Contacts of the strand formed by residues 162 - 167 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C LEU* 3.8 18.4 - - + -
105C LEU* 3.7 27.1 - - + -
111C PHE* 3.3 15.7 - - + -
113C TYR* 4.2 11.7 - - + -
151C VAL* 3.7 27.3 - - + +
154C ILE* 3.9 13.7 - - + -
155C LEU* 4.0 14.4 - - + +
158C ALA* 3.7 18.8 - - + -
160C SER 3.7 4.9 - - - +
161C GLN* 1.3 79.6 - - - +
163C VAL* 1.3 64.2 + - - +
230C SER* 3.0 11.0 + - - -
231C GLY 2.9 23.9 + - - +
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Residues in contact with VAL 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C PHE 2.9 7.1 + - - -
112C LEU* 3.3 13.5 - - + +
113C TYR* 2.7 40.2 + - - +
161C GLN* 3.5 18.2 - - + +
162C ILE* 1.3 79.8 - - - +
164C GLY* 1.3 58.7 + - - +
165C PHE* 3.5 34.7 - - + -
224C PHE* 4.1 5.6 - - + -
229C VAL 3.0 28.5 - - - +
230C SER* 4.1 2.0 - - - -
231C GLY 3.2 9.6 - - - +
233C PHE* 4.0 11.9 - - + -
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Residues in contact with GLY 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TYR* 3.4 33.3 + - - -
115C SER* 4.8 1.8 - - - -
162C ILE* 5.3 0.2 - - - +
163C VAL* 1.3 76.6 - - - +
165C PHE* 1.3 63.7 + - - -
166C ARG 3.7 0.5 + - - -
231C GLY 2.9 9.9 + - - +
232C ILE* 3.4 7.5 - - - +
233C PHE* 2.9 28.4 + - - +
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Residues in contact with PHE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU* 4.2 13.2 - - + -
113C TYR 2.9 18.5 + - - +
114C ALA* 3.8 2.3 - - - -
115C SER* 2.8 24.5 + - - +
163C VAL* 3.5 24.9 - - + -
164C GLY* 1.3 72.2 - - - -
166C ARG* 1.3 61.1 + - - +
167C TYR* 3.1 35.7 + + + -
220C VAL* 3.6 18.4 - - + -
221C ASN* 3.3 36.6 - - - -
224C PHE* 3.5 47.1 - + + -
233C PHE* 3.5 11.2 - + + +
235C LEU* 4.1 8.1 - - + -
283C LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C SER* 3.3 15.8 + - - +
116C SER 3.3 22.2 - - - +
117C ALA* 3.6 3.4 - - - +
119C THR* 3.2 17.1 + - - +
120C TYR* 3.1 45.6 + - + -
129C GLU* 3.8 7.4 - - - +
134C GLU* 2.8 37.8 + - - -
145C PHE* 5.6 0.4 - - - -
148C ASP* 2.8 29.7 + - - +
152C ARG* 4.0 2.6 - - - +
164C GLY 3.7 1.6 + - - -
165C PHE* 1.3 69.6 - - - +
167C TYR* 1.3 62.5 + - - +
168C PHE* 3.2 8.8 - - - -
232C ILE* 4.1 17.0 - - + +
233C PHE 2.7 18.7 + - - +
234C ASN* 3.7 7.4 - - - +
235C LEU* 2.9 19.2 + - - -
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Residues in contact with TYR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.5 15.8 - - + +
75C GLU* 2.7 31.0 + - - -
114C ALA* 3.5 17.0 - - + +
115C SER 4.1 3.0 + - - -
117C ALA* 3.0 22.3 + - - +
165C PHE* 3.1 30.8 + - + -
166C ARG* 1.3 72.0 - - - +
168C PHE* 1.3 63.1 + - - +
170C VAL* 3.7 8.3 - - + -
217C VAL* 3.6 20.4 - - + -
221C ASN* 3.1 21.0 + - - -
235C LEU* 3.5 30.1 - - + -
400C NAP 3.3 45.9 - + + -
402C BMA 4.9 0.5 + - - -
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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