Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 1OVM
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 GLY 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL 3.0 7.1 + - - +
97A LEU* 3.9 5.6 - - - -
98A HIS* 2.9 27.5 + - - +
134A THR* 4.0 4.0 - - - +
136A ALA 3.3 10.8 - - - -
152A VAL* 5.2 0.9 - - - -
156A MET* 3.4 26.0 - - - -
162A PRO* 1.3 75.1 - - - +
164A TYR* 1.3 61.7 + - - +
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Residues in contact with TYR 164 (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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75A PHE* 5.9 0.7 - - - -
79A GLU* 2.5 30.7 + - - -
83A MET* 5.9 0.4 - - + -
86A ILE* 6.5 0.2 - - + -
97A LEU* 4.4 0.2 - - - +
98A HIS* 3.5 25.8 - + + -
100A VAL* 3.2 26.7 - - + +
127A TYR* 3.5 44.9 + + - +
130A SER* 3.5 28.5 - - - -
134A THR* 3.9 11.0 - - + -
136A ALA 2.9 8.7 + - - -
137A GLN* 3.0 19.7 - - + +
138A ALA 2.9 26.0 + - - -
152A VAL* 4.5 1.5 - - - +
156A MET* 5.0 0.2 - - - +
163A GLY* 1.3 75.6 - - - +
165A LEU* 1.3 70.5 + - - +
166A MET* 3.9 14.4 - - + +
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Residues in contact with LEU 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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11A LEU* 3.9 30.3 - - + -
97A LEU* 4.0 17.7 - - + -
98A HIS 2.9 12.4 + - - +
99A ILE* 3.5 10.3 - - + +
100A VAL* 3.0 25.6 + - - +
138A ALA* 3.5 5.2 - - + -
140A LEU* 3.9 38.1 - - + -
148A GLU 4.5 3.6 - - - +
149A ILE* 4.3 9.6 - - + -
152A VAL* 3.7 34.3 - - + -
153A LEU* 5.6 0.4 - - + -
164A TYR* 1.3 85.5 - - - +
166A MET* 1.3 61.5 + - - +
167A LEU 3.5 0.7 + - - -
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Residues in contact with MET 166 (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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75A PHE* 4.5 8.5 - - + -
100A VAL* 3.7 11.7 - - + +
102A ALA* 3.7 17.5 - - + -
108A GLN* 3.1 40.6 - - - +
123A PHE 4.4 14.8 - - - +
124A ARG* 4.8 3.6 - - - +
127A TYR* 5.2 5.2 - - - -
138A ALA 2.9 13.7 + - - +
139A VAL* 3.5 38.4 - - + -
140A LEU* 3.0 26.4 + - - +
164A TYR* 3.9 17.9 - - + +
165A LEU* 1.3 71.4 - - - +
167A LEU* 1.3 59.3 + - - +
168A PRO* 3.2 15.1 - - + +
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Residues in contact with LEU 167 (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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7A VAL* 4.5 6.5 - - + -
8A ALA* 5.1 3.4 - - - -
11A LEU* 4.1 15.3 - - + -
30A TYR 4.8 0.2 - - - +
34A PHE* 3.9 36.6 - - + -
99A ILE* 4.4 14.6 - - + -
100A VAL 2.9 14.0 + - - +
101A GLY* 3.5 5.3 - - - -
102A ALA* 3.0 20.6 + - - -
140A LEU* 3.9 20.0 - - + -
165A LEU 3.5 1.2 + - - +
166A MET* 1.3 73.2 - - - +
168A PRO* 1.3 74.9 - - + +
169A ALA* 3.4 1.7 + - - -
171A VAL* 4.0 12.3 - - + -
172A ALA* 4.0 28.5 - - + +
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Residues in contact with PRO 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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102A ALA 3.5 9.4 - - - +
103A PRO 3.5 11.7 - - - +
105A THR* 3.9 11.9 - - + +
108A GLN* 4.3 1.1 - - - +
139A VAL* 5.0 1.1 - - + -
140A LEU 3.2 28.0 - - - +
166A MET* 3.2 30.1 - - + +
167A LEU* 1.3 86.0 - - + +
169A ALA* 1.3 66.7 + - - +
170A ASP* 3.5 16.2 - - - +
171A VAL* 3.0 26.2 + - + +
172A ALA 3.1 9.2 + - - -
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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