Contacts of the strand formed by residues 96 - 103 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ARG* 1.3 94.1 - - + +
97B VAL* 1.3 62.9 + - - +
118B GLU* 3.7 28.8 + - - +
119B SER* 3.6 27.7 - - - +
166B ALA 4.0 20.6 - - - +
167B PHE* 3.9 9.2 - - + -
168B ASP* 2.9 38.4 + - - +
169B VAL 3.4 6.4 + - - +
198B LYS* 5.0 7.4 - - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.8 24.7 - - + -
94B PRO* 5.0 2.5 - - + -
95B ARG 4.9 0.4 - - - -
96B LYS* 1.3 80.5 - - - +
98B LEU* 1.3 66.7 + - - +
99B ILE* 4.2 1.1 - - + -
111B VAL* 3.9 27.6 - - + -
117B VAL* 4.0 13.7 - - + -
119B SER 2.9 11.1 + - - +
120B VAL* 3.3 8.9 - - + -
121B VAL 2.8 31.0 + - - -
167B PHE* 3.8 7.6 - - - -
169B VAL* 3.3 25.1 - - + +
171B ILE* 4.3 9.9 - - + -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 1.3 75.0 - - - +
99B ILE* 1.3 73.9 + - - +
100B ILE* 3.9 11.4 - - + -
121B VAL* 3.4 27.4 - - + +
123B CYS 4.6 1.3 - - - +
159B PHE* 3.6 26.7 - - + -
160B MET* 3.7 38.1 - - + -
167B PHE* 3.7 32.0 - - + -
169B VAL 2.9 8.3 + - - +
170B ILE* 3.7 15.5 - - + -
171B ILE* 2.7 28.1 + - - +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.5 7.2 - - + -
98B LEU* 1.3 80.0 - - - +
100B ILE* 1.3 74.1 + - - +
101B GLY 4.2 5.8 - - - +
102B GLY* 4.3 8.7 - - - -
107B VAL* 3.9 17.7 - - + -
108B LEU* 3.6 40.6 - - + +
111B VAL* 4.3 5.4 - - + -
120B VAL* 3.7 22.4 - - + -
121B VAL 2.7 12.9 + - - +
122B GLN* 3.2 18.4 - - + +
123B CYS 2.8 26.5 + - - -
171B ILE* 3.3 9.6 - - + +
173B ASP* 4.5 7.4 - - + -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.9 18.2 - - + -
99B ILE* 1.3 70.8 - - - +
101B GLY* 1.3 66.2 + - - +
123B CYS* 3.7 26.0 - - + -
156B GLY* 3.8 22.7 - - - -
159B PHE* 3.9 8.3 - - + -
160B MET* 3.6 22.7 - - + -
170B ILE* 4.6 1.3 - - + -
171B ILE 2.8 14.7 + - - +
172B THR* 4.3 4.4 - - + +
173B ASP* 2.9 31.9 + - - +
184B LEU* 3.8 22.0 - - + -
189B TYR* 3.3 27.4 - - - +
501B MTA 4.0 3.8 - - + -
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.3 0.7 - - - -
100B ILE* 1.3 76.0 - - - +
102B GLY* 1.3 64.8 + - - -
103B GLY 3.4 2.6 + - - -
122B GLN* 3.3 22.5 + - - +
123B CYS 2.9 11.5 + - - -
124B GLU* 3.6 8.2 - - - +
173B ASP 3.6 2.7 - - - -
174B SER* 5.4 0.9 - - - -
184B LEU* 5.7 0.2 - - - -
501B MTA 3.5 33.6 + - - -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.3 7.9 - - - -
100B ILE 3.7 1.2 + - - -
101B GLY* 1.3 71.7 - - - -
103B GLY* 1.3 65.0 + - - +
104B ASP* 3.2 4.7 - - - -
105B GLY* 3.0 14.2 + - - -
107B VAL* 5.4 3.4 - - - -
122B GLN* 2.8 19.6 + - - +
173B ASP* 3.2 38.3 + - - -
501B MTA 3.8 2.5 - - - -
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLY* 1.3 75.8 - - - +
104B ASP* 1.3 57.0 + - - +
122B GLN* 4.2 0.7 - - - -
124B GLU* 3.1 24.6 + - - -
129B VAL* 4.0 8.3 - - - -
130B ILE* 3.8 9.1 - - - -
133B SER* 3.6 12.5 + - - -
144B TYR* 2.7 24.3 + - - -
501B MTA 3.5 16.5 - - - -
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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