Contacts of the strand formed by residues 162 - 167 (chain J) in PDB entry 2X86
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 162 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101J LEU* 3.8 18.8 - - + -
105J LEU* 3.7 26.5 - - + -
111J PHE* 3.3 15.9 - - + -
113J TYR* 4.2 12.1 - - + -
151J VAL* 3.7 26.5 - - + -
154J ILE* 3.9 13.9 - - + -
155J LEU* 4.0 13.9 - - + +
158J ALA* 3.7 18.4 - - + -
160J SER 3.7 5.2 - - - +
161J GLN* 1.3 78.8 - - - +
163J VAL* 1.3 63.0 + - - +
230J SER* 3.0 10.9 + - - -
231J GLY* 2.9 24.5 + - - +
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Residues in contact with VAL 163 (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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111J PHE 2.9 7.3 + - - -
112J LEU* 3.3 13.1 - - + -
113J TYR* 2.7 40.0 + - - +
161J GLN* 3.5 18.8 - - + +
162J ILE* 1.3 79.4 - - - +
164J GLY* 1.3 59.3 + - - +
165J PHE* 3.5 34.5 - - + -
224J PHE* 4.1 6.1 - - + -
229J VAL 3.0 28.3 - - - +
230J SER* 4.1 1.8 - - - -
231J GLY 3.2 9.4 - - - +
233J PHE* 4.0 11.7 - - + -
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Residues in contact with GLY 164 (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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113J TYR* 3.4 33.3 + - - -
115J SER* 4.8 1.6 - - - -
151J VAL* 6.0 0.2 - - - +
163J VAL* 1.3 76.9 - - - +
165J PHE* 1.3 63.4 + - - -
166J ARG 3.7 0.2 + - - -
231J GLY 2.9 10.3 + - - +
232J ILE* 3.4 7.6 - - - +
233J PHE 2.9 28.6 + - - +
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Residues in contact with PHE 165 (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 LEU* 4.2 12.3 - - + -
113J TYR 2.9 17.2 + - - +
114J ALA* 3.8 2.1 - - - -
115J SER* 2.8 24.2 + - - +
163J VAL* 3.5 26.0 - - + -
164J GLY* 1.3 73.3 - - - -
166J ARG* 1.3 61.3 + - - +
167J TYR* 3.1 35.7 + + + -
220J VAL* 3.6 19.3 - - + -
221J ASN* 3.3 37.9 - - - -
224J PHE* 3.5 46.4 - + + -
233J PHE* 3.5 12.3 - + + -
235J LEU* 4.1 8.1 - - + -
283J LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 166 (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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115J SER* 3.3 14.7 + - - +
116J SER 3.3 21.5 - - - +
117J ALA* 3.6 3.4 - - - +
119J THR* 3.2 17.1 + - - +
120J TYR* 3.1 46.1 + - + -
129J GLU* 3.8 8.4 - - - +
134J GLU* 2.8 36.8 + - - -
145J PHE* 5.6 0.4 - - - -
148J ASP* 2.8 29.5 + - - +
152J ARG* 3.9 2.4 - - - +
164J GLY 3.7 1.2 + - - -
165J PHE* 1.3 70.4 - - - +
167J TYR* 1.3 62.5 + - - +
168J PHE* 3.2 8.7 - - - -
232J ILE* 4.1 17.4 - - + +
233J PHE 2.7 19.4 + - - +
234J ASN* 3.7 8.1 - - - +
235J LEU* 2.9 19.6 + - - -
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Residues in contact with TYR 167 (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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11J ILE* 3.5 24.4 - - + +
75J GLU* 2.8 30.7 + - - -
114J ALA* 3.5 18.1 - - + +
115J SER 4.1 3.2 + - - -
116J SER* 4.2 0.2 + - - -
117J ALA* 3.0 22.2 + - - +
165J PHE* 3.1 31.1 + - + -
166J ARG* 1.3 71.6 - - - +
168J PHE* 1.3 62.7 + - - +
170J VAL* 3.7 11.7 - - + -
217J VAL* 3.6 20.9 - - + -
221J ASN* 3.1 21.4 + - - -
235J LEU* 3.5 29.4 - - + -
400J NAP 3.5 32.4 - + + -
402J BMA 4.6 0.3 + - - -
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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