 - - + -
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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