Contacts of the strand formed by residues 164 - 168 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE 3.4 1.2 + - - -
9B LEU* 3.4 22.2 - - + +
10B PHE 2.8 24.6 + - - -
162B ALA* 3.7 2.9 - - - +
163B ARG* 1.3 86.6 - - + +
165B CYS* 1.3 73.1 + - - +
192B ILE* 3.4 14.6 - - + +
194B THR* 4.6 2.0 - - + +
307B LEU* 4.2 12.6 - - + -
310B LEU* 3.7 37.5 - - + +
311B VAL* 3.8 30.3 - - + -
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Residues in contact with CYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 3.2 35.4 - - + +
159B VAL* 4.8 6.1 - - - -
162B ALA* 3.9 12.3 - - - -
164B VAL* 1.3 79.9 - - - +
166B TYR* 1.3 54.3 + - - +
167B ILE* 5.5 0.4 - - + -
182B VAL* 4.1 13.0 - - + -
185B HIS* 6.0 3.8 - - - -
186B ALA* 5.3 8.5 - - - -
191B ARG* 5.6 2.7 - - - -
192B ILE 2.7 10.7 + - - +
193B PHE* 4.0 24.0 - - + -
194B THR* 2.6 38.6 + - - +
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Residues in contact with TYR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.9 2.0 - - + -
10B PHE 2.8 11.2 + - - +
11B GLY* 3.1 24.3 - - - -
65B SER* 4.7 4.7 + - - -
66B THR* 3.8 25.4 - - + +
69B SER* 4.0 16.7 + - - -
70B ILE* 5.1 3.8 - - + -
165B CYS* 1.3 73.2 - - - +
167B ILE* 1.3 65.1 + - - +
168B ALA* 3.9 11.3 - - - +
194B THR* 3.0 31.2 - - - +
195B LEU 4.1 4.5 - - - -
196B ASN* 2.9 38.5 + - + +
221B PHE* 4.0 14.6 - + - -
300B ASP* 5.3 0.3 + - - -
303B VAL* 3.7 27.6 - - + +
307B LEU* 3.7 28.3 - - + -
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 5.1 2.2 - - + -
11B GLY* 5.0 0.9 - - - -
12B MET* 3.0 41.7 - - + +
66B THR* 4.0 0.7 - - - -
165B CYS* 5.5 0.2 - - + -
166B TYR* 1.3 83.3 - - - +
168B ALA* 1.3 73.6 + - - +
171B PHE* 3.7 23.8 - - + -
179B VAL* 4.1 25.6 - - + -
182B VAL* 4.3 14.1 - - + -
193B PHE* 3.5 31.0 - - + -
194B THR 3.1 6.5 + - - -
195B LEU* 3.2 35.5 - - + +
196B ASN 3.4 0.3 + - - -
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 6.3 0.2 - - - -
65B SER* 4.2 11.9 - - - +
66B THR* 2.9 34.3 + - - +
166B TYR* 3.9 13.4 - - - +
167B ILE* 1.3 75.4 - - - +
169B GLY* 1.3 63.6 + - - +
170B PHE* 3.0 11.3 + - + +
171B PHE* 3.0 19.3 + - + +
172B LEU* 4.5 0.9 + - - +
195B LEU* 4.7 0.9 - - - +
196B ASN* 3.8 8.7 - - + -
198B SER* 3.5 12.1 - - - +
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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