Contacts of the strand formed by residues 164 - 168 (chain C) in PDB entry 2I6A
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 VAL 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C ILE 3.2 1.4 + - - -
9C LEU* 3.5 14.3 - - + +
10C PHE 2.9 24.1 + - - -
162C ALA* 3.5 3.5 - - - +
163C ARG* 1.3 88.3 - - + +
165C CYS* 1.3 68.6 + - - +
192C ILE* 3.4 17.7 - - + +
194C THR* 4.4 3.4 - - + -
307C LEU* 4.0 23.8 - - + +
310C LEU* 3.1 38.8 - - + +
311C VAL* 4.0 24.5 - - + -
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Residues in contact with CYS 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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10C PHE* 3.1 18.2 - - + +
159C VAL* 4.9 6.5 - - - -
162C ALA* 4.2 13.2 - - - -
164C VAL* 1.3 80.4 - - - +
166C TYR* 1.3 61.2 + - - +
167C ILE* 5.7 0.4 - - + -
182C VAL* 3.7 24.9 - - + -
185C HIS* 5.9 4.5 - - - -
186C ALA* 5.2 7.6 - - - -
191C ARG* 5.7 5.2 - - - -
192C ILE 2.9 10.4 + - - +
193C PHE* 3.8 22.0 - - + -
194C THR* 2.8 32.8 + - - +
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Residues in contact with TYR 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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9C LEU* 4.6 4.2 - - + +
10C PHE 2.7 11.9 + - - +
11C GLY* 2.9 27.8 - - - -
12C MET 3.5 1.2 + - - -
65C SER* 4.6 3.8 + - - -
66C THR* 3.8 26.0 - - + +
69C SER* 3.8 17.6 + - - -
70C ILE* 5.0 3.6 - - + -
165C CYS* 1.3 72.3 - - - +
167C ILE* 1.3 79.2 + - - +
168C ALA* 4.0 8.5 - - - +
194C THR* 3.1 25.6 - - - +
195C LEU 3.9 6.3 - - - -
196C ASN* 3.0 32.5 + - + +
221C PHE* 3.9 22.9 - + - -
300C ASP* 5.5 0.3 + - - -
303C VAL* 3.7 17.1 - - + +
307C LEU* 4.0 28.9 - - + -
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Residues in contact with ILE 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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10C PHE* 4.8 3.6 - - + -
12C MET* 3.0 53.8 - - + +
66C THR* 4.1 0.9 - - - -
166C TYR* 1.3 87.4 - - - +
168C ALA* 1.3 65.8 + - - +
171C PHE* 3.6 27.8 - - + -
179C VAL* 4.4 23.8 - - + -
182C VAL* 4.7 9.2 - - + -
193C PHE* 4.2 19.5 - - + -
194C THR 3.2 4.1 + - - +
195C LEU* 3.1 32.9 - - + +
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Residues in contact with ALA 168 (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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65C SER* 4.0 17.5 - - - +
66C THR* 2.9 25.8 + - - +
166C TYR* 4.0 12.5 - - - +
167C ILE* 1.3 76.6 - - - +
169C GLY* 1.3 66.7 + - - +
170C PHE* 3.0 8.3 + - + +
171C PHE* 3.0 19.1 + - + +
172C LEU* 4.4 1.0 + - - +
195C LEU* 4.2 1.9 - - - +
196C ASN* 3.8 9.0 - - + -
198C SER* 3.4 11.9 - - - +
500C 5I5 6.2 0.2 - - + -
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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