Contacts of the strand formed by residues 146 - 151 (chain C) in PDB entry 2O1S
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 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C TYR* 4.4 2.9 + - - -
73C GLN* 3.4 9.5 - - + +
75C ILE* 4.8 2.2 - - + -
130C GLY* 3.6 32.1 - - - +
133C ILE* 3.7 18.3 + - + +
134C ALA* 3.6 25.7 - - - -
137C ALA* 4.5 4.9 - - - +
144C ARG 4.2 0.6 + - - -
145C ARG* 1.3 78.3 + - - +
147C VAL* 1.3 67.6 + - - +
148C CYS* 4.5 5.8 - - - -
173C ASP 4.4 5.7 + - - -
174C MSE 3.4 13.8 - - + +
175C LEU* 2.9 23.0 + - - +
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 4.0 9.2 - - + -
67C TYR* 3.5 38.8 - - + +
73C GLN 2.9 17.8 + - - +
74C LEU* 3.8 20.9 - - + +
75C ILE* 2.8 26.3 + - - +
146C THR* 1.3 77.0 - - - +
148C CYS* 1.3 69.3 + - - +
149C VAL* 5.0 0.4 - - + -
175C LEU* 3.1 17.0 - - + +
177C ILE* 3.7 29.6 - - + -
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Residues in contact with CYS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE* 3.4 12.6 - - - +
126C SER* 3.5 41.1 - - - +
127C ILE* 4.3 2.9 - - + +
130C GLY* 3.9 10.1 - - - -
146C THR* 4.5 2.9 - - - -
147C VAL* 1.3 80.5 - - - +
149C VAL* 1.3 58.3 + - - +
150C ILE 4.0 0.8 + - - +
174C MSE 3.8 25.6 - - - -
175C LEU 2.7 10.9 + - - +
176C VAL* 3.4 8.9 - - + +
177C ILE* 2.6 35.9 + - - +
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU* 3.9 17.0 - - + -
63C LEU* 3.8 29.2 - - + -
74C LEU* 4.2 8.7 - - + -
75C ILE 2.8 9.8 + - - +
76C TRP* 3.5 35.4 - - + -
77C ASP* 2.8 30.4 + - - +
81C GLN* 4.4 6.4 + - - +
126C SER* 4.3 0.6 + - - -
147C VAL* 5.0 0.2 - - + -
148C CYS* 1.3 76.0 - - - +
150C ILE* 1.3 60.7 + - - +
177C ILE* 3.4 14.8 - - + +
179C ASN* 4.0 17.9 - - + +
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ASP* 3.6 27.1 - - - +
124C SER* 4.5 4.9 - - - -
126C SER* 3.8 9.0 - - - +
127C ILE* 3.8 23.1 - - + -
148C CYS 5.4 0.2 - - - +
149C VAL* 1.3 75.6 - - - +
151C GLY* 1.3 71.0 + - - +
154C ALA* 3.7 7.9 - - + +
155C ILE* 3.6 35.9 - - + +
160C ALA* 4.5 2.5 - - + -
176C VAL* 4.0 22.0 - - + -
177C ILE 2.8 16.2 + - - +
178C LEU* 3.3 6.6 - - + +
179C ASN* 2.8 26.9 + - - -
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Residues in contact with GLY 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ASP* 4.6 2.2 + - - +
81C GLN* 5.2 6.3 - - - +
150C ILE* 1.3 80.3 - - - +
152C ASP* 1.3 61.2 + - - -
153C GLY 3.2 2.9 - - - -
154C ALA* 3.3 2.5 + - - +
155C ILE* 3.0 28.2 + - - +
178C LEU* 3.8 0.7 - - - -
179C ASN* 3.4 17.0 - - - +
3002C TPP 3.1 22.7 + - - -
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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