Contacts of the strand formed by residues 266 - 273 (chain E) in PDB entry 1WOH
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 THR 266 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221E GLY 5.2 2.0 - - - -
222E GLN 2.9 11.3 + - - +
223E ASN* 3.4 23.2 - - - +
224E VAL 2.9 25.5 + - - -
265E ASN* 1.3 71.7 - - - +
267E VAL* 1.3 63.2 + - - +
268E VAL* 3.5 10.1 + - + +
305E LEU* 4.9 15.7 - - - +
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Residues in contact with VAL 267 (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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112E ARG* 4.7 2.1 - - - +
113E VAL* 3.8 23.1 - - + +
224E VAL* 3.4 9.2 - - + +
226E PHE* 3.8 31.2 - - + -
261E ALA 4.8 1.1 - - - +
262E ALA* 4.0 17.0 - - - +
265E ASN* 3.5 8.4 + - + +
266E THR* 1.3 74.6 - - - +
268E VAL* 1.3 64.4 + - - +
269E GLY 3.7 22.7 - - - +
270E LEU* 5.4 0.7 - - + -
300E VAL* 3.8 37.6 - - + +
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Residues in contact with VAL 268 (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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108E ARG* 4.2 8.5 + - - +
112E ARG 4.5 5.0 - - - +
113E VAL* 5.0 0.2 - - - -
114E PRO* 3.0 19.8 - - - +
131E PHE* 3.2 36.6 - - + -
134E VAL* 4.6 8.7 - - + -
137E LEU* 4.1 12.3 - - + -
223E ASN* 4.1 23.6 - - + +
224E VAL 2.8 24.9 + - - +
225E TYR* 4.1 4.7 - - + -
266E THR* 3.8 16.4 - - + +
267E VAL* 1.3 76.0 - - - +
269E GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 269 (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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113E VAL* 4.4 4.9 - - - +
114E PRO* 3.4 20.4 - - - -
131E PHE* 4.5 0.4 - - - -
225E TYR* 3.6 13.5 - - - -
226E PHE 3.0 21.6 + - - -
267E VAL* 3.5 12.6 - - - +
268E VAL* 1.3 82.3 - - - +
270E LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 270 (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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113E VAL* 5.7 2.7 - - + -
114E PRO 3.1 7.7 + - - +
115E VAL* 3.4 21.1 - - + -
116E PHE* 2.8 28.2 + - - -
225E TYR* 4.3 4.3 - - - -
226E PHE* 3.0 34.1 - - + +
228E VAL* 4.6 12.1 - - + -
258E LEU* 5.0 0.9 - - + -
267E VAL* 5.4 1.1 - - + -
269E GLY* 1.3 75.7 - - - +
271E ASP* 1.3 78.6 + - - +
272E LEU* 4.2 2.9 - - + +
293E VAL* 4.5 19.5 - - + -
296E THR* 3.6 34.3 - - + +
297E LEU* 6.3 3.6 - - + -
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Residues in contact with ASP 271 (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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116E PHE* 3.2 20.0 - - + +
124E SER* 3.0 22.8 + - - -
127E LEU* 4.0 5.8 - - + -
225E TYR* 2.7 34.9 + - - +
226E PHE 2.8 7.5 + - - +
227E SER* 2.9 23.5 + - - -
228E VAL* 2.9 19.4 + - - +
270E LEU* 1.3 82.3 - - - +
272E LEU* 1.3 60.2 + - - +
273E VAL* 3.9 16.2 - - + +
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Residues in contact with LEU 272 (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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55E LEU* 4.0 24.6 - - + +
116E PHE 2.9 10.5 + - - +
117E LEU* 3.9 3.6 - - + -
118E GLY* 2.9 24.4 + - - +
228E VAL* 3.4 32.5 - - + +
230E VAL* 3.5 23.8 - - + -
270E LEU* 4.6 2.2 - - + -
271E ASP* 1.3 72.8 - - - +
273E VAL* 1.3 61.8 + - - +
275E LEU* 4.5 5.6 - - + +
289E MET* 4.3 25.4 - - + +
292E LEU* 4.5 5.4 - - + -
293E VAL* 4.1 28.7 - - + -
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Residues in contact with VAL 273 (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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118E GLY* 4.1 4.0 - - - +
119E GLY 3.4 10.3 - - - +
120E ASP 4.1 0.2 - - - +
121E HIS* 3.6 39.3 - - + +
123E VAL* 3.6 30.7 - - + -
124E SER* 4.3 2.7 - - - +
228E VAL 3.0 12.1 + - - +
229E ASP* 3.8 7.9 - - - -
230E VAL* 3.0 25.4 + - - +
271E ASP* 3.9 19.7 - - + +
272E LEU* 1.3 79.7 - - - +
274E GLU* 1.3 70.4 + - + +
275E LEU 3.3 4.7 + - - +
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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