Contacts of the strand formed by residues 198 - 208 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLN* 4.2 17.0 - - + +
191A ILE 3.3 8.7 - - - +
192A LEU* 4.2 19.3 - - + -
193A ARG* 5.9 0.2 - - - -
196A GLY 4.2 5.4 - - - +
197A GLU* 1.3 80.5 + - - +
199A LYS* 1.3 83.3 + - - +
200A ALA* 4.5 3.4 - - + +
190B GLN* 6.3 0.4 - - - +
198B VAL* 4.0 36.7 + - + +
200B ALA* 4.5 8.1 - - + -
196C GLY 4.2 2.8 - - - +
197C GLU* 4.5 8.1 - - - +
198C VAL* 4.6 16.0 + - + +
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Residues in contact with LYS 199 (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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189A VAL 3.8 0.3 - - - +
190A GLN* 3.4 2.3 - - - -
191A ILE* 2.7 46.6 + - + +
193A ARG* 6.6 0.2 - - - +
198A VAL* 1.3 80.2 - - - +
200A ALA* 1.3 61.4 + - - +
201A PHE* 4.4 17.0 - - + -
195C ASN* 3.3 27.8 + - - +
196C GLY* 3.1 11.2 - - - +
197C GLU* 2.9 32.9 + - - +
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Residues in contact with ALA 200 (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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188A LEU* 4.2 4.9 - - + -
189A VAL 3.2 8.5 - - - +
190A GLN* 4.2 17.0 - - + +
198A VAL* 4.9 1.1 - - + -
199A LYS* 1.3 75.0 - - - +
201A PHE* 1.3 64.7 + - - +
190C GLN* 5.6 1.8 - - - +
192C LEU* 3.5 27.8 - - + +
193C ARG 4.6 0.5 - - - +
196C GLY* 2.8 28.3 + - - +
198C VAL* 3.4 20.6 - - + +
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Residues in contact with PHE 201 (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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3A GLU* 5.6 4.3 - - + -
7A LEU* 4.2 35.7 - - + -
8A LEU* 3.8 39.5 - - + -
11A TYR* 5.7 1.6 - + - -
187A ARG 3.6 1.6 - - - +
188A LEU* 3.6 2.1 - - - +
189A VAL* 2.9 33.5 + - - +
191A ILE* 4.1 22.0 - - + -
199A LYS* 4.4 12.1 - - + -
200A ALA* 1.3 78.5 - - - +
202A LEU* 1.3 60.8 + - - +
203A VAL 4.0 0.6 + - - -
192C LEU* 4.1 4.9 - - - -
193C ARG 5.4 0.9 - - - -
194C PRO 3.7 14.1 - - - -
195C ASN 3.8 8.3 - - - -
196C GLY* 3.7 29.8 - - - -
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Residues in contact with LEU 202 (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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3A GLU* 3.1 24.4 - - - +
173A TRP* 3.7 29.4 - - + -
186A LYS* 4.7 1.6 - - + -
187A ARG 3.5 11.0 - - - +
188A LEU* 4.3 3.4 - - + +
201A PHE* 1.3 73.1 - - - +
203A VAL* 1.3 77.5 + - - +
204A ASP* 4.5 7.6 - - + +
160C ASN* 3.8 33.7 - - + +
161C GLU 5.6 0.2 - - - +
167C LYS* 4.2 34.5 + - + +
169C VAL* 4.2 13.7 - - + -
192C LEU* 4.0 15.6 - - + +
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Residues in contact with VAL 203 (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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3A GLU* 3.6 8.3 - - + +
4A LEU* 3.9 32.8 - - + +
8A LEU* 3.8 28.0 - - + -
185A PHE* 4.0 19.5 - - + +
186A LYS* 3.3 4.3 - - - -
187A ARG* 2.7 51.2 + - + +
202A LEU* 1.3 78.2 - - - +
204A ASP* 1.3 64.7 + - - +
205A ASP* 3.5 23.8 - - - +
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Residues in contact with ASP 204 (chain A).
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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1A MET* 3.5 16.5 + - - +
3A GLU* 3.2 11.2 + - - +
184A ARG* 2.9 31.4 + - - -
185A PHE 3.4 3.6 - - - +
186A LYS* 2.7 39.6 + - + +
202A LEU* 4.5 13.9 - - + +
203A VAL* 1.3 77.7 - - - +
205A ASP* 1.3 65.2 + - - +
160C ASN* 3.9 9.9 + - - -
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Residues in contact with ASP 205 (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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1A MET* 3.0 13.9 - - + +
2A TYR* 2.7 32.7 + - - -
3A GLU* 3.8 0.7 - - - +
4A LEU* 5.2 1.2 - - - +
5A TYR* 4.6 4.0 + - - -
118A TYR* 3.0 39.6 + - + +
184A ARG* 3.6 6.3 - - - -
185A PHE* 2.9 40.1 + - + +
203A VAL* 3.5 19.7 - - - +
204A ASP* 1.3 74.5 - - - +
206A GLU* 1.3 62.2 + - - +
207A LEU* 3.6 7.1 + - + -
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Residues in contact with GLU 206 (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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1A MET* 5.4 2.8 - - - +
117A MET 4.5 1.7 - - - +
118A TYR* 4.6 9.7 - - - +
177A GLU* 5.3 2.8 - - - +
182A LYS* 3.5 44.3 + - + +
183A LEU 3.6 4.0 - - - +
184A ARG* 3.0 35.2 + - - +
204A ASP 4.4 0.2 + - - -
205A ASP* 1.3 71.4 - - - +
207A LEU* 1.3 68.9 + - - +
208A ASN* 4.7 4.5 + - - +
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Residues in contact with LEU 207 (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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117A MET* 3.4 37.9 - - + +
118A TYR* 3.8 42.0 - - + +
182A LYS* 3.4 9.6 - - - +
183A LEU* 2.7 47.3 + - + +
185A PHE* 3.8 28.5 - - + -
205A ASP* 4.1 9.6 - - + +
206A GLU* 1.3 83.6 - - - +
208A ASN* 1.3 63.9 + - - +
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Residues in contact with ASN 208 (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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117A MET* 2.7 55.2 + - - +
118A TYR 3.7 5.7 + - - -
119A PHE 3.2 33.8 - - - +
120A ASP* 3.5 12.7 - - - +
180A VAL 5.5 0.2 - - - +
181A GLN 3.5 5.7 - - - +
182A LYS* 2.8 34.7 + - - +
206A GLU* 4.7 2.8 + - - -
207A LEU* 1.3 78.1 - - - +
209A ILE* 1.3 63.6 + - - +
210A TYR* 3.7 15.1 - - + -
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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