Contacts of the strand formed by residues 160 - 166 (chain V) in PDB entry 1O19
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 THR 160 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153V LEU* 4.4 5.6 - - + -
154V ASP 3.2 9.6 - - - +
155V SER* 2.6 25.6 + - - +
159V VAL* 1.4 71.8 - - - +
161V HIS* 1.3 76.1 + - - +
162V ASN* 5.0 2.9 - - - +
177V ARG* 3.3 6.2 - - - +
178V LEU* 2.9 46.3 + - + -
180V LEU 3.1 16.9 + - - -
181V ALA* 4.3 0.2 - - - +
261V LEU* 5.1 0.3 - - - +
274V ILE* 3.6 31.4 - - + +
277V THR* 6.1 0.4 - - + -
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Residues in contact with HIS 161 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73V HIS 5.2 0.9 - - - -
108V ALA* 4.9 7.0 - - + -
109V PRO* 3.6 42.3 - - + +
110V LEU* 5.2 3.4 + - - +
152V VAL 4.1 0.2 - - - -
153V LEU* 3.4 4.5 - - - -
154V ASP* 2.7 40.0 + - + +
159V VAL* 4.0 31.3 - - + +
160V THR* 1.3 81.2 + - - +
162V ASN* 1.3 67.6 + - - +
163V VAL* 4.2 11.2 - - + -
175V ILE* 4.0 7.8 - - + +
176V MET 3.0 16.8 - - - -
177V ARG* 3.7 28.8 + - + +
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Residues in contact with ASN 162 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151V ILE* 4.5 5.6 - - + +
152V VAL 3.2 7.1 + - - +
153V LEU* 3.6 21.2 - - - +
160V THR* 5.0 2.3 - - - +
161V HIS* 1.3 75.6 + - - +
163V VAL* 1.3 62.7 + - - +
164V PRO* 3.5 2.4 - - - +
175V ILE* 3.2 24.4 - - - +
176V MET* 2.9 13.1 + - - +
178V LEU* 5.8 0.3 + - - +
277V THR* 2.9 31.0 - - - +
278V THR* 3.4 34.6 + - - +
281V SER* 3.6 20.2 - - - +
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Residues in contact with VAL 163 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109V PRO* 3.5 34.1 - - + -
136V ILE* 5.1 2.2 - - + -
138V ALA* 3.4 22.0 - - + -
139V VAL* 5.0 0.9 - - + -
151V ILE* 4.2 0.6 - - - +
152V VAL* 2.9 28.4 + - - +
154V ASP* 5.8 0.4 - - + -
161V HIS* 4.2 9.9 - - + -
162V ASN* 1.3 78.4 - - - +
164V PRO* 1.3 64.1 - - - +
165V ILE* 3.5 17.2 + - + +
170V ALA* 3.6 31.0 - - + -
175V ILE* 3.9 15.7 - - + -
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Residues in contact with PRO 164 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150V GLY 3.7 6.5 - - - +
151V ILE* 3.9 15.9 - - + -
162V ASN 3.5 6.7 - - - +
163V VAL* 1.3 82.9 - - - +
165V ILE* 1.4 60.2 + - - +
170V ALA* 3.6 0.5 - - - -
171V LEU* 2.8 35.5 + - + +
174V ALA* 3.7 15.9 - - + -
175V ILE* 4.0 18.2 - - + +
281V SER* 3.4 20.6 - - - +
285V CYS* 3.8 21.3 - - - -
293V LEU* 4.4 9.0 - - + -
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Residues in contact with ILE 165 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138V ALA* 3.7 9.6 - - + +
139V VAL* 3.5 40.8 - - + +
142V LEU* 3.9 18.4 - - + -
148V THR 3.4 16.8 - - - +
149V THR* 3.1 23.2 - - - +
150V GLY 2.9 13.0 + - - +
152V VAL* 4.5 2.7 - - + -
163V VAL* 3.6 20.6 - - + +
164V PRO* 1.4 74.3 - - - +
166V TYR* 1.3 62.3 + - - +
168V GLY* 3.6 25.4 - - - +
169V TYR 3.7 2.9 - - - -
170V ALA* 3.6 15.9 - - + -
171V LEU* 4.7 1.3 - - - -
293V LEU* 4.3 2.4 - - - +
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Residues in contact with TYR 166 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149V THR* 3.6 18.6 - - + -
165V ILE* 1.3 72.6 - - - +
167V GLU* 1.3 89.8 + - + +
168V GLY 2.9 4.6 + - - -
169V TYR* 3.1 26.9 + - + +
171V LEU* 4.3 21.2 - - + +
289V ILE* 3.7 35.9 - - + -
292V ASP* 4.0 16.6 + - - -
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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