Contacts of the strand formed by residues 179 - 182 (chain E) in PDB entry 1O94
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 179 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E VAL* 3.3 22.2 - - + +
118E ALA* 5.2 2.5 - - + -
131E GLY* 3.4 32.3 - - - +
132E ILE* 5.0 1.9 - - + +
134E VAL* 4.2 4.0 - - + -
135E ALA* 3.9 30.7 - - + +
138E LEU* 3.9 12.6 - - + -
140E TRP* 3.8 21.8 - - + -
141E PRO 3.0 5.9 + - - -
142E HIS* 3.2 23.9 - - - +
143E ALA 3.3 4.3 + - - +
178E ALA* 1.3 71.9 - - - +
180E LEU* 1.3 70.1 + - - +
181E THR* 5.0 1.6 - - + -
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Residues in contact with LEU 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E MET* 4.2 13.5 - - + -
116E VAL 3.0 6.6 + - - +
117E PHE* 3.5 27.1 - - + -
118E ALA* 3.0 24.9 + - - +
143E ALA* 3.5 13.5 - - + -
146E VAL* 4.1 5.8 - - + -
149E LEU* 3.6 33.4 - - + -
158E ALA* 5.7 0.2 - - + -
160E ILE* 4.1 18.8 - - + -
174E ILE* 3.9 26.0 - - + -
178E ALA* 4.5 3.6 - - + -
179E VAL* 1.3 83.1 - - - +
181E THR* 1.3 64.4 + - - +
182E ILE* 4.0 16.4 + - + +
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Residues in contact with THR 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ALA* 3.1 7.4 - - + +
119E GLY 3.7 14.8 - - - +
120E VAL* 3.7 11.5 + - - +
131E GLY* 4.2 20.6 - - - +
132E ILE* 4.0 29.4 - - + +
143E ALA 3.2 6.5 + - - -
144E ALA* 3.2 8.7 - - - +
145E VAL* 3.0 22.7 + - - +
146E VAL* 2.9 28.1 + - - +
179E VAL* 5.0 0.9 - - + -
180E LEU* 1.3 77.2 - - - +
182E ILE* 1.3 61.5 + - - +
100F LEU* 5.9 0.3 - - - +
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Residues in contact with ILE 182 (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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38E TRP* 3.3 12.8 - - - +
41E PHE* 4.2 2.7 - - + +
42E SER* 3.7 41.1 - - - +
45E GLU* 5.1 4.9 - - + -
117E PHE* 4.2 21.1 - - + -
118E ALA 2.7 15.2 + - - +
119E GLY* 4.0 1.8 - - - -
120E VAL* 3.1 18.9 + - - +
146E VAL* 3.9 18.8 - - + +
149E LEU* 5.2 0.9 - - + -
180E LEU* 4.1 23.1 - - + +
181E THR* 1.3 77.6 - - - +
183E GLN* 1.3 62.6 + - - +
186E ILE* 3.6 36.8 - - + -
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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