Contacts of the strand formed by residues 263 - 267 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LEU* 3.8 29.4 - - + -
203B SER 3.3 4.4 + - - +
204B LEU* 3.4 8.9 - - + +
205B VAL 3.0 24.6 + - - -
261B ALA* 3.1 5.6 - - - +
262B ASP* 1.3 83.6 - - - +
264B VAL* 1.3 63.9 + - - +
265B LEU 4.1 0.2 - - - -
289B LEU* 4.7 0.2 - - - -
297B LYS* 3.2 12.8 - - + +
299B MET* 3.8 18.2 - - + -
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 3.6 25.1 - - + -
207B VAL* 4.0 10.8 - - + -
258B ILE* 4.5 9.0 - - + -
259B PRO 4.8 3.4 - - - +
261B ALA* 5.1 3.8 - - + +
263B ALA* 1.3 74.3 - - - +
265B LEU* 1.3 57.3 + - - +
266B PHE* 3.7 26.5 - - + -
285B CYS* 4.2 14.1 - - + -
288B ALA* 6.0 3.1 - - + -
289B LEU* 3.8 24.2 - - + -
297B LYS 3.0 9.6 + - - +
298B LEU* 3.6 8.2 - - + +
299B MET* 2.7 34.9 + - - +
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 5.0 8.3 - - + -
198B PHE* 5.7 0.4 - - + -
204B LEU* 4.1 17.7 - - + -
205B VAL 2.8 17.2 + - - +
206B ASP* 3.8 12.9 - - - +
207B VAL* 3.0 32.1 + - - +
214B THR* 3.9 18.8 - - + -
218B ILE* 3.9 28.0 - - + -
263B ALA 4.1 0.2 - - - -
264B VAL* 1.3 73.8 - - - +
266B PHE* 1.3 63.6 + - - +
267B LYS* 4.2 8.2 + - + +
299B MET* 3.2 31.9 - - + +
301B ALA* 4.4 20.4 - - + -
363B LEU* 5.0 4.0 - - + -
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Residues in contact with PHE 266 (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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207B VAL* 3.6 29.4 - - + -
253B MET* 4.3 1.3 - - - -
258B ILE* 4.2 7.6 - - + -
264B VAL* 3.7 19.7 - - + -
265B LEU* 1.3 75.0 - - - +
267B LYS* 1.3 60.3 + - - +
268B TRP 3.7 0.7 + - - -
269B VAL* 3.9 18.5 + - + -
270B LEU* 3.6 36.8 - - + +
281B MET* 3.8 31.9 - - + -
282B LEU* 4.8 4.9 - - + -
285B CYS* 4.0 18.6 - - - -
298B LEU* 3.7 25.4 - - + -
299B MET 2.8 10.7 + - - +
300B ILE* 3.6 5.4 - - + +
301B ALA 2.9 25.9 + - - +
302B ASP* 4.9 0.7 - - - +
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 4.1 5.1 + - - +
182B ASP* 2.7 28.9 + - - -
183B SER* 2.9 32.1 + - - +
186B PHE* 4.2 21.5 - - + -
190B LEU* 5.9 0.4 - - + -
206B ASP* 5.0 5.9 + - - +
207B VAL 4.6 2.0 + - - -
208B GLY 5.5 1.0 - - - +
214B THR* 4.1 15.9 - - + +
265B LEU* 4.0 16.2 + - + +
266B PHE* 1.3 70.2 - - - +
268B TRP* 1.3 90.8 + - + +
269B VAL* 3.2 13.8 + - - +
301B ALA* 3.4 22.7 - - + +
361B ARG* 3.8 11.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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