Contacts of the strand formed by residues 164 - 168 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE 3.3 2.0 + - - -
9A LEU* 3.4 18.3 - - + +
10A PHE 2.9 24.4 + - - -
162A ALA* 3.6 3.3 - - - +
163A ARG* 1.3 86.4 - - + +
165A CYS* 1.3 75.0 + - - +
192A ILE* 3.6 17.9 - - + +
194A THR* 4.4 2.7 - - + -
307A LEU* 4.4 14.6 - - + +
310A LEU* 3.1 37.9 - - + +
311A VAL* 3.8 24.9 - - + -
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Residues in contact with CYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.8 0.4 - - - -
10A PHE* 3.2 23.3 - - + +
159A VAL* 5.0 8.5 - - - -
162A ALA* 4.4 10.8 - - - -
163A ARG 5.5 0.4 - - - -
164A VAL* 1.3 79.2 - - - +
166A TYR* 1.3 60.8 + - - +
167A ILE* 5.8 0.4 - - + -
182A VAL* 4.1 22.4 - - + -
185A HIS* 5.9 4.3 - - - -
186A ALA* 5.3 7.6 - - - -
191A ARG* 5.5 3.6 - - - -
192A ILE 2.8 14.5 + - - +
193A PHE* 4.0 18.6 - - + -
194A THR* 2.9 32.1 + - - +
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.8 2.5 - - + -
10A PHE 2.8 11.3 + - - +
11A GLY* 3.1 25.6 - - - -
12A MET 3.6 1.4 + - - -
65A SER* 4.6 2.4 + - - -
66A THR* 3.8 24.7 - - + +
69A SER* 3.9 25.7 + - - -
70A ILE* 5.4 2.7 - - + -
165A CYS* 1.3 74.7 - - - +
167A ILE* 1.3 68.4 + - - +
168A ALA* 4.0 8.1 - - - +
194A THR* 3.0 27.1 - - - +
195A LEU* 3.8 13.9 - - - -
196A ASN* 2.3 39.6 + - + +
221A PHE* 3.8 24.0 - + - -
303A VAL* 3.8 9.7 - - + +
307A LEU* 3.6 27.4 - - + -
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 5.0 2.7 - - + -
12A MET* 3.5 45.3 - - + +
66A THR* 3.8 3.1 - - - -
166A TYR* 1.3 84.7 - - - +
168A ALA* 1.3 76.5 + - - +
171A PHE* 3.7 18.6 - - + -
172A LEU* 6.5 0.2 - - + -
179A VAL* 3.9 26.9 - - + -
182A VAL* 4.2 10.8 - - + -
193A PHE* 3.8 27.4 - - + -
194A THR 3.2 6.2 + - - +
195A LEU* 3.1 34.4 - - + +
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY* 6.2 0.2 - - - -
65A SER* 3.8 20.2 - - - +
66A THR* 2.7 24.7 + - - +
166A TYR* 4.0 8.5 - - - +
167A ILE* 1.3 85.4 - - - +
169A GLY* 1.3 63.7 + - - +
170A PHE* 3.0 14.3 + - + +
171A PHE* 3.1 10.6 + - + +
172A LEU 4.6 0.2 + - - -
195A LEU* 4.6 0.2 - - - +
196A ASN* 3.7 9.9 - - + -
198A SER* 3.5 11.4 - - - +
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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