Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 2R32
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LYS* 3.7 22.9 - - - -
62A PHE 3.2 17.3 - - - +
63A GLY 3.7 11.2 - - - -
64A PRO* 4.1 17.9 - - + -
85A TRP* 3.9 6.7 - - - -
98A TYR* 4.1 16.8 - + - -
99A GLY* 3.9 19.5 - - - -
100A GLN* 3.0 66.5 + - + +
136A VAL* 4.7 1.6 - - - +
150A LEU* 5.0 1.5 - - - +
162A ASN* 4.4 5.4 - - - -
163A THR* 1.3 82.2 - - - +
165A TRP* 1.3 67.3 + - - +
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Residues in contact with TRP 165 (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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61A LYS* 3.4 4.9 - - - +
62A PHE* 2.8 30.2 + - + +
69A TRP* 3.5 20.0 - + - -
85A TRP* 2.9 50.4 + + - +
87A LEU* 3.8 20.6 - - + -
97A ILE* 3.9 13.5 - - + -
98A TYR 3.2 12.8 - - - +
99A GLY* 3.9 1.8 - - - -
117A LEU* 5.0 2.5 - - + -
136A VAL* 4.0 14.8 - - + -
148A ILE* 3.4 44.6 - - + -
150A LEU* 3.6 29.1 - - + +
164A TYR* 1.3 79.6 - - - +
166A GLY* 1.3 93.3 + - - +
167A ILE* 4.1 12.1 - - + -
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA 3.1 14.8 - - - -
61A LYS* 3.9 1.8 - - - -
69A TRP* 5.4 0.4 - - - -
97A ILE* 3.5 2.1 - - - -
98A TYR* 2.8 49.4 + - - +
165A TRP* 1.3 89.5 - - - +
167A ILE* 1.3 60.9 + - - -
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A MET* 3.2 8.6 - - - +
60A ALA* 3.0 42.2 + - + +
78A CYS* 6.1 1.3 - - - -
79A VAL* 4.4 7.6 - - + -
87A LEU* 3.4 30.1 - - + -
89A ILE* 4.0 11.0 - - + -
95A TYR* 3.7 34.1 - - + -
96A LEU 3.3 12.3 - - - +
97A ILE* 3.7 20.6 - - + -
98A TYR* 3.6 4.4 - - - -
142A LEU* 3.9 13.7 - - + -
148A ILE* 4.8 2.5 - - + -
165A TRP* 4.1 7.2 - - + -
166A GLY* 1.3 75.0 - - - +
168A ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 168 (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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57A PRO* 3.6 25.8 - - + -
58A CYS 3.5 5.2 - - - +
59A MET* 3.7 30.3 - - + -
95A TYR* 3.3 8.2 - - - -
96A LEU* 2.9 59.7 + - + +
98A TYR* 5.3 5.6 - - + -
167A ILE* 1.3 75.1 - - - +
169A LEU* 1.3 73.3 + - - +
170A LEU* 4.2 12.6 - - + -
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PRO* 4.0 12.8 - - - +
58A CYS* 3.0 24.3 + - + +
78A CYS* 4.3 13.4 - - + -
91A GLN* 4.0 15.9 - - - +
92A ASN 4.7 2.5 - - - +
93A GLY* 4.2 4.0 - - - -
94A LEU 3.7 7.4 - - - +
95A TYR* 3.6 38.9 - - + +
168A ILE* 1.3 80.5 - - - +
170A LEU* 1.3 60.8 + - - +
171A ALA* 3.5 27.8 - - - +
172A ASN* 3.6 21.3 - - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 2.8 39.4 + - + +
96A LEU* 4.1 31.4 - - + +
139A THR* 4.3 14.1 - - + +
168A ILE* 4.2 24.9 - - + -
169A LEU* 1.3 75.2 - - - +
171A ALA* 1.3 61.9 + - + +
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Residues in contact with ALA 171 (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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93A GLY* 3.5 2.3 - - - -
94A LEU* 2.9 37.6 + - + -
169A LEU* 3.5 6.8 - - - +
170A LEU* 1.3 85.0 - - + +
172A ASN* 1.3 63.6 + - - +
173A PRO* 3.5 14.2 - - + +
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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