Contacts of the strand formed by residues 73 - 76 (chain A) 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 GLN 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR* 5.5 0.2 - - - -
70A PRO 3.1 15.4 + - - -
71A PHE 2.9 20.2 + - - -
72A ASP* 1.3 71.6 - - - +
74A LEU* 1.3 60.3 + - - +
75A ILE* 4.8 1.6 - - + +
114A GLU 5.8 1.0 + - - -
117A VAL* 3.4 35.1 - - + +
133A ILE* 3.7 30.4 - - + +
144A ARG* 3.6 28.7 - - - +
145A ARG 2.8 12.5 + - - +
146A THR* 3.5 3.6 - - + +
147A VAL* 3.0 31.0 + - - +
382B ILE* 4.3 10.2 - - - +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.5 17.3 - - + -
64A HIS* 3.7 31.0 - - + +
67A TYR* 6.2 1.1 - - + -
69A THR* 4.3 14.6 - - + -
72A ASP 3.8 2.6 + - - -
73A GLN* 1.3 72.7 - - - +
75A ILE* 1.3 85.8 + - - +
76A TRP* 3.5 38.5 + - + +
85A HIS* 4.0 4.4 - - + +
115A TYR 4.5 5.4 - - - +
117A VAL* 3.4 24.2 + - - +
147A VAL* 3.5 22.2 - - + +
149A VAL* 4.3 13.7 - - + -
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 4.8 0.9 - - + +
74A LEU* 1.3 84.6 - - - +
76A TRP* 1.3 70.4 + - - +
77A ASP 4.1 0.2 + - - -
117A VAL* 4.1 16.2 - - + -
118A LEU* 4.2 20.6 - - + +
126A SER* 3.6 29.2 - - - +
129A ALA* 4.5 2.9 - - + -
130A GLY* 3.7 25.4 - - - +
133A ILE* 3.4 28.7 - - + -
146A THR* 4.8 5.4 - - + -
147A VAL 2.9 11.5 + - - +
148A CYS* 3.3 9.0 - - - +
149A VAL* 2.8 27.5 + - - +
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Residues in contact with TRP 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A THR* 4.2 12.1 - - + -
59A LEU* 4.3 2.2 - - + -
60A THR* 3.3 31.0 - - + -
63A LEU* 4.1 18.4 - - + -
74A LEU* 3.5 27.8 - - + +
75A ILE* 1.3 81.4 - - - +
77A ASP* 1.3 63.1 + - - +
79A GLY* 4.3 7.4 - - - -
81A GLN* 3.8 37.0 - - + +
82A ALA* 4.2 8.5 - - + -
85A HIS* 3.3 46.8 + + + -
108A PRO* 4.4 10.7 - - + +
118A LEU 5.3 0.9 + - - +
120A VAL* 3.3 25.8 - - - +
149A VAL* 3.6 37.0 - - + -
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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