Contacts of the helix formed by residues 188 - 199 (chain A) in PDB entry 1JWO
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A HIS* 3.8 6.5 - - - -
186A PHE* 3.7 5.0 - - - +
187A CYS* 1.3 90.9 - - - +
189A LEU* 1.3 63.9 + - - +
190A MET* 3.1 40.5 - - + +
191A ASP* 2.5 45.0 + - - +
192A MET 3.1 5.4 + - - -
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Residues in contact with LEU 189 (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 LEU* 4.6 13.0 - - + -
122A TRP* 4.5 12.3 - - + -
146A VAL* 3.9 19.5 - - + -
156A TYR* 3.5 46.0 - - + -
171A VAL* 4.3 9.0 - - + -
177A HIS* 3.6 18.5 + - + +
188A ASN* 1.3 73.6 - - - +
190A MET* 1.3 55.7 + - + +
191A ASP 2.4 17.2 + - - -
192A MET* 2.7 51.1 + - + +
193A VAL* 2.8 18.8 + - + +
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Residues in contact with MET 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.1 40.6 - - + +
120A MET* 3.7 22.9 - - + +
122A TRP* 4.0 14.8 - - + -
188A ASN* 3.0 39.5 - - + +
189A LEU* 1.3 73.8 - - + +
191A ASP* 1.3 65.1 + - - +
193A VAL* 4.7 0.4 - - - -
194A GLU* 4.7 6.0 - - - +
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Residues in contact with ASP 191 (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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186A PHE* 3.7 11.6 - - + -
187A CYS* 4.7 6.4 + - - +
188A ASN* 2.5 47.3 + - - +
189A LEU 2.4 9.1 + - - -
190A MET* 1.3 68.0 - - - +
192A MET* 1.3 66.3 + - - +
193A VAL 3.0 2.8 - - - +
194A GLU* 3.7 17.5 - - - +
195A HIS* 3.0 20.8 + - - +
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Residues in contact with MET 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.6 17.3 - - + -
171A VAL* 3.5 31.0 - - + -
177A HIS* 5.2 2.2 - - - -
178A LEU* 4.8 8.3 - - - -
179A THR* 4.5 9.2 - - - +
186A PHE* 3.6 31.6 - - + -
188A ASN 3.1 5.9 + - - +
189A LEU* 2.7 42.6 + - + +
191A ASP* 1.3 76.6 - - - +
193A VAL* 1.3 70.1 + - + +
195A HIS* 3.0 2.1 + - - +
196A TYR* 2.9 52.2 + - + -
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Residues in contact with VAL 193 (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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122A TRP* 3.7 51.6 - - + +
144A PHE* 4.1 21.3 - - + -
146A VAL* 4.7 9.6 - - + -
158A LEU* 5.0 2.0 - - + -
189A LEU* 2.8 23.0 + - + +
190A MET* 4.7 0.2 - - - -
191A ASP 4.3 0.9 - - - +
192A MET* 1.3 83.0 - - + +
194A GLU* 1.3 68.0 + - - +
196A TYR* 3.2 2.6 + - - +
197A SER* 3.1 21.1 + - - +
207A LEU* 4.5 16.7 - - + +
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Residues in contact with GLU 194 (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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190A MET 4.7 3.4 - - - +
191A ASP* 3.7 21.8 + - - +
193A VAL* 1.3 78.3 - - - +
195A HIS* 1.3 71.4 + - - +
197A SER* 2.8 29.2 + - - -
198A LYS* 3.4 31.0 + - - +
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Residues in contact with HIS 195 (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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184A VAL* 4.0 18.2 - - + +
186A PHE* 3.2 30.0 - + + -
191A ASP 3.0 18.0 + - - +
192A MET 3.1 4.0 - - - +
194A GLU* 1.3 80.4 - - - +
196A TYR* 1.3 87.2 + + - +
197A SER 2.7 11.1 + - - -
198A LYS* 2.7 21.8 + - - +
199A ASP* 3.5 26.8 + - + +
202A ALA* 5.4 1.8 - - + -
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Residues in contact with TYR 196 (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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158A LEU* 5.6 4.9 - - + -
179A THR* 4.1 18.4 + - + -
180A ILE* 3.7 31.7 - - - +
184A VAL* 4.8 1.8 + - + +
186A PHE* 4.0 14.6 - + - -
192A MET* 2.9 52.0 + - + +
193A VAL 3.2 3.1 + - - +
195A HIS* 1.3 89.5 + + - +
197A SER* 1.3 58.7 + - - +
198A LYS 3.5 0.4 - - - -
199A ASP 3.9 8.7 - - - +
200A LYS* 3.6 7.1 - - - -
202A ALA* 3.1 25.4 - - + -
203A ILE* 3.1 36.8 - - + -
205A THR 4.7 0.7 - - - +
206A LYS* 4.0 5.2 - - - +
207A LEU* 3.1 38.4 + - + -
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Residues in contact with SER 197 (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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144A PHE* 5.1 3.6 - - - -
193A VAL* 3.1 14.3 + - - +
194A GLU* 2.8 28.7 + - - -
195A HIS 2.7 2.0 + - - -
196A TYR* 1.3 80.0 - - - +
198A LYS* 1.3 62.3 + - - +
206A LYS* 3.8 15.8 - - - +
207A LEU* 3.8 25.6 + - - +
208A VAL* 5.2 2.8 + - - -
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Residues in contact with LYS 198 (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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194A GLU* 3.4 34.7 + - - +
195A HIS* 2.7 16.3 + - - +
197A SER* 1.3 79.7 - - - +
199A ASP* 1.3 58.0 + - + +
206A LYS* 3.7 21.6 + - - +
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Residues in contact with ASP 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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195A HIS* 3.5 19.9 + - + +
196A TYR* 3.9 20.1 - - - -
197A SER 3.9 0.8 - - - -
198A LYS* 1.3 79.9 - - + +
200A LYS* 1.3 68.7 + - - +
201A GLY* 3.6 16.6 + - - +
202A ALA* 5.4 0.5 - - - +
206A LYS* 5.3 2.0 - - - +
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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