Contacts of the strand formed by residues 263 - 267 (chain A) in PDB entry 4EVI
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 ALA 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 3.8 27.1 - - + -
203A SER 3.3 6.1 + - - +
204A LEU* 3.3 9.4 - - + +
205A VAL 2.9 25.1 + - - -
261A ALA* 3.5 5.0 - - - +
262A ASP* 1.3 81.3 - - - +
264A VAL* 1.3 64.4 + - - +
265A LEU 4.0 0.2 - - - -
289A LEU* 4.6 0.2 - - - -
297A LYS* 3.2 13.7 - - + +
299A MET* 4.0 17.7 - - - -
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.7 16.2 - - + -
207A VAL* 3.9 17.7 - - + -
258A ILE* 5.0 5.2 - - + -
259A PRO 5.2 1.6 - - - +
261A ALA* 5.0 3.4 - - + +
263A ALA* 1.3 76.0 - - - +
265A LEU* 1.3 55.6 + - - +
266A PHE* 3.6 29.2 - - + -
285A CYS* 4.0 17.9 - - - -
288A ALA* 5.9 3.8 - - + -
289A LEU* 3.9 23.8 - - + -
297A LYS 3.1 8.3 + - - +
298A LEU* 3.6 8.0 - - + +
299A MET* 2.7 34.4 + - - +
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Residues in contact with LEU 265 (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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190A LEU* 5.3 6.1 - - + -
198A PHE* 5.9 1.1 - - + -
204A LEU* 4.0 18.2 - - + -
205A VAL 2.8 15.4 + - - +
206A ASP* 3.6 24.6 - - - +
207A VAL* 2.8 34.1 + - - +
214A THR* 4.0 11.9 - - + -
218A ILE* 3.9 28.0 - - + -
263A ALA 4.0 0.2 - - - -
264A VAL* 1.3 73.9 - - - +
266A PHE* 1.3 73.2 + - - +
267A LYS* 4.4 2.9 - - + +
299A MET* 3.2 31.9 - - + +
300A ILE 4.9 0.2 - - - -
301A ALA* 4.3 16.6 - - + -
363A LEU* 5.0 2.9 - - + -
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Residues in contact with PHE 266 (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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207A VAL* 3.6 33.2 - - + -
253A MET* 4.4 1.6 - - - -
258A ILE* 4.5 0.9 - - + -
264A VAL* 3.6 25.1 - - + -
265A LEU* 1.3 73.0 - - - +
267A LYS* 1.3 59.9 + - - +
268A TRP 3.9 0.9 + - - -
269A VAL* 3.8 19.5 + - + -
270A LEU* 3.8 35.2 - - + +
281A MET* 3.7 31.4 - - + -
282A LEU* 4.4 8.3 - - + -
285A CYS* 4.1 15.7 - - - -
298A LEU* 3.7 24.9 - - + -
299A MET 2.9 10.3 + - - +
300A ILE* 3.5 4.9 - - + +
301A ALA 2.9 25.6 + - - +
302A ASP* 5.0 0.9 - - - +
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Residues in contact with LYS 267 (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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182A ASP* 2.8 28.3 + - - +
183A SER* 3.2 14.1 + - - +
186A PHE* 3.5 33.2 - - + -
206A ASP* 4.8 4.6 + - - +
207A VAL 4.6 1.4 + - - -
214A THR* 3.5 25.1 - - + +
265A LEU* 4.0 10.3 + - + +
266A PHE* 1.3 72.1 - - - +
268A TRP* 1.3 81.3 + - + +
269A VAL* 3.1 5.5 + - - +
301A ALA* 3.3 25.6 - - + +
361A ARG* 3.8 5.4 - - - +
401A SAH 2.5 63.2 + - - +
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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