Contacts of the strand formed by residues 263 - 267 (chain B) in PDB entry 4M83
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 HIS 263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B TRP* 4.9 4.7 - + - -
227B PRO* 4.7 22.8 - - + +
230B ALA* 4.4 15.0 - - + +
232B LYS 2.8 11.4 + - - +
233B VAL* 3.2 10.6 - - + +
234B VAL* 3.0 26.6 + - - +
256B PHE* 5.8 0.7 - - - -
261B GLY 4.6 0.2 - - - +
262B TRP* 1.3 76.5 - - - +
264B LEU* 1.3 76.5 + - - +
265B VAL* 4.0 7.3 - - + +
282B ASP 4.6 3.7 + - - -
283B ASN* 3.3 35.0 + - + +
284B VAL 4.3 0.4 + - - -
285B GLU* 2.9 37.9 + - + +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B VAL* 3.6 26.0 - - + +
236B VAL* 3.6 28.3 - - + -
252B CYS 3.6 22.2 - - - +
253B VAL* 4.1 5.4 - - - -
256B PHE* 4.0 15.5 - - + -
263B HIS* 1.3 81.3 - - - +
265B VAL* 1.3 74.2 - - - +
266B LEU* 3.8 17.7 - - + -
283B ASN* 2.8 7.5 + - - +
284B VAL* 3.6 36.4 - - + -
285B GLU 3.2 24.3 + - - -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TRP* 3.6 33.0 - - + -
233B VAL* 4.4 6.5 - - + -
234B VAL 2.8 15.8 + - - +
235B LEU* 3.5 22.3 - - + +
236B VAL 2.9 27.5 + - - -
263B HIS* 4.0 4.7 - - - +
264B LEU* 1.3 81.2 - - - +
266B LEU* 1.3 62.7 + - - +
285B GLU* 3.5 11.2 - - + +
287B HIS* 3.8 26.9 - - + +
290B VAL* 5.1 2.0 - - + -
295B ILE* 4.0 14.4 - - + -
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 3.7 30.1 - - + -
249B TYR* 4.3 10.3 - - + +
252B CYS* 3.8 20.9 - - + -
253B VAL* 3.4 32.5 - - + -
264B LEU* 3.8 14.8 - - + -
265B VAL* 1.3 74.1 - - - +
267B GLN* 1.3 59.2 + - - +
268B ILE* 3.8 7.4 - - + -
277B LEU* 3.8 9.0 - - + -
284B VAL* 4.2 4.3 - - + -
285B GLU 2.9 8.7 + - - -
286B VAL* 3.5 31.1 - - + +
287B HIS* 2.9 33.4 + - - +
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Residues in contact with GLN 267 (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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235B LEU* 4.7 2.5 - - + -
236B VAL* 2.9 23.7 + - - +
237B SER* 2.9 25.0 + - - +
238B LEU* 3.9 2.4 - - - +
239B GLY 2.4 33.5 + - - +
240B SER* 5.7 0.2 - - - -
243B THR* 5.3 1.6 + - - -
249B TYR* 3.7 13.1 + - - -
266B LEU* 1.3 73.2 - - - +
268B ILE* 1.3 59.4 + - - +
269B GLY* 2.8 21.8 + - - -
287B HIS 3.7 3.1 - - - -
288B ASP 3.0 8.3 - - - +
290B VAL* 3.5 20.4 - - + -
502B UDP 2.9 29.3 - - + +
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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