Contacts of the strand formed by residues 262 - 265 (chain B) in PDB entry 4AUQ
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 ILE 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B VAL 3.9 0.4 - - - -
261B SER* 1.3 84.2 - - - +
263B VAL* 1.3 69.3 + - - +
264B PHE* 4.0 9.8 + - + -
269B HIS 4.0 0.2 - - - +
270B LEU* 3.1 6.4 - - - -
271B VAL* 2.8 42.4 + - + +
273B ALA* 3.8 30.7 - - + -
276B ALA* 4.1 11.2 - - + -
292B ARG* 3.7 33.9 - - + -
293B VAL 3.5 3.4 - - - +
294B ARG* 4.2 22.9 - - + +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B SER 4.1 1.0 + - - -
262B ILE* 1.3 74.2 - - - +
264B PHE* 1.3 78.3 + - - +
265B VAL* 3.8 3.1 + - + +
268B GLY* 3.7 16.6 - - - +
269B HIS 3.6 9.2 - - - +
270B LEU* 4.0 13.9 - - + -
291B SER 3.8 0.3 - - - +
292B ARG* 3.5 4.9 - - - -
293B VAL* 2.9 56.8 + - + +
295B THR* 3.9 13.6 - - + +
263E VAL* 4.3 13.5 - - + -
265E VAL* 6.0 1.1 - - + -
293E VAL* 4.6 6.3 - - + -
295E THR* 3.8 16.6 - - + -
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Residues in contact with PHE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 4.2 10.5 - - + -
263B VAL* 1.3 77.8 - - - +
265B VAL* 1.3 61.8 + - - +
267B CYS* 4.0 13.7 - - - -
268B GLY* 2.7 30.2 + - - -
269B HIS 2.9 19.2 + - - +
271B VAL* 3.7 36.1 - - + -
276B ALA* 4.4 1.6 - - + -
279B LEU* 4.2 18.8 - - + -
282B CYS* 4.1 16.8 - - + -
283B PRO* 4.0 15.5 - - + -
289B VAL* 3.6 36.8 - - + -
291B SER 3.7 0.7 - - - -
292B ARG* 3.7 33.9 - - + -
293E VAL* 4.5 0.2 - - - +
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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
----------------------------------------------------------
263B VAL* 4.2 4.3 - - + +
264B PHE* 1.3 76.8 - - - +
266B PRO* 1.3 72.6 - - + +
267B CYS 3.6 0.7 - - - -
288B PRO 4.9 1.1 - - - -
289B VAL* 3.9 1.4 - - - -
290B ARG* 2.9 48.6 + - + +
291B SER* 3.0 36.5 + - - +
293B VAL* 3.8 22.2 - - + -
265E VAL* 5.0 4.0 - - + -
291E SER* 6.1 1.1 - - - +
293E VAL* 4.1 23.6 - - + -
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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
------------------------------------------------------------
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