Contacts of the strand formed by residues 162 - 167 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101T LEU* 3.8 19.1 - - + -
105T LEU* 3.7 26.7 - - + -
111T PHE* 3.3 15.7 - - + -
113T TYR* 4.2 11.9 - - + -
151T VAL* 3.7 26.2 - - + -
154T ILE* 3.9 13.2 - - + -
155T LEU* 4.0 14.4 - - + +
158T ALA* 3.7 18.4 - - + -
160T SER 3.7 5.2 - - - +
161T GLN* 1.3 79.0 - - - +
163T VAL* 1.3 65.2 + - - +
164T GLY 5.3 0.2 - - - +
230T SER* 3.0 11.4 + - - -
231T GLY* 2.9 23.4 + - - +
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Residues in contact with VAL 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T PHE 2.9 7.9 + - - -
112T LEU* 3.3 12.9 - - + -
113T TYR* 2.7 39.8 + - - +
161T GLN* 3.5 18.6 - - + +
162T ILE* 1.3 79.8 - - - +
164T GLY* 1.3 58.8 + - - +
165T PHE* 3.5 35.6 - - + -
224T PHE* 4.1 5.8 - - + -
229T VAL 3.0 28.5 - - - +
230T SER* 4.1 1.8 - - - -
231T GLY 3.2 9.6 - - - +
233T PHE* 4.0 12.1 - - + -
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Residues in contact with GLY 164 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T TYR* 3.4 34.0 + - - -
115T SER* 4.8 2.0 - - - -
162T ILE* 5.3 0.2 - - - +
163T VAL* 1.3 76.2 - - - +
165T PHE* 1.3 63.7 + - - -
166T ARG 3.7 0.2 + - - -
231T GLY 2.9 9.9 + - - +
232T ILE* 3.4 7.5 - - - +
233T PHE* 2.9 28.6 + - - +
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Residues in contact with PHE 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112T LEU* 4.2 12.8 - - + -
113T TYR 2.9 17.9 + - - +
114T ALA* 3.8 2.1 - - - -
115T SER* 2.8 24.7 + - - +
163T VAL* 3.5 25.8 - - + -
164T GLY* 1.3 72.4 - - - -
166T ARG* 1.3 61.1 + - - +
167T TYR* 3.1 34.7 + + + -
220T VAL* 3.6 19.3 - - + -
221T ASN* 3.3 37.2 - - - -
224T PHE* 3.4 46.2 - + + -
233T PHE* 3.5 11.0 - + + -
234T ASN 5.6 0.2 - - - -
235T LEU* 4.1 7.6 - - + -
283T LEU* 5.5 0.4 - - + -
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Residues in contact with ARG 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115T SER* 3.4 15.6 + - - +
116T SER 3.3 22.0 - - - +
117T ALA* 3.6 2.7 - - - +
119T THR* 3.2 17.5 + - - +
120T TYR* 3.1 45.4 + - + -
129T GLU* 3.8 7.6 - - - +
134T GLU* 2.8 38.2 + - - -
145T PHE* 5.6 0.2 - - - -
148T ASP* 2.8 29.7 + - - +
152T ARG* 3.9 1.8 - - - +
164T GLY 3.7 1.2 + - - -
165T PHE* 1.3 70.6 - - - +
167T TYR* 1.3 62.2 + - - +
168T PHE* 3.2 8.8 - - - -
232T ILE* 4.1 16.7 - - + +
233T PHE 2.7 19.0 + - - +
234T ASN* 3.7 8.3 - - - +
235T LEU 2.9 19.5 + - - -
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Residues in contact with TYR 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T ILE* 3.5 23.7 - - + +
75T GLU* 2.8 29.8 + - - -
114T ALA* 3.5 17.9 - - + +
115T SER 4.1 3.2 + - - -
117T ALA* 3.0 22.2 + - - +
165T PHE* 3.1 29.9 + - + -
166T ARG* 1.3 71.5 - - - +
168T PHE* 1.3 63.4 + - - +
170T VAL* 3.7 12.8 - - + -
217T VAL* 3.6 20.2 - - + -
221T ASN* 3.1 22.2 + - - -
235T LEU* 3.5 29.8 - - + -
400T NAP 3.6 32.8 - + + -
402T BMA 4.8 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