Contacts of the strand formed by residues 266 - 273 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221D GLY 5.7 1.6 - - - -
222D GLN 2.9 15.0 + - - +
223D ASN* 3.5 19.4 + - - +
224D VAL 2.9 23.5 + - - -
265D ASN* 1.3 71.2 - - - +
267D VAL* 1.3 65.0 + - - +
268D VAL* 3.3 9.5 + - + +
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Residues in contact with VAL 267 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D ARG* 4.8 2.1 - - - +
113D VAL* 3.9 23.6 - - + +
224D VAL* 3.4 10.5 - - + +
226D PHE* 3.7 35.0 - - + -
261D ALA 4.8 0.9 - - - +
262D ALA* 4.0 16.4 - - - +
265D ASN 3.5 7.9 + - - +
266D THR* 1.3 74.5 - - - +
268D VAL* 1.3 61.9 + - - +
269D GLY 3.8 21.5 - - - +
270D LEU* 5.5 0.9 - - + -
300D VAL* 3.9 32.8 - - + +
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Residues in contact with VAL 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ARG* 4.4 6.1 - - - +
112D ARG 4.4 5.3 - - - +
113D VAL* 5.0 0.4 - - - -
114D PRO* 3.3 17.9 - - - +
131D PHE* 3.3 38.6 - - + -
134D VAL* 4.4 10.8 - - + -
137D LEU* 4.2 9.6 - - + -
223D ASN* 4.2 20.9 - - + +
224D VAL 2.8 21.9 + - - +
225D TYR* 4.1 9.2 - - + -
266D THR* 3.5 20.6 - - + +
267D VAL* 1.3 74.2 - - - +
269D GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 4.4 5.1 - - - +
114D PRO* 3.5 20.0 - - - -
131D PHE* 4.6 1.6 - - - -
225D TYR* 3.5 13.6 - - - -
226D PHE* 2.9 24.3 + - - +
267D VAL* 3.5 11.3 - - - +
268D VAL* 1.3 81.0 - - - +
270D LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 5.7 2.7 - - + -
114D PRO 3.1 8.3 + - - +
115D VAL* 3.4 25.5 - - + -
116D PHE* 2.8 29.4 + - - -
225D TYR* 4.4 3.9 - - - -
226D PHE* 3.0 32.1 - - + +
228D VAL* 4.4 13.0 - - + -
258D LEU* 5.1 0.9 - - + -
267D VAL* 5.5 1.3 - - + -
269D GLY* 1.3 75.7 - - - +
271D ASP* 1.3 78.0 + - - +
272D LEU* 4.2 2.9 - - + +
293D VAL* 4.5 19.5 - - + -
296D THR* 3.9 30.7 - - + +
297D LEU* 6.3 3.6 - - + -
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Residues in contact with ASP 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D PHE* 3.2 19.3 - - + +
124D SER* 2.9 25.7 + - - -
127D LEU* 4.0 6.3 - - + -
225D TYR* 2.6 32.9 + - - +
226D PHE 2.9 7.5 + - - -
227D SER* 2.9 23.9 + - - -
228D VAL* 2.8 20.1 + - - +
270D LEU* 1.3 82.5 - - - +
272D LEU* 1.3 60.9 + - - +
273D VAL* 3.9 14.1 - - + +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.0 20.9 - - + -
116D PHE 2.9 9.7 + - - +
117D LEU* 3.8 9.6 - - + -
118D GLY* 2.8 26.7 + - - +
228D VAL* 3.4 32.3 - - + +
230D VAL* 3.6 26.5 - - + -
270D LEU* 4.7 2.2 - - + -
271D ASP* 1.3 73.1 - - - +
273D VAL* 1.3 61.4 + - - +
275D LEU* 4.5 6.1 - - + -
289D MET* 4.3 20.4 - - + +
292D LEU* 4.5 4.7 - - + -
293D VAL* 4.1 28.7 - - + -
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Residues in contact with VAL 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D GLY* 4.1 4.7 - - - +
119D GLY 3.4 10.3 - - - +
120D ASP 4.0 4.5 - - - +
121D HIS* 3.6 38.6 - - + +
123D VAL* 3.7 29.8 - - + -
124D SER* 4.3 2.5 - - - +
228D VAL 2.9 15.8 + - - +
229D ASP* 3.9 5.4 - - - -
230D VAL* 3.1 23.6 + - - +
271D ASP* 3.9 18.8 - - + +
272D LEU* 1.3 79.9 - - - +
274D GLU* 1.3 72.1 + - + +
275D LEU 3.3 4.2 + - - -
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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