Contacts of the strand formed by residues 263 - 268 (chain A) in PDB entry 4M7P
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 TRP 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLY 5.6 0.9 - - - +
231A ALA* 5.2 0.6 - - - -
233A LYS* 3.2 35.6 - - + +
234A VAL 5.0 0.4 - - - -
235A VAL* 3.9 14.6 - - + -
257A PHE* 3.7 32.3 - + + +
260A LEU* 3.0 45.5 + - + +
261A PRO 3.5 14.8 + - - -
262A GLY* 1.3 82.5 + - - +
264A HIS* 1.3 64.2 + - - +
284A ASN* 2.8 24.7 + - - +
302A LEU* 4.0 14.6 - - + -
361A ALA* 3.9 17.7 - - + -
362A LEU* 3.9 22.7 - - + +
365A VAL* 3.6 39.7 - - + -
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Residues in contact with HIS 264 (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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225A TRP* 4.1 16.2 - + - -
228A PRO* 3.8 23.1 - - + +
230A GLY 5.3 2.9 - - - +
231A ALA* 4.0 21.3 - - + -
233A LYS 2.8 7.7 + - - +
234A VAL* 3.3 7.1 - - + +
235A VAL* 2.9 28.4 + - - +
263A TRP* 1.3 76.6 - - - +
265A LEU* 1.3 64.7 + - - +
266A VAL* 4.1 2.7 + - + +
283A ASP 4.8 3.3 + - - -
284A ASN* 3.6 26.8 - - + -
285A VAL 4.4 0.6 + - - -
286A GLU* 3.0 52.9 + - + +
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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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235A VAL* 3.5 22.7 - - + +
237A VAL* 3.6 27.1 - - + -
253A CYS 3.4 31.6 - - - +
254A VAL* 4.1 3.4 - - - -
257A PHE* 4.0 21.5 - - + +
264A HIS* 1.3 73.8 + - - +
266A VAL* 1.3 62.5 + - - +
267A LEU* 3.7 22.7 - - + -
284A ASN 2.9 15.9 + - - +
285A VAL* 3.4 19.5 - - + -
286A GLU* 2.9 28.4 + - - +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TRP* 3.8 42.4 - - + +
234A VAL* 4.8 3.1 - - + -
235A VAL 2.9 9.7 + - - +
236A LEU* 3.2 31.6 - - + -
237A VAL* 2.6 36.0 + - - +
264A HIS* 4.1 5.4 + - - +
265A LEU* 1.3 74.3 - - - +
267A LEU* 1.3 60.3 + - - +
286A GLU* 3.4 13.5 - - + +
288A HIS* 5.1 5.2 - - + -
291A VAL* 4.1 13.9 - - + -
296A ILE* 4.0 14.4 - - + -
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Residues in contact with LEU 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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237A VAL* 3.8 21.8 - - + -
250A TYR* 3.9 20.6 - - + +
253A CYS* 3.8 16.8 - - + -
254A VAL* 4.3 8.1 - - + -
265A LEU* 3.7 31.2 - - + -
266A VAL* 1.3 78.6 - - - +
268A GLN* 1.3 63.0 + - - +
269A ILE* 6.1 0.2 - - + -
278A LEU* 3.8 22.9 - - + -
285A VAL* 4.5 0.9 - - + -
286A GLU 2.9 7.3 + - - +
287A VAL* 3.3 35.0 - - + -
288A HIS* 3.0 27.0 + - - +
291A VAL* 4.6 0.3 - - - +
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Residues in contact with GLN 268 (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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237A VAL 3.3 17.8 + - - +
238A SER* 3.3 25.8 + - - +
239A LEU* 5.6 1.0 - - - -
250A TYR* 2.8 31.0 + - - -
267A LEU* 1.3 79.1 - - - +
269A ILE* 1.3 61.3 + - - +
271A ARG* 4.9 12.6 + - + +
288A HIS 3.3 6.5 - - - +
289A ASP 3.5 15.9 - - - +
290A TRP* 2.8 5.1 - - - -
291A VAL* 2.1 63.9 + - + +
293A GLN* 5.8 0.6 - - - +
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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