Contacts of the strand formed by residues 266 - 273 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C GLY 5.3 1.4 - - - -
222C GLN 2.9 9.1 + - - +
223C ASN* 3.5 22.5 + - - +
224C VAL 2.9 26.0 + - - -
265C ASN* 1.3 71.5 - - - +
267C VAL* 1.3 65.4 + - - +
268C VAL* 3.4 10.7 + - + +
305C LEU* 5.5 10.0 - - - +
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ARG* 4.7 2.1 - - - +
113C VAL* 4.1 20.7 - - + +
224C VAL* 3.4 10.1 - - + +
226C PHE* 3.7 36.1 - - + -
261C ALA 4.9 0.7 - - - +
262C ALA* 4.0 16.4 - - + +
265C ASN 3.6 6.4 + - - +
266C THR* 1.3 76.6 - - - +
268C VAL* 1.3 62.3 + - - +
269C GLY 3.8 22.9 - - - +
270C LEU* 5.4 0.9 - - + -
300C VAL* 3.8 34.9 - - + +
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Residues in contact with VAL 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG* 4.3 8.8 - - - +
112C ARG 4.5 4.5 - - - +
113C VAL* 5.0 0.7 - - - -
114C PRO* 3.2 17.3 - - - +
131C PHE* 3.2 37.1 - - + -
134C VAL* 4.6 9.0 - - + -
137C LEU* 4.1 11.9 - - + -
223C ASN* 4.2 22.0 - - + +
224C VAL 2.8 25.3 + - - +
225C TYR* 4.0 6.7 - - - +
266C THR* 3.8 16.2 - - + +
267C VAL* 1.3 76.4 - - - +
269C GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 4.3 5.4 - - - +
114C PRO* 3.5 19.1 - - - -
131C PHE* 4.5 0.7 - - - -
225C TYR* 3.6 13.1 - - - -
226C PHE 2.9 23.0 + - - -
267C VAL* 3.5 12.8 - - - +
268C VAL* 1.3 82.1 - - - +
270C LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 5.5 3.1 - - + -
114C PRO 3.1 8.7 + - - +
115C VAL* 3.4 23.3 - - + -
116C PHE* 2.8 28.9 + - - -
225C TYR* 4.5 3.3 - - - -
226C PHE* 3.1 28.0 - - + -
228C VAL* 4.6 11.7 - - + -
258C LEU* 5.1 0.7 - - + -
267C VAL* 5.4 1.1 - - + -
269C GLY* 1.3 76.5 - - - +
271C ASP* 1.3 80.6 + - - +
272C LEU* 4.2 3.4 - - + +
293C VAL* 4.5 19.3 - - + +
296C THR* 3.6 35.2 - - + +
297C LEU* 6.5 2.7 - - + -
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Residues in contact with ASP 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PHE* 3.1 18.8 - - + +
124C SER* 3.1 23.0 + - - -
127C LEU* 4.0 6.1 - - + -
225C TYR* 2.5 33.8 + - - +
226C PHE 2.8 7.5 + - - -
227C SER* 2.9 23.1 + - - -
228C VAL* 2.9 20.8 + - - +
270C LEU* 1.3 82.6 - - - +
272C LEU* 1.3 60.4 + - - +
273C VAL* 3.7 15.0 - - + +
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 4.0 21.0 - - + +
116C PHE 2.8 10.5 + - - +
117C LEU* 3.7 9.4 - - + -
118C GLY* 2.8 26.5 + - - +
228C VAL* 3.4 22.7 - - + +
230C VAL* 3.6 23.1 - - + -
270C LEU* 4.6 2.7 - - + -
271C ASP* 1.3 73.3 - - - +
273C VAL* 1.3 60.8 + - - +
275C LEU* 4.6 4.9 - - + -
289C MET* 3.0 38.1 - - + +
292C LEU* 4.5 2.5 - - + -
293C VAL* 4.1 28.0 - - + -
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLY* 4.3 3.8 - - - -
119C GLY 3.6 9.6 - - - +
120C ASP 4.2 4.7 - - - +
121C HIS* 3.6 35.0 - - + +
123C VAL* 3.8 27.8 - - + -
124C SER* 4.3 3.1 - - - +
228C VAL 2.9 16.3 + - - +
229C ASP* 3.8 9.4 - - - -
230C VAL* 3.0 29.7 + - - +
271C ASP* 3.7 20.9 - - + +
272C LEU* 1.3 80.6 - - - +
274C GLU* 1.3 65.6 + - + +
275C LEU 3.4 3.4 - - - -
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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