Contacts of the strand formed by residues 96 - 103 (chain A) in PDB entry 2O07
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 LYS 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 1.3 85.2 - - + +
97A VAL* 1.3 62.5 + - - +
118A GLU* 5.7 2.9 - - + +
119A SER* 3.7 17.7 - - - +
166A ALA 3.9 21.8 - - - +
167A PHE* 3.8 9.3 - - + -
168A ASP* 2.8 40.8 + - - +
169A VAL 3.4 5.5 + - - -
198A LYS* 5.1 7.2 - - - +
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Residues in contact with VAL 97 (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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88A LEU* 4.0 13.9 - - + -
94A PRO* 4.9 2.2 - - + -
95A ARG 4.7 0.4 - - - -
96A LYS* 1.3 81.7 - - - +
98A LEU* 1.3 71.9 + - - +
99A ILE* 4.5 0.9 - - + -
111A VAL* 4.0 20.2 - - + -
117A VAL* 4.0 31.2 - - + -
119A SER 3.0 10.9 + - - +
120A VAL* 3.3 8.8 - - + -
121A VAL* 2.9 25.3 + - - +
167A PHE* 3.9 7.0 - - - -
169A VAL* 3.3 18.2 - - + +
171A ILE* 4.3 18.2 - - + -
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Residues in contact with LEU 98 (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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97A VAL* 1.3 74.8 - - - +
99A ILE* 1.3 64.9 + - - +
100A ILE* 3.7 16.8 - - + -
121A VAL* 3.3 28.7 - - + +
123A CYS 4.7 1.3 - - - +
159A PHE* 3.6 25.6 - - + -
160A MET* 3.7 38.6 - - + -
167A PHE* 3.7 33.4 - - + -
169A VAL 2.9 6.1 + - - -
170A ILE* 3.2 12.9 - - + -
171A ILE* 2.8 26.7 + - - +
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Residues in contact with ILE 99 (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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97A VAL* 4.5 7.2 - - + -
98A LEU* 1.3 77.1 - - - +
100A ILE* 1.3 75.7 + - - +
101A GLY 4.0 4.5 - - - +
102A GLY* 4.2 8.1 - - - -
107A VAL* 3.8 22.0 - - + -
108A LEU* 3.6 34.3 - - + +
111A VAL* 4.1 6.5 - - + -
120A VAL* 3.6 25.6 - - + -
121A VAL 2.9 12.0 + - - +
122A GLN* 3.3 23.4 - - + +
123A CYS 2.9 25.3 + - - -
171A ILE* 3.2 10.1 - - + +
173A ASP* 4.5 3.1 - - + -
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Residues in contact with ILE 100 (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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98A LEU* 3.7 34.3 - - + -
99A ILE* 1.3 72.4 - - - +
101A GLY* 1.3 66.1 + - - +
102A GLY 3.7 0.2 + - - -
123A CYS* 3.6 18.8 - - + +
156A GLY* 3.8 23.8 - - - -
159A PHE* 3.9 7.4 - - + -
160A MET* 3.6 15.0 - - + -
170A ILE* 4.5 2.5 - - + -
171A ILE 2.8 12.2 + - - +
172A THR* 3.7 11.9 - - + +
173A ASP* 2.8 30.0 + - - +
174A SER* 5.7 0.9 - - - -
189A TYR* 3.4 28.0 - - + +
501A MTA 4.0 12.6 - - + +
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Residues in contact with GLY 101 (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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99A ILE* 4.3 0.4 - - - -
100A ILE* 1.3 74.0 - - - +
102A GLY* 1.3 64.6 + - - -
103A GLY 3.3 3.0 + - - -
122A GLN* 3.3 22.9 + - - +
123A CYS 2.8 12.6 + - - -
124A GLU* 3.6 8.6 - - - +
173A ASP 3.5 7.0 - - - -
174A SER* 5.2 0.9 - - - -
501A MTA 3.6 28.9 + - - -
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Residues in contact with GLY 102 (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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99A ILE* 4.2 4.0 - - - -
100A ILE 3.7 1.0 + - - -
101A GLY* 1.3 72.4 - - - -
103A GLY* 1.3 65.5 + - - +
104A ASP* 3.2 3.6 - - - -
105A GLY* 2.9 14.5 + - - -
107A VAL* 5.4 3.6 - - - -
108A LEU 5.8 0.4 + - - -
122A GLN* 2.9 23.1 + - - +
173A ASP* 3.0 38.8 + - - -
501A MTA 3.8 2.6 - - - -
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Residues in contact with GLY 103 (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 GLY* 1.3 76.8 - - - +
104A ASP* 1.3 57.9 + - - +
122A GLN* 4.3 0.9 - - - -
124A GLU* 3.1 26.5 + - - -
129A VAL* 3.9 7.6 - - - -
130A ILE* 3.9 7.4 - - - -
133A SER* 3.7 10.9 + - - -
144A TYR* 2.7 24.5 + - - -
501A MTA 3.5 14.9 - - - -
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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