Contacts of the strand formed by residues 263 - 268 (chain J) in PDB entry 6O81
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 263 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J SER* 5.6 0.4 - - - +
128J LEU* 3.4 34.5 - - + +
130J MET* 5.1 0.4 - - - -
166J ARG* 3.3 28.2 - - - +
167J LEU* 3.4 39.0 + - + +
229J ILE* 5.0 1.8 - - - +
232J LEU* 3.4 43.7 - - + +
233J VAL* 3.7 12.6 - - + +
236J GLN* 4.3 8.4 - - + +
261J LEU* 3.8 14.4 - - + -
262J ASP* 1.3 76.8 - - - +
264J TYR* 1.3 66.0 + - - +
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Residues in contact with TYR 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J LEU* 4.0 28.3 - - + +
124J TYR* 3.2 47.3 - + + +
126J ALA* 3.7 17.3 - - + -
128J LEU 2.9 10.4 + - - +
129J ALA* 3.2 7.4 - - + -
130J MET* 2.9 26.0 + - - +
163J THR* 6.0 0.2 - - - -
165J LYS* 3.3 31.6 - - + -
166J ARG* 3.6 30.2 + - + +
167J LEU* 4.1 3.7 - - - +
262J ASP* 3.6 25.0 - - + +
263J ILE* 1.3 80.5 - - - +
265J SER* 1.3 62.3 + - - +
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Residues in contact with SER 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J VAL* 5.9 0.2 - - - -
120J LEU* 4.2 6.4 - - - +
130J MET* 3.0 19.3 - - - -
132J MET* 4.9 9.8 - - - +
158J ILE* 5.4 2.1 - - - +
160J VAL* 4.4 11.1 - - - +
164J GLY 3.7 4.9 - - - +
165J LYS* 2.7 32.2 + - - +
167J LEU* 3.7 21.9 - - - +
264J TYR* 1.3 76.4 - - - +
266J PHE* 1.3 60.8 + - - +
267J ILE* 4.0 16.3 - - - +
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Residues in contact with PHE 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J VAL* 5.4 3.8 - - + -
116J GLU* 3.1 46.4 - - + +
117J VAL* 5.2 2.7 - - + -
120J LEU* 4.0 16.5 - - + +
130J MET 2.9 9.8 + - - +
131J LEU* 3.4 13.7 - - + +
132J MET* 2.9 28.2 + - - +
164J GLY 5.1 4.3 - - - -
165J LYS* 6.1 2.5 - - + -
265J SER* 1.3 74.9 + - - +
267J ILE* 1.3 84.3 + - - +
268J LYS* 3.7 11.7 - - + -
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Residues in contact with ILE 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J MET* 3.5 13.5 - - + +
134J LYS* 3.8 20.9 - - - -
158J ILE* 5.8 1.8 - - + -
160J VAL* 5.6 6.5 - - + -
164J GLY 4.8 11.0 + - - +
196J HIS* 5.1 17.9 - - + +
199J LEU* 3.7 45.5 - - + -
265J SER* 4.0 15.9 - - - +
266J PHE* 1.3 93.9 - - - +
268J LYS* 1.3 65.2 + - - +
269J GLU* 4.0 1.7 + - - +
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Residues in contact with LYS 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J VAL* 4.0 25.4 - - + -
131J LEU* 3.9 16.8 - - + -
132J MET 2.9 15.5 + - - +
133J ARG* 4.0 17.9 - - + +
134J LYS* 4.0 18.5 + - - +
266J PHE* 3.7 14.2 + - + -
267J ILE* 1.3 78.8 - - - +
269J GLU* 1.3 61.0 + - - +
270J ALA 3.8 1.6 - - - +
271J ASN 5.1 1.7 - - - +
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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