Contacts of the strand formed by residues 263 - 267 (chain A) in PDB entry 2JG7
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 ARG 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A VAL* 3.6 39.5 + - - +
239A ASP* 3.4 35.2 + - - +
240A LEU* 3.4 13.8 - - + -
241A LEU 3.0 22.5 + - - -
257A VAL* 3.7 5.3 - - - +
260A ARG* 5.3 0.9 + - - -
261A PHE 5.7 0.2 - - - +
262A GLY* 1.3 74.7 - - - -
264A LYS* 1.3 61.3 + - - +
486A GLN 4.7 7.9 - - - +
488A MET 4.7 4.1 + - - -
489A ARG* 3.8 24.0 - - - +
470B GLU* 2.9 34.2 + - - +
471B LYS* 5.1 6.5 - - - +
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.8 5.6 - - - +
241A LEU* 3.4 8.5 - - + +
253A VAL* 6.4 0.4 - - + -
254A ALA* 4.0 26.5 - - - +
257A VAL* 3.9 13.9 - - + -
258A GLN* 3.0 30.5 + - - +
262A GLY 4.0 15.6 + - - -
263A ARG* 1.3 76.6 - - - +
265A LEU* 1.3 60.8 + - - +
266A LEU* 4.1 24.9 - - + -
486A GLN* 5.5 1.6 - - - +
258B GLN* 3.0 29.8 - - - +
264B LYS* 4.8 3.5 - - - +
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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
----------------------------------------------------------
175A ASN* 4.6 1.6 - - - +
240A LEU* 4.2 9.6 - - + -
241A LEU 2.9 8.7 + - - +
242A SER* 3.4 19.7 - - - +
243A PHE* 2.8 30.1 + - - +
264A LYS* 1.3 73.6 - - - +
266A LEU* 1.3 62.3 + - - +
267A GLU* 3.7 26.5 - - + -
476A GLY* 4.0 8.3 - - - -
477A ARG 3.4 23.8 - - - +
478A GLU* 4.0 4.9 - - + -
486A GLN* 3.7 30.1 - - + +
487A TYR* 3.6 29.8 - - + +
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Residues in contact with LEU 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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241A LEU 5.3 0.4 - - - +
243A PHE* 3.7 18.2 - - + -
250A GLY 4.4 12.3 - - - +
253A VAL* 5.0 2.9 - - + -
254A ALA* 3.7 28.5 - - + +
264A LYS* 4.1 26.2 - - + -
265A LEU* 1.3 80.7 - - - +
267A GLU* 1.3 63.2 + - - +
268A LEU* 4.1 11.2 - - + -
469A GLY 5.6 0.7 + - - -
473A THR 3.3 8.7 - - - +
474A GLY* 3.5 26.4 + - - +
475A GLY 3.9 0.2 + - - -
476A GLY* 3.0 28.2 + - - +
258B GLN* 4.2 9.4 - - - +
261B PHE* 4.2 14.8 - - + -
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Residues in contact with GLU 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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243A PHE 2.9 9.0 + - - +
244A THR* 3.3 15.4 - - - +
245A GLY 3.2 22.5 + - - -
265A LEU* 3.7 11.2 - - + -
266A LEU* 1.3 73.6 - - - +
268A LEU* 1.3 58.6 + - - +
467A PHE* 2.7 26.8 - - - +
468A GLY* 3.4 16.5 - - - -
469A GLY 4.4 1.4 + - - -
473A THR 3.8 0.9 - - - -
476A GLY 3.3 17.6 - - - +
478A GLU* 3.4 37.0 - - - +
1510A NAD 3.1 35.7 + - - +
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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
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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