Contacts of the strand formed by residues 159 - 164 (chain B) in PDB entry 2WO6
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 TYR 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLU 3.6 1.0 - - - +
154B LYS* 3.2 5.0 - - - -
155B TRP* 2.8 55.4 + - + +
156B MET* 4.7 6.3 - - - -
158B ARG* 1.3 93.3 + - + +
160B GLU* 1.3 63.1 + - - +
161B ILE* 3.7 3.3 + - + -
176B ALA* 4.3 10.5 - - + -
177B TYR 3.4 2.7 - - - +
178B ASP* 3.8 33.9 - - + -
185B VAL* 4.2 13.9 - - + -
187B ILE* 4.0 15.9 - - + -
226B ARG* 3.0 38.5 + - - +
228B PHE* 3.4 34.6 - + - -
237B VAL* 3.8 8.7 - - + +
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLY* 5.9 3.4 - - - +
153B GLU 3.7 4.9 - - - -
154B LYS* 4.2 23.3 - - + +
158B ARG 4.7 0.2 - - - +
159B TYR* 1.3 71.6 - - - +
161B ILE* 1.3 65.7 + - - +
162B ASP* 3.4 1.9 + - - +
176B ALA* 3.1 2.4 - - - -
177B TYR* 2.8 55.2 + - + +
179B ARG* 3.5 46.0 + - + +
184B TRP* 4.8 0.5 - - - -
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 3.9 27.8 - - + -
150B LYS 4.1 11.2 - - - +
152B GLY* 2.7 33.3 + - - -
153B GLU* 2.8 25.4 + - + +
155B TRP* 3.6 52.9 - - + +
159B TYR* 4.6 2.9 - - + +
160B GLU* 1.3 72.5 - - - +
162B ASP* 1.3 59.6 + - - +
163B SER 4.1 7.2 - - - +
174B VAL* 4.2 15.3 - - + -
175B LYS 3.9 5.2 - - - +
176B ALA* 3.9 17.7 - - + -
187B ILE* 4.6 2.0 - - + -
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Residues in contact with ASP 162 (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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151B ASN* 3.2 24.9 + - - +
152B GLY 4.4 0.6 + - - +
160B GLU 3.4 1.6 + - - +
161B ILE* 1.3 74.4 - - - +
163B SER* 1.3 86.0 + - - +
175B LYS* 2.8 31.6 + - + +
184B TRP* 3.7 32.0 - - + -
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 4.5 3.8 - - - -
151B ASN* 3.7 17.3 - - - -
161B ILE* 3.8 2.3 - - - +
162B ASP* 1.3 100.2 + - - +
164B LEU* 1.3 63.8 + - - +
165B ILE* 3.6 14.0 + - - +
174B VAL* 3.2 8.5 - - - +
175B LYS* 2.9 29.9 + - - +
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Residues in contact with LEU 164 (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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149B VAL* 3.9 24.9 - - + +
151B ASN* 4.5 1.8 + - - -
163B SER* 1.3 74.7 - - - +
165B ILE* 1.3 62.4 + - - +
166B GLY 3.8 9.6 - - - +
167B LYS* 4.0 26.2 - - + -
172B GLN* 3.6 44.6 - - + +
173B VAL 3.7 10.5 - - - +
174B VAL* 4.4 2.9 - - + +
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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