Contacts of the strand formed by residues 265 - 270 (chain C) in PDB entry 5E5R
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 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C PHE* 5.6 0.7 - - + -
197C ILE* 3.6 15.5 - - + +
198C GLY 4.6 1.1 - - - -
199C ALA* 3.9 16.2 - - + +
253C THR* 3.8 4.4 - - - +
254C GLY 2.9 30.9 + - - -
255C SER* 3.4 27.8 - - - +
256C LEU* 3.5 24.2 - - + +
262C SER 4.2 1.3 - - - +
263C GLU 3.8 0.2 - - - -
264C ILE* 1.3 81.0 - - + +
266C GLU* 1.3 70.9 + - - +
267C TRP* 3.4 35.8 + - + +
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Residues in contact with GLU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LEU* 4.0 20.6 - - + +
140C PRO* 4.8 9.2 - - + -
143C PHE* 6.3 0.7 - - + -
196C ILE* 3.7 31.8 - - + +
197C ILE 2.9 13.8 + - - +
198C GLY* 3.5 2.9 - - - -
199C ALA 3.0 22.3 + - - +
251C ARG* 2.6 37.6 + - - +
252C TYR 4.1 1.5 - - - +
253C THR* 2.6 30.0 + - - +
265C VAL* 1.3 73.3 - - - +
267C TRP* 1.3 62.0 + - - +
268C ILE* 4.9 0.2 - - - +
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Residues in contact with TRP 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C SER* 3.1 20.3 + - - -
163C HIS* 3.8 20.6 - + - -
175C GLN* 3.5 41.5 - - + -
177C PHE* 4.4 11.0 - + - -
199C ALA* 3.3 34.8 - - + -
200C MET 4.3 2.0 - - - -
201C ALA* 4.1 13.2 - - + -
250C TYR 4.5 0.4 - - - -
251C ARG* 2.6 30.3 + - - -
252C TYR* 3.1 41.6 + + + +
254C GLY* 3.9 13.2 - - - -
255C SER 3.1 28.7 + - - +
256C LEU* 5.2 0.2 - - - -
257C THR* 3.7 16.8 - - + -
265C VAL* 3.4 21.1 - - + +
266C GLU* 1.3 71.0 - - - +
268C ILE* 1.3 60.7 + - - +
269C VAL* 4.1 3.4 - - + -
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Residues in contact with ILE 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 3.8 25.4 - - + -
134C VAL* 5.8 0.2 - - + -
137C ALA* 4.8 1.3 - - + -
139C LEU* 3.9 29.2 - - + -
199C ALA 2.7 15.3 + - - +
200C MET* 3.3 20.3 - - + +
201C ALA* 2.6 34.7 + - - +
249C TYR* 3.7 29.6 - - + -
250C TYR 3.6 2.7 - - - -
251C ARG* 3.7 14.1 - - - -
266C GLU 4.9 0.7 - - - +
267C TRP* 1.3 76.7 - - - +
269C VAL* 1.3 57.3 + - - +
270C PHE* 3.9 21.1 + - + -
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Residues in contact with VAL 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 4.0 29.8 - - + -
163C HIS* 4.3 19.3 - - + +
165C ILE* 5.0 1.3 - - + -
201C ALA* 3.6 18.6 - - + +
203C PHE* 3.6 35.9 - - + -
249C TYR* 3.3 2.1 - - - -
250C TYR* 2.8 43.7 + - + +
252C TYR* 4.4 13.5 - - + -
267C TRP* 4.6 3.8 - - + -
268C ILE* 1.3 75.2 - - - +
270C PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 3.4 34.3 - - + -
200C MET* 4.1 23.3 - - + -
201C ALA 3.1 12.0 + - - +
202C ILE* 3.7 36.6 - - + -
203C PHE* 3.5 24.0 + - - +
242C LEU* 4.6 7.6 - - + -
243C PRO* 3.9 21.1 - - + -
245C SER 5.0 0.7 - - - -
246C LEU* 3.6 37.7 - - + -
248C SER 4.5 2.2 - - - +
249C TYR* 3.7 14.4 - - + -
268C ILE* 4.2 13.5 - - + -
269C VAL* 1.3 75.2 - - - +
271C ARG* 1.3 63.3 + - - +
272C ARG 4.5 2.8 - - - +
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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