Contacts of the strand formed by residues 223 - 229 (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 ASN 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C VAL* 3.5 25.3 - - + +
135C PRO* 3.0 40.4 + - - +
136C ASP* 4.3 4.7 + - - +
137C LEU* 3.7 3.9 - - - +
138C HIS* 2.8 29.6 + - - +
222C GLN* 1.3 72.2 - - - +
224C VAL* 1.3 59.3 + - - +
266C THR* 3.5 25.0 - - - +
268C VAL* 4.2 7.8 - - + +
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Residues in contact with VAL 224 (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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138C HIS* 3.2 10.1 - - + +
140C VAL* 3.6 25.4 - - + -
219C PRO* 3.9 16.2 - - + -
222C GLN* 3.9 1.8 - - + +
223C ASN* 1.3 77.4 - - - +
225C TYR* 1.3 67.4 + - - +
226C PHE* 3.7 22.0 - - + -
261C ALA* 5.2 0.4 - - + -
265C ASN* 3.5 38.8 - - + +
266C THR 2.9 11.3 + - - +
267C VAL* 3.4 10.5 - - + +
268C VAL* 2.8 30.5 + - - +
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Residues in contact with TYR 225 (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* 3.9 9.3 - + - -
124C SER* 4.8 0.4 - - - -
127C LEU* 3.7 18.8 - - + +
128C LEU* 3.6 33.3 - - + +
131C PHE* 3.8 39.7 - + - -
137C LEU* 4.1 9.2 - - + +
138C HIS 2.9 11.1 + - - +
139C VAL* 3.3 16.1 - - + +
140C VAL 3.0 24.4 + - - +
224C VAL* 1.3 73.9 - - - +
226C PHE* 1.3 70.4 + - - +
227C SER* 4.1 5.8 - - - -
268C VAL* 4.0 8.7 - - + -
269C GLY 3.6 14.1 - - - -
271C ASP* 2.5 41.2 + - + +
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Residues in contact with PHE 226 (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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140C VAL* 3.6 19.7 - - + -
224C VAL* 3.7 13.9 - - + -
225C TYR* 1.3 77.7 - - - +
227C SER* 1.3 60.7 + - - +
228C VAL* 4.1 1.6 - - + -
258C LEU* 3.7 33.4 - - + -
261C ALA* 3.5 34.1 - - + -
262C ALA* 3.8 8.3 - - + -
267C VAL* 3.7 38.1 - - + -
269C GLY 2.9 8.8 + - - +
270C LEU* 3.1 32.4 - - + -
271C ASP 2.8 24.7 + - - -
296C THR* 4.2 16.6 - - + -
300C VAL* 4.5 0.2 - - + -
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Residues in contact with SER 227 (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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121C HIS* 3.0 26.5 + - - -
139C VAL* 4.4 2.7 - - - -
140C VAL 3.0 11.7 + - - +
141C GLN* 3.4 4.2 - - - +
142C LEU 3.0 27.0 + - - +
163C PHE* 3.5 20.6 - - - -
225C TYR* 3.9 8.0 + - - -
226C PHE* 1.3 73.7 - - - +
228C VAL* 1.3 60.2 + - - +
271C ASP* 2.9 24.4 + - - -
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Residues in contact with VAL 228 (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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142C LEU* 4.0 15.0 - - + -
226C PHE* 4.9 0.2 - - + -
227C SER* 1.3 77.2 - - - +
229C ASP* 1.3 63.4 + - - +
230C VAL 3.6 0.7 + - - -
233C PHE* 3.9 17.7 - - + -
258C LEU* 4.1 31.0 - - + -
270C LEU* 4.6 12.3 - - + -
271C ASP* 2.9 17.6 + - - +
272C LEU* 3.4 22.6 - - + +
273C VAL* 2.9 29.8 + - - +
289C MET* 4.1 1.1 - - + -
292C LEU* 3.9 17.5 - - + -
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Residues in contact with ASP 229 (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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121C HIS* 3.1 21.2 + - + +
142C LEU* 2.9 22.9 + - - +
143C ASP* 3.0 24.8 - - - +
145C HIS* 5.2 0.5 + - - -
147C ASP* 4.0 2.3 - - - +
227C SER 3.9 1.2 + - - -
228C VAL* 1.3 74.8 - - - +
230C VAL* 1.3 66.7 + - - +
231C ASP* 2.9 35.3 + - - +
232C GLY* 2.9 15.4 + - - -
233C PHE* 4.5 1.6 + - - -
273C VAL* 3.5 6.9 - - - +
274C GLU* 3.3 25.5 - - - +
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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