Contacts of the strand formed by residues 192 - 202 (chain B) in PDB entry 2WHR
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 GLY 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B PRO* 4.4 3.4 - - - +
112B THR 3.3 8.3 - - - -
114B VAL* 4.0 7.9 - - - -
145B VAL* 3.8 12.7 - - - +
187B ILE* 3.0 18.6 + - - -
188B ALA* 3.3 14.9 - - - +
190B PHE 3.4 1.8 - - - -
191B GLY* 1.3 81.5 - - - +
193B ASP* 1.3 60.2 + - - -
194B PRO* 3.3 11.4 - - - +
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PRO* 3.7 30.7 - - - +
112B THR 2.6 21.5 + - - +
113B PRO* 4.2 4.0 - - + +
114B VAL* 3.7 8.0 - - - +
192B GLY* 1.3 71.4 - - - -
194B PRO* 1.3 69.9 - - - +
195B MET* 2.9 33.9 + - - +
196B SER* 2.9 34.6 + - - +
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Residues in contact with PRO 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PRO* 5.6 1.8 - - + -
184B GLN* 3.1 55.2 + - - +
187B ILE* 3.8 19.5 - - + -
188B ALA* 4.4 15.3 - - + -
192B GLY 3.3 9.8 - - - +
193B ASP* 1.3 90.5 - - - +
195B MET* 1.3 61.1 + - + +
196B SER 3.3 0.9 - - - -
197B VAL* 3.4 4.5 - - + +
223B HIS* 3.0 15.8 + - - -
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Residues in contact with MET 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ASP* 2.9 20.1 + - - +
194B PRO* 1.3 82.4 - - + +
196B SER* 1.3 60.1 + - - +
223B HIS* 2.9 28.8 + - + -
224B ARG* 5.2 1.0 + - - -
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PRO* 3.6 21.6 - - - +
114B VAL 2.9 25.3 + - - +
193B ASP* 2.9 24.3 + - - +
195B MET* 1.3 80.2 - - - +
197B VAL* 1.3 60.5 + - - +
198B THR* 4.2 0.7 - - - -
223B HIS* 3.4 2.5 - - - -
224B ARG* 3.0 24.0 + - - +
484B ALA 3.4 9.4 + - - -
485B ARG 4.7 2.1 + - - -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 3.5 12.3 - - + +
116B ILE* 3.6 34.1 - - + -
183B VAL* 4.5 7.0 - - + -
184B GLN* 3.6 13.5 - - - +
193B ASP 3.9 2.9 - - - +
194B PRO* 3.4 27.8 - - + +
196B SER* 1.3 75.9 - - - +
198B THR* 1.3 65.3 + - - +
199B LEU* 4.4 3.1 - - + -
221B LEU 3.9 17.3 - - - +
222B PHE* 3.7 7.4 - - + +
223B HIS* 2.7 43.1 + - + +
224B ARG* 3.3 5.1 + - - -
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Residues in contact with THR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL 2.9 11.8 + - - -
115B LEU* 3.4 9.3 - - + +
116B ILE* 2.8 26.5 + - - +
196B SER* 5.1 0.7 + - - -
197B VAL* 1.3 75.9 - - - +
199B LEU* 1.3 73.4 + - - +
200B PHE* 3.8 2.5 + - + +
224B ARG* 3.4 26.4 + - + +
226B VAL* 4.0 19.3 - - + -
480B TRP 5.7 0.7 - - - +
483B PHE* 4.1 7.9 - - + -
484B ALA* 3.3 37.1 + - + +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 3.5 30.1 - - + +
118B ILE* 4.9 4.5 - - + -
180B LEU* 4.0 24.9 - - + -
197B VAL* 4.4 0.7 - - + -
198B THR* 1.3 75.4 - - - +
200B PHE* 1.3 54.6 + - - +
209B VAL* 3.8 26.2 - - + -
212B HIS* 4.1 22.0 - - + -
222B PHE* 3.6 50.3 - - + -
224B ARG 3.0 9.1 + - - +
225B ALA* 3.2 1.9 - - - -
226B VAL 2.7 31.9 + - - +
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Residues in contact with PHE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 3.8 30.3 - - + -
116B ILE 2.9 19.5 + - - +
117B TRP* 3.2 51.1 - + + -
118B ILE* 2.9 23.1 + - - +
138B LEU* 4.7 3.1 - - + -
146B LEU* 4.3 14.6 - - + -
198B THR* 4.4 1.8 - - + -
199B LEU* 1.3 75.2 - - - +
201B GLY* 1.3 57.7 + - - +
209B VAL* 4.1 4.5 - - - -
226B VAL* 3.3 30.5 - - + -
228B GLN* 3.7 13.9 - - - +
454B ILE* 4.4 8.1 - - + -
455B PHE* 3.7 22.9 - + - -
480B TRP* 3.8 18.4 - + - -
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Residues in contact with GLY 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TRP* 3.6 10.2 - - - -
118B ILE 3.3 16.4 - - - -
200B PHE* 1.3 76.9 - - - +
202B GLU* 1.3 60.0 + - - -
205B GLY 3.9 9.0 - - - -
206B ALA* 3.4 10.6 - - - +
209B VAL* 4.0 1.0 - - - +
226B VAL 3.2 6.7 + - - +
228B GLN* 2.9 28.6 + - - +
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B TRP* 5.6 1.7 - - - -
117B TRP* 3.6 22.6 - - + -
118B ILE 3.7 2.8 + - - -
120B GLY* 3.3 14.2 + - - -
133B TYR* 5.3 1.4 + - - -
201B GLY* 1.3 73.9 - - - +
203B SER* 1.3 76.9 + - - +
204B ALA 3.2 0.3 + - - -
205B GLY 2.9 15.6 + - - -
206B ALA 3.4 3.0 - - - +
228B GLN* 3.0 13.0 - - - +
229B SER* 4.1 2.1 - - - -
447B HIS* 3.5 19.1 + - - -
448B GLY* 3.3 25.3 + - - -
450B GLU* 3.4 22.7 - - - +
451B ILE* 3.7 21.8 - - + +
1545B K27 5.3 0.2 + - - -
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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