Contacts of the strand formed by residues 96 - 102 (chain E) in PDB entry 2P5V
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 VAL 96 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90E VAL* 4.0 21.8 - - + +
93E TRP* 3.2 20.9 + - + +
94E PRO 4.0 2.3 - - - +
95E GLU* 1.3 76.2 - - - +
97E LEU* 1.3 60.3 + - - +
98E SER 3.5 25.6 - - - +
110E LEU* 4.1 21.5 - - + -
111E GLN 3.5 6.1 - - - +
112E ALA* 4.0 8.5 - - + -
123E PHE* 3.8 28.9 - - + -
147F LYS* 2.8 33.9 + - + +
149F THR* 4.5 1.0 - - - +
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Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E PRO 3.9 9.0 - - - +
95E GLU 3.7 14.1 - - - +
96E VAL* 1.3 76.4 - - - +
98E SER* 1.3 62.8 + - - +
111E GLN* 2.8 14.4 + - + +
113E PHE* 4.2 20.0 - - + -
147F LYS* 3.9 3.1 - - - +
148F HIS* 3.3 3.3 + - - -
149F THR* 2.8 52.7 + - + +
150F THR* 3.9 9.6 - - - +
151F SER 3.4 27.6 - - - +
152F LEU* 3.8 20.9 - - + -
153F PRO* 4.0 11.0 - - + -
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Residues in contact with SER 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E VAL* 3.5 7.0 - - - +
97E LEU* 1.3 82.6 - - - +
99E CYS* 1.3 61.1 + - - +
100E PHE* 3.7 15.7 - - - -
109E LEU 4.2 1.3 + - - -
110E LEU* 3.2 3.8 - - - -
111E GLN* 2.9 57.7 + - - +
147F LYS* 3.1 13.2 - - - -
148F HIS* 3.6 22.5 - - - -
149F THR 5.3 0.2 - - - -
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Residues in contact with CYS 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E PHE* 4.1 11.4 - - - -
90E VAL* 3.6 25.4 - - + -
98E SER* 1.3 76.6 - - - +
100E PHE* 1.3 66.3 + - - +
108E TYR* 3.9 22.9 - - - -
109E LEU 3.3 4.5 - - - -
110E LEU* 3.7 25.1 - - + -
146F ILE* 2.9 40.9 + - + -
147F LYS* 2.8 15.0 + - + +
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Residues in contact with PHE 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E SER* 3.7 23.6 - - - -
99E CYS* 1.3 79.6 - - - +
101E ALA* 1.3 61.8 - - - +
102E LEU* 3.6 21.0 + - + +
108E TYR* 3.2 6.2 - - - -
109E LEU* 2.8 41.6 + - + +
111E GLN* 5.2 1.3 - - - -
69F GLN* 3.5 27.4 - - - -
71F PHE* 3.6 28.3 - + - -
111F GLN* 4.5 3.1 - - - -
142F VAL* 3.8 16.6 - - + -
144F LYS 3.5 3.4 - - - +
145F GLU* 3.6 36.3 - - + -
148F HIS* 4.1 22.7 - + + -
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LEU* 4.9 3.1 - - + -
83E ARG* 4.3 11.7 - - - +
100E PHE* 1.3 71.8 - - - +
102E LEU* 1.3 53.6 + - - +
107E ASP 3.2 10.5 - - - +
108E TYR* 3.8 24.2 - - + -
142F VAL* 3.6 5.0 - - - -
143F LEU* 2.7 40.9 + - + -
144F LYS* 2.9 29.4 + - + +
146F ILE* 4.5 1.7 - - + +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ARG* 4.5 10.8 - - - +
100E PHE* 3.8 22.7 - - + +
101E ALA* 1.3 79.1 - - - +
103E THR* 1.3 62.5 + - - +
104E GLY 3.3 3.5 + - - +
106E THR* 3.7 21.0 - - + +
107E ASP* 3.0 10.6 + - - +
109E LEU* 3.7 35.0 - - + +
71F PHE* 3.6 28.3 - - + -
73F ARG* 6.0 0.4 - - - +
140F SER* 4.3 18.8 - - - +
141F PHE 3.3 16.8 - - - +
142F VAL* 3.8 6.5 - - - -
143F LEU* 3.3 15.8 - - - +
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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