Contacts of the strand formed by residues 198 - 208 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A VAL* 4.6 17.4 + - + +
199A LYS* 4.4 3.8 - - - -
200A ALA* 3.4 28.7 - - + +
196B GLY 4.1 3.5 - - - +
197B GLU* 4.7 7.3 - - - +
198B VAL* 4.6 13.1 + - + +
190C GLN* 4.3 17.0 - - + +
191C ILE 3.4 8.7 - - - +
192C LEU* 4.0 15.3 - - + -
193C ARG* 6.1 0.7 - - - -
196C GLY 3.2 17.5 - - - +
197C GLU* 1.3 80.9 + - - +
199C LYS* 1.3 83.2 + - - +
200C ALA* 4.6 3.1 - - + +
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Residues in contact with LYS 199 (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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195B ASN* 2.8 31.4 + - - +
196B GLY 3.1 9.0 - - - +
197B GLU* 2.7 31.7 + - - +
189C VAL 3.8 0.3 - - - +
190C GLN* 3.4 2.1 - - - -
191C ILE* 2.7 48.7 + - + +
193C ARG* 6.6 0.4 - - + -
198C VAL* 1.3 79.7 - - - +
200C ALA* 1.3 59.7 + - - +
201C PHE* 4.3 16.2 - - + -
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Residues in contact with ALA 200 (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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190B GLN* 5.6 1.1 - - - +
192B LEU* 3.6 25.3 - - + +
193B ARG 4.7 0.5 - - - +
196B GLY* 2.8 29.3 + - - +
198B VAL* 3.4 21.5 - - + +
188C LEU* 4.1 4.7 - - + -
189C VAL 3.2 9.6 - - - +
190C GLN* 4.1 18.2 - - + +
198C VAL* 4.9 1.1 - - + -
199C LYS* 1.3 75.2 - - - +
201C PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 201 (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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192B LEU* 3.9 5.8 - - - -
193B ARG 5.3 1.1 - - - -
194B PRO 3.7 12.8 - - - -
195B ASN* 3.7 8.1 - - - -
196B GLY* 3.5 33.9 - - - -
3C GLU* 5.6 3.6 - - + -
7C LEU* 3.7 38.4 - - + -
8C LEU* 3.7 38.4 - - + -
11C TYR* 5.9 1.1 - + - -
187C ARG 3.6 1.7 - - - +
188C LEU* 3.7 1.7 - - - +
189C VAL* 2.9 34.3 + - - +
191C ILE* 4.0 22.0 - - + -
199C LYS* 4.3 12.1 - - + -
200C ALA* 1.3 77.4 - - - +
202C LEU* 1.3 60.3 + - - +
203C VAL 4.0 0.2 + - - -
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Residues in contact with LEU 202 (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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160B ASN* 3.7 36.1 - - + +
161B GLU 5.7 0.2 - - - +
167B LYS* 4.6 32.4 + - + +
169B VAL* 4.2 11.9 - - + -
192B LEU* 3.9 15.8 - - + +
3C GLU* 3.2 24.0 - - - +
173C TRP* 3.9 26.7 - - + -
186C LYS* 4.5 3.1 - - + -
187C ARG 3.5 10.3 - - - +
188C LEU* 4.3 4.3 - - + +
201C PHE* 1.3 73.2 - - - +
203C VAL* 1.3 78.0 + - - +
204C ASP* 3.7 6.7 + - + +
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Residues in contact with VAL 203 (chain C).
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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3C GLU* 3.7 7.2 - - + +
4C LEU* 4.0 28.9 - - + +
8C LEU* 3.8 28.9 - - + -
185C PHE* 4.1 12.1 - - + +
186C LYS* 3.2 6.2 - - - -
187C ARG* 2.7 62.5 + - + +
202C LEU* 1.3 76.0 - - - +
204C ASP* 1.3 60.2 + - - +
205C ASP* 3.3 27.1 - - - +
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Residues in contact with ASP 204 (chain C).
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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160B ASN* 4.3 8.9 + - - -
1C MET* 3.2 24.4 + - - +
3C GLU* 3.2 13.6 + - - +
184C ARG* 3.0 32.2 + - - -
185C PHE 3.6 2.9 - - - -
186C LYS* 3.0 34.2 + - + +
202C LEU* 3.7 14.8 + - + +
203C VAL* 1.3 74.7 - - - +
205C ASP* 1.3 60.8 + - - +
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Residues in contact with ASP 205 (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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1C MET* 2.9 18.1 - - + +
2C TYR* 2.8 30.9 + - - -
4C LEU* 5.1 2.6 - - - +
5C TYR* 4.9 3.3 + - - -
118C TYR* 3.4 33.6 + - + +
183C LEU 3.6 0.2 - - - +
184C ARG* 3.6 6.6 - - - -
185C PHE* 2.9 41.5 + - + +
203C VAL* 3.3 23.2 - - - +
204C ASP* 1.3 73.7 + - - +
206C GLU* 1.3 60.5 + - - +
207C LEU* 3.7 8.6 + - + -
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Residues in contact with GLU 206 (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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1C MET* 3.6 33.7 - - + +
117C MET 4.5 1.4 - - - +
118C TYR* 4.6 7.4 - - - +
177C GLU* 5.4 2.3 - - - +
182C LYS* 3.5 45.2 + - + +
183C LEU 3.6 5.6 - - - +
184C ARG* 4.0 25.6 + - + +
205C ASP* 1.3 73.6 - - - +
207C LEU* 1.3 68.4 + - - +
208C ASN* 4.9 3.5 + - - +
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Residues in contact with LEU 207 (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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117C MET* 3.3 39.0 - - + +
118C TYR* 3.7 41.1 - - + +
182C LYS* 3.4 9.8 - - - +
183C LEU* 2.7 51.0 + - + +
185C PHE* 4.1 25.1 - - + -
205C ASP* 4.4 9.4 - - + +
206C GLU* 1.3 83.5 - - - +
208C ASN* 1.3 63.2 + - - +
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Residues in contact with ASN 208 (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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117C MET* 2.6 56.1 + - - +
118C TYR 3.7 4.6 + - - -
119C PHE 3.1 28.0 - - - +
120C ASP* 3.4 10.8 - - - +
180C VAL 5.5 0.2 - - - +
181C GLN 3.6 5.9 - - - +
182C LYS* 2.7 34.0 + - - +
206C GLU* 4.9 2.4 + - - -
207C LEU* 1.3 77.5 - - - +
209C ILE* 1.3 63.5 + - - +
210C TYR* 3.7 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