Contacts of the strand formed by residues 266 - 273 (chain F) in PDB entry 1WOI
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221F GLY 5.3 1.3 - - - -
222F GLN 2.9 12.0 + - - +
223F ASN* 3.4 23.6 + - - +
224F VAL 2.8 26.7 + - - -
265F ASN* 1.3 71.1 - - - +
267F VAL* 1.3 63.5 + - - +
268F VAL* 3.4 11.6 + - + +
304F VAL* 6.6 0.2 - - + -
305F LEU* 4.4 20.2 - - - +
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Residues in contact with VAL 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ARG 4.6 1.6 - - - +
113F VAL* 3.9 24.5 - - + +
224F VAL* 3.3 9.4 - - + +
226F PHE* 3.7 42.6 - - + -
261F ALA 4.9 1.1 - - - +
262F ALA* 3.9 20.6 - - - +
265F ASN 3.5 7.4 + - - +
266F THR* 1.3 73.9 - - - +
268F VAL* 1.3 62.6 + - - +
269F GLY 3.9 15.7 - - - +
270F LEU* 5.5 1.1 - - + -
296F THR* 6.0 0.2 - - + -
300F VAL* 4.0 28.8 - - + +
304F VAL* 6.2 1.6 - - - +
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Residues in contact with VAL 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ARG* 4.4 6.8 - - - +
112F ARG 4.6 4.0 - - - +
113F VAL* 4.9 0.9 - - - -
114F PRO* 3.1 21.2 - - - +
131F PHE* 3.2 33.4 - - + -
134F VAL* 4.3 12.6 - - + -
137F LEU* 3.9 15.3 - - + -
223F ASN* 4.2 17.9 - - + +
224F VAL 2.9 24.4 + - - +
225F TYR* 4.0 5.6 - - + -
266F THR* 3.9 19.3 - - + +
267F VAL* 1.3 76.5 - - - +
269F GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F VAL* 4.3 4.5 - - - +
114F PRO* 3.5 19.7 - - - -
131F PHE* 4.6 0.7 - - - -
225F TYR* 3.6 14.2 - - - -
226F PHE* 2.9 24.6 + - - +
267F VAL* 3.5 11.5 - - - +
268F VAL* 1.3 83.0 - - - +
270F LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F VAL* 5.6 2.7 - - + -
114F PRO 3.1 9.3 + - - +
115F VAL* 3.4 24.3 - - + -
116F PHE* 2.8 29.5 + - - -
225F TYR* 4.4 3.3 - - - -
226F PHE* 3.2 26.5 - - + -
228F VAL* 4.6 12.1 - - + -
258F LEU* 5.2 0.9 - - + -
267F VAL* 5.5 1.3 - - + -
269F GLY* 1.3 75.7 - - - +
271F ASP* 1.3 80.0 + - - +
272F LEU* 4.1 3.1 - - + +
293F VAL* 4.4 22.0 - - + +
296F THR* 3.7 34.8 - - + +
297F LEU* 6.4 2.9 - - + -
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Residues in contact with ASP 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F PHE* 3.1 19.1 - - + +
124F SER* 2.6 27.7 + - - -
127F LEU* 4.1 5.2 - - + -
225F TYR* 2.7 32.2 + - - +
226F PHE 3.0 7.9 + - - -
227F SER* 2.8 24.1 + - - -
228F VAL* 2.9 19.8 + - - +
270F LEU* 1.3 83.1 - - - +
272F LEU* 1.3 59.9 + - - +
273F VAL* 3.8 14.3 - - + +
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Residues in contact with LEU 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 3.8 22.8 - - + +
116F PHE 2.9 9.8 + - - +
117F LEU* 3.8 7.7 - - + -
118F GLY* 2.8 28.3 + - - +
228F VAL* 3.5 21.3 - - + +
230F VAL* 3.8 20.0 - - + -
270F LEU* 4.5 2.5 - - + -
271F ASP* 1.3 74.0 - - - +
273F VAL* 1.3 58.5 + - - +
275F LEU* 4.4 6.9 - - + +
289F MET* 3.0 39.9 - - + +
292F LEU* 4.6 3.1 - - + -
293F VAL* 4.0 29.6 - - + -
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Residues in contact with VAL 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F GLY* 4.3 2.9 - - - -
119F GLY 3.5 9.4 - - - +
120F ASP 4.2 0.9 - - - +
121F HIS* 3.6 41.7 - - + +
123F VAL* 3.8 28.5 - - + -
124F SER* 4.2 3.6 - - - +
228F VAL 2.9 10.8 + - - +
229F ASP* 3.7 15.0 - - + +
230F VAL* 3.0 29.0 + - - +
271F ASP* 3.8 19.1 - - + +
272F LEU* 1.3 81.0 - - - +
274F GLU* 1.3 62.6 + - + +
275F LEU 3.2 7.4 + - - +
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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