Contacts of the strand formed by residues 223 - 229 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A VAL* 3.5 25.7 - - + +
135A PRO* 3.0 42.4 + - - +
136A ASP 4.6 2.6 + - - +
137A LEU* 3.9 2.4 - - - +
138A HIS* 2.9 28.4 + - - +
222A GLN* 1.3 73.0 + - - +
224A VAL* 1.3 59.6 + - - +
266A THR* 3.3 25.9 + - - +
268A VAL* 4.1 7.0 - - + +
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A HIS* 3.4 12.3 - - + +
140A VAL* 3.6 24.9 - - + -
219A PRO* 3.9 16.4 - - + -
222A GLN* 4.0 1.8 - - + +
223A ASN* 1.3 78.2 - - - +
225A TYR* 1.3 71.0 + - - +
226A PHE* 3.9 17.5 - - + -
261A ALA* 5.3 0.7 - - + -
265A ASN* 3.7 35.7 - - + +
266A THR 2.8 12.2 + - - +
267A VAL* 3.3 10.7 - - + +
268A VAL* 2.8 31.5 + - - +
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Residues in contact with TYR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 3.7 9.7 - + - -
124A SER* 4.8 0.4 - - - -
127A LEU* 3.7 17.3 - - + +
128A LEU* 3.7 32.0 - - + +
131A PHE* 3.8 39.5 - + - -
137A LEU* 4.1 8.5 - - + +
138A HIS 2.9 12.4 + - - +
139A VAL* 3.3 15.3 - - + -
140A VAL 2.9 24.1 + - - +
224A VAL* 1.3 75.2 - - - +
226A PHE* 1.3 73.4 + - - +
227A SER* 4.1 6.5 - - - -
268A VAL* 4.0 7.2 - - + -
269A GLY 3.6 13.7 - - - -
271A ASP* 2.7 43.1 + - + +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 3.5 20.2 - - + -
224A VAL* 3.9 12.3 - - + -
225A TYR* 1.3 76.0 - - - +
227A SER* 1.3 61.4 + - - +
228A VAL* 4.0 1.8 - - + -
258A LEU* 3.7 34.3 - - + -
261A ALA* 3.4 35.7 - - + -
262A ALA* 3.8 12.3 - - + -
267A VAL* 3.6 39.9 - - + -
269A GLY 2.9 10.1 + - - +
270A LEU* 3.1 27.4 - - + -
271A ASP 2.9 25.3 + - - -
296A THR* 4.3 13.9 - - + -
300A VAL* 4.4 0.4 - - + -
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Residues in contact with SER 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A HIS* 3.0 26.5 + - - -
139A VAL* 4.3 3.8 - - - -
140A VAL 3.0 10.3 + - - +
141A GLN* 3.4 3.4 - - - +
142A LEU 2.9 27.4 + - - +
163A PHE* 3.6 21.5 - - - -
225A TYR* 3.9 7.5 + - - -
226A PHE* 1.3 73.7 - - - +
228A VAL* 1.3 59.6 + - - +
271A ASP* 2.8 26.0 + - - -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.1 12.6 - - + -
227A SER* 1.3 77.7 - - - +
229A ASP* 1.3 63.9 + - - +
230A VAL 3.7 0.7 + - - -
233A PHE* 4.0 17.5 - - + -
258A LEU* 4.2 32.8 - - + -
270A LEU* 4.6 13.2 - - + -
271A ASP* 2.9 18.4 + - - +
272A LEU* 3.5 20.9 - - + +
273A VAL* 2.9 28.9 + - - -
289A MET* 4.3 1.1 - - + -
292A LEU* 3.9 18.4 - - + -
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A HIS* 3.3 21.1 + - + +
142A LEU* 3.0 21.7 + - - +
143A ASP* 3.0 24.8 - - - +
145A HIS* 4.9 0.5 + - - -
147A ASP* 4.0 2.6 - - - +
227A SER 3.9 0.8 + - - -
228A VAL* 1.3 75.9 - - - +
230A VAL* 1.3 65.6 + - - +
231A ASP* 2.9 35.6 + - - +
232A GLY* 2.9 14.6 + - - -
233A PHE* 4.5 1.9 + - - -
273A VAL* 3.6 6.3 - - - -
274A GLU* 3.3 26.4 - - - +
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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