Contacts of the strand formed by residues 146 - 151 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D TYR* 4.8 3.3 + - - -
73D GLN* 3.4 3.8 - - - +
75D ILE* 3.8 21.5 - - + -
130D GLY 3.5 24.7 - - - +
133D ILE* 3.9 13.2 + - + +
134D ALA* 3.5 30.3 + - + +
137D ALA* 4.6 4.9 - - - +
144D ARG* 4.2 0.4 + - - +
145D ARG* 1.3 77.9 + - - +
147D VAL* 1.3 64.3 + - - +
148D CYS* 4.4 5.6 - - - -
173D ASP 4.4 5.6 + - - -
174D MSE 3.4 9.5 - - + -
175D LEU* 3.0 23.3 + - - +
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU* 3.9 14.1 - - + -
67D TYR* 3.9 33.9 - - + +
73D GLN 2.9 12.4 + - - +
74D LEU* 3.9 20.4 - - + +
75D ILE* 2.9 27.9 + - - +
146D THR* 1.3 75.5 - - - +
148D CYS* 1.3 67.7 + - - +
149D VAL* 4.9 0.9 - - + -
175D LEU* 3.0 16.2 - - + +
177D ILE* 3.7 29.8 - - + -
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Residues in contact with CYS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ILE* 3.4 11.2 - - - -
126D SER* 3.0 28.0 - - - +
127D ILE* 4.4 4.0 - - + +
130D GLY* 3.7 19.7 - - - -
146D THR* 4.4 1.6 - - - -
147D VAL* 1.3 79.4 - - - +
149D VAL* 1.3 57.0 + - - +
150D ILE* 4.1 0.9 - - + -
174D MSE 3.6 30.5 - - - -
175D LEU 2.7 10.8 + - - +
176D VAL* 3.1 12.6 - - + +
177D ILE* 2.4 35.7 + - - +
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 4.0 17.3 - - + -
63D LEU* 3.9 22.4 - - + -
74D LEU* 4.8 2.9 - - + -
75D ILE 3.0 10.4 + - - +
76D TRP* 3.6 42.6 - - + -
77D ASP* 2.9 29.6 + - - +
81D GLN* 4.4 7.3 + - - +
126D SER* 4.0 0.2 + - - -
147D VAL* 4.9 1.1 - - + -
148D CYS* 1.3 77.3 - - - +
150D ILE* 1.3 62.5 + - - +
177D ILE* 3.4 17.3 - - + +
179D ASN* 4.0 16.8 - - + -
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Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ASP* 2.9 37.2 - - + +
81D GLN* 5.0 0.2 - - - -
124D SER* 5.2 2.2 - - - -
126D SER* 3.5 15.9 - - - +
127D ILE* 4.4 15.3 - - + -
148D CYS 4.8 1.1 - - - +
149D VAL* 1.3 73.7 - - - +
151D GLY* 1.3 65.1 + - - +
154D ALA* 4.5 5.4 - - + -
155D ILE* 3.5 18.2 - - + -
176D VAL* 4.1 18.8 - - + -
177D ILE 2.9 15.5 + - - +
178D LEU* 3.4 26.6 - - + +
179D ASN* 2.8 23.2 + - - -
277D PHE* 4.9 0.2 - - + -
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Residues in contact with GLY 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ASP* 4.7 1.0 - - - +
78D VAL* 5.7 0.6 - - - +
81D GLN* 4.6 9.7 - - - +
150D ILE* 1.3 78.2 - - - +
152D ASP* 1.3 65.0 + - - -
153D GLY 3.2 2.9 - - - -
154D ALA* 3.3 4.2 + - - +
155D ILE* 3.1 21.8 + - - +
178D LEU* 4.1 0.9 - - - -
179D ASN* 3.8 15.0 - - - -
4002D DPO 3.2 22.6 + - - -
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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