Contacts of the strand formed by residues 198 - 208 (chain B) in PDB entry 1WZN
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 VAL 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A GLY 4.3 1.4 - - - +
197A GLU* 4.3 10.9 - - - +
198A VAL* 4.0 26.1 - - + +
190B GLN* 4.3 17.0 - - + +
191B ILE 3.5 7.0 - - - +
192B LEU* 4.1 16.4 - - + -
193B ARG* 6.3 0.2 - - - -
196B GLY 3.3 17.5 + - - +
197B GLU* 1.3 79.7 + - - +
199B LYS* 1.3 91.0 + - - +
200B ALA* 4.8 0.4 - - + -
198C VAL* 4.6 11.7 + - + +
199C LYS* 4.5 2.9 - - - -
200C ALA* 3.4 28.7 - - + +
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Residues in contact with LYS 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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195A ASN* 3.3 26.6 + - - +
196A GLY 3.2 9.2 - - - +
197A GLU* 2.7 31.7 + - - +
166B GLU* 6.2 0.2 - - - +
189B VAL 3.8 0.7 - - - +
190B GLN* 3.5 1.6 - - - -
191B ILE* 2.7 47.1 + - + +
193B ARG* 6.3 6.7 - - + +
198B VAL* 1.3 80.8 - - - +
200B ALA* 1.3 59.6 + - - +
201B PHE* 4.2 17.9 - - + -
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Residues in contact with ALA 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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190A GLN* 5.5 1.8 - - - +
192A LEU* 3.5 34.9 - - + +
193A ARG 4.7 0.9 - - - +
196A GLY* 2.8 26.1 + - - +
198A VAL* 4.5 13.2 - - + +
188B LEU* 4.3 4.9 - - + -
189B VAL 3.2 8.5 - - - +
190B GLN* 4.1 18.2 - - + +
198B VAL* 4.8 0.9 - - + -
199B LYS* 1.3 76.4 - - - +
201B PHE* 1.3 63.9 + - - +
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Residues in contact with PHE 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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192A LEU* 3.9 5.6 - - - -
193A ARG 5.4 0.9 - - - -
194A PRO 3.8 11.0 - - - -
195A ASN* 3.7 8.7 - - - -
196A GLY* 3.6 33.9 - - - -
3B GLU* 5.7 3.4 - - + -
7B LEU* 4.1 37.0 - - + -
8B LEU* 3.8 37.4 - - + +
11B TYR* 6.0 0.7 - + - -
187B ARG 3.6 1.4 - - - +
188B LEU* 3.6 2.1 - - - +
189B VAL* 2.9 35.3 + - - +
191B ILE* 4.0 22.4 - - + -
199B LYS* 4.2 14.8 - - + -
200B ALA* 1.3 77.4 - - - +
202B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 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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160A ASN* 3.7 33.4 - - + +
167A LYS* 4.4 32.6 + - + +
169A VAL* 4.2 12.3 - - + -
192A LEU* 3.9 16.5 - - + +
3B GLU* 3.1 24.8 - - - +
173B TRP* 3.8 30.1 - - + -
186B LYS* 4.7 1.3 - - + -
187B ARG 3.5 9.0 - - - +
188B LEU* 4.5 2.5 - - + +
201B PHE* 1.3 73.7 - - - +
203B VAL* 1.3 79.9 + - - +
204B ASP* 3.9 8.4 + - + +
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Residues in contact with VAL 203 (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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3B GLU* 3.7 7.6 - - + +
4B LEU* 4.0 28.7 - - + +
8B LEU* 3.9 28.7 - - + -
185B PHE* 4.3 19.3 - - + -
186B LYS* 3.3 5.2 - - - -
187B ARG* 2.7 54.1 + - + +
202B LEU* 1.3 77.9 - - - +
204B ASP* 1.3 63.6 + - - +
205B ASP* 3.5 23.8 - - - +
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Residues in contact with ASP 204 (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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160A ASN* 4.4 7.7 + - - -
1B MET* 3.5 21.1 + - - +
3B GLU* 3.2 12.0 + - - +
184B ARG* 2.8 34.3 + - - +
185B PHE 3.5 4.2 - - - +
186B LYS* 3.2 32.1 + - + +
202B LEU* 4.5 13.9 - - + +
203B VAL* 1.3 77.3 - - - +
205B ASP* 1.3 61.7 + - - +
206B GLU 4.3 0.3 + - - -
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Residues in contact with ASP 205 (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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1B MET* 3.2 11.7 - - + +
2B TYR* 2.8 31.2 + - - -
3B GLU* 3.9 1.0 - - - +
4B LEU* 5.2 2.1 - - - +
5B TYR* 4.6 4.0 + - - -
118B TYR* 2.8 39.9 + - + +
184B ARG* 3.6 6.4 + - - -
185B PHE* 3.0 41.7 + - + +
203B VAL* 3.5 19.7 - - - +
204B ASP* 1.3 74.8 - - - +
206B GLU* 1.3 61.6 + - - +
207B LEU* 3.6 8.1 + - + -
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Residues in contact with GLU 206 (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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1B MET* 5.4 2.6 - - - +
117B MET 4.4 1.7 - - - +
118B TYR* 4.6 9.7 - - - +
182B LYS* 3.1 45.5 + - + +
183B LEU 3.6 2.9 - - - +
184B ARG* 3.2 35.1 + - - +
205B ASP* 1.3 73.0 - - - +
207B LEU* 1.3 67.9 + - - +
208B ASN* 4.7 4.0 + - - -
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Residues in contact with LEU 207 (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 MET* 3.3 43.1 - - + +
118B TYR* 3.9 38.8 - - + +
182B LYS* 3.4 11.4 - - - +
183B LEU* 2.7 45.7 + - + +
185B PHE* 4.0 25.4 - - + -
205B ASP* 4.3 10.3 - - + +
206B GLU* 1.3 84.6 - - - +
208B ASN* 1.3 63.8 + - - +
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Residues in contact with ASN 208 (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 MET* 2.7 57.2 + - - +
118B TYR 3.7 4.2 + - - -
119B PHE 3.2 36.6 + - - +
120B ASP* 3.5 10.3 - - - +
181B GLN 3.5 4.9 - - - +
182B LYS* 2.7 34.5 + - - +
206B GLU* 4.7 3.2 + - - -
207B LEU* 1.3 78.6 - - - +
209B ILE* 1.3 62.7 + - - +
210B TYR* 3.7 15.3 + - + +
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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