Contacts of the strand formed by residues 159 - 167 (chain B) in PDB entry 2C0O
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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118B LEU* 3.3 19.6 - - + +
124B PHE* 3.5 39.5 - + - -
149B ILE* 4.2 11.2 - - + -
150B ARG 3.3 10.5 - - - +
151B ASP* 3.7 11.0 - - - -
152B SER* 3.9 3.2 - - - +
157B GLY 4.8 10.1 - - - -
158B SER* 1.3 86.5 - - - +
160B SER* 1.3 66.9 + - - +
178B LYS* 4.2 1.7 - - - +
179B ILE* 2.9 38.4 + - + +
181B THR* 5.4 4.9 - - + +
187B PHE* 4.0 27.6 - + - -
198B LEU* 4.0 16.6 - - + -
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Residues in contact with SER 160 (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 ILE* 3.1 7.4 - - - +
150B ARG* 2.8 66.6 + - - +
152B SER* 3.9 2.3 - - - +
159B TYR* 1.3 77.8 + - - +
161B LEU* 1.3 60.7 + - - +
177B TYR 3.4 12.0 + - - -
178B LYS* 4.2 3.5 - - - +
179B ILE* 3.8 6.7 - - - -
501B PTR 2.7 32.3 + - - -
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Residues in contact with LEU 161 (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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147B PHE* 4.2 8.7 - - + -
148B MET 3.5 9.0 - - - +
149B ILE* 3.4 23.6 - - + -
160B SER* 1.3 73.6 - - - +
162B SER* 1.3 62.3 + - - +
163B VAL* 3.7 15.9 - - + -
175B LYS 3.7 0.9 - - - +
176B HIS* 3.2 5.7 - - - +
177B TYR* 2.8 52.2 + - + +
179B ILE* 3.7 9.7 - - + +
189B ILE* 3.4 27.8 - - + -
201B LEU* 4.8 6.5 - - + -
205B TYR* 5.4 0.7 - - + -
212B LEU* 4.2 13.0 - - + -
216B LEU* 4.0 22.9 - - + -
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Residues in contact with SER 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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133B ALA* 4.5 2.5 - - - -
137B LEU* 3.7 21.2 - - - +
147B PHE* 3.1 25.5 - - - +
148B MET* 3.0 23.1 + - - -
150B ARG* 2.9 23.5 + - - +
160B SER 4.1 0.2 + - - -
161B LEU* 1.3 71.1 - - - +
163B VAL* 1.3 62.4 + - - +
174B VAL* 4.0 0.4 - - - -
175B LYS 3.3 3.1 - - - -
176B HIS* 2.5 35.3 + - - -
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Residues in contact with VAL 163 (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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137B LEU* 4.8 0.7 - - - -
145B GLY* 3.9 11.0 - - - +
146B SER 3.6 8.3 - - - +
147B PHE* 4.1 0.4 - - + -
161B LEU* 3.7 24.2 - - + -
162B SER* 1.3 78.1 - - - +
164B ARG* 1.3 75.0 + - - +
165B ASP* 3.9 1.1 + - + +
174B VAL* 3.2 7.2 - - - +
175B LYS* 2.7 41.3 + - + +
177B TYR* 4.0 21.8 - - + -
212B LEU* 5.0 2.9 - - + -
214B GLN* 4.4 15.5 - - + +
216B LEU* 3.8 26.2 - - + -
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Residues in contact with ARG 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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137B LEU* 3.4 25.4 + - + +
138B LEU* 3.5 28.0 + - + +
139B ALA 4.2 3.2 + - - -
142B ASN* 2.5 48.1 + - - +
143B MET* 3.4 23.1 - - - +
144B LEU* 4.4 1.6 - - + -
145B GLY* 2.8 23.2 + - - +
146B SER* 2.9 20.2 + - - +
163B VAL* 1.3 73.5 - - - +
165B ASP* 1.3 61.9 + - - +
172B ASP* 3.6 33.8 + - - +
173B THR 3.4 14.1 - - - +
174B VAL* 4.6 3.4 - - + +
214B GLN* 3.1 14.4 - - - +
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Residues in contact with ASP 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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144B LEU* 3.6 11.0 - - - +
163B VAL* 4.6 0.9 - - + +
164B ARG* 1.3 77.9 - - - +
166B TYR* 1.3 79.8 + - - +
167B ASP* 5.3 1.9 - - - +
172B ASP* 3.7 5.9 - - - +
173B THR* 3.0 35.9 + - - +
175B LYS* 2.9 32.7 + - + +
213B CYS* 2.9 35.2 - - + +
214B GLN* 3.4 15.5 + - + +
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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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144B LEU* 3.8 17.5 - - + -
165B ASP* 1.3 92.9 + - - +
167B ASP* 1.3 81.0 + - - +
168B PRO* 3.8 19.2 + - + +
171B GLY* 3.2 38.4 - - - -
172B ASP* 3.4 19.5 - - - +
173B THR* 4.1 1.5 + - - +
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Residues in contact with ASP 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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169A ARG* 5.9 0.7 + - - -
165B ASP* 5.5 1.4 - - - +
166B TYR* 1.3 88.7 - - - +
168B PRO* 1.3 66.8 - - + +
169B ARG* 3.6 11.2 - - + +
170B GLN* 3.3 33.0 - - + +
171B GLY* 2.7 30.2 + - - -
173B THR* 4.0 15.8 + - - +
175B LYS* 4.6 10.5 + - - -
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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