Contacts of the helix formed by residues 191 - 201 (chain A) in PDB entry 2WMH
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 GLU 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A TYR* 3.8 19.1 - - - +
190A HIS* 1.3 89.1 - - - +
192A LYS* 1.3 65.1 + - - +
193A TRP* 2.8 40.3 + - - +
194A PHE* 3.4 0.6 + - + -
195A TRP* 3.2 24.7 + - - -
223A PRO* 3.5 26.8 - - + +
225A ARG* 3.8 22.1 - - + -
226A ASP* 3.5 17.3 - - + +
230A THR* 3.1 19.3 + - - +
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Residues in contact with LYS 192 (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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191A GLU* 1.3 73.4 - - - +
193A TRP* 1.3 65.1 + - - +
194A PHE 3.1 0.2 + - - -
196A GLU* 2.9 30.7 + - - +
226A ASP* 2.9 37.6 + - - +
229A GLY* 3.7 21.3 - - - -
230A THR* 4.9 0.4 - - - -
233A ILE* 3.5 27.0 - - + +
354A ILE* 4.0 10.5 + - + +
355A SER* 3.9 30.5 - - - +
357A LEU 4.6 4.2 + - - -
358A ASN* 4.6 20.6 + - - +
361A TYR* 4.6 4.6 - - - -
369A GLU* 2.8 38.9 + - - -
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Residues in contact with TRP 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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160A TYR 3.3 26.2 - - - -
163A TYR* 4.1 30.5 - + + -
191A GLU* 2.8 33.9 + - + +
192A LYS* 1.3 78.8 - - - +
194A PHE* 1.3 75.4 + + + +
196A GLU* 3.5 13.7 + - - +
197A THR* 2.7 50.0 + - + -
226A ASP* 4.6 3.8 + - - -
355A SER* 3.8 11.3 - - - +
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Residues in contact with PHE 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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159A ASN* 3.7 25.4 - - + -
160A TYR* 3.7 13.9 - - + -
163A TYR* 3.6 24.5 - + - -
167A LEU* 5.3 0.7 - - + -
187A TRP* 4.2 6.3 - + - -
189A ASP* 3.2 40.8 - - + -
190A HIS 3.2 27.1 - - - +
191A GLU 3.4 1.1 + - - +
192A LYS 3.1 0.8 - - - -
193A TRP* 1.3 106.6 - + + +
195A TRP* 1.3 70.8 + + - +
197A THR* 3.0 4.2 + - - -
198A ILE* 2.9 54.8 + - + +
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Residues in contact with TRP 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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187A TRP* 3.7 33.4 - + - -
189A ASP* 3.1 37.3 + - + -
190A HIS* 3.8 4.2 - - - +
191A GLU 3.2 20.3 + - - +
192A LYS 4.2 1.3 - - - +
194A PHE* 1.3 78.8 - + - +
196A GLU* 1.3 66.3 + - - +
198A ILE* 3.4 29.4 + - + +
199A MET* 3.3 17.2 + - - +
217A LEU* 4.0 24.5 - - + -
218A ALA 3.4 23.6 - - - -
230A THR* 3.8 12.5 - - + +
233A ILE* 3.8 20.9 - - + -
234A VAL* 3.4 24.1 - - + +
237A PHE* 3.6 31.3 - + + -
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Residues in contact with GLU 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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192A LYS 2.9 19.5 + - - +
193A TRP* 3.6 7.9 - - - +
195A TRP* 1.3 76.7 - - - +
197A THR* 1.3 63.2 + - - +
200A ASN* 3.1 19.7 + - - +
233A ILE* 4.4 7.0 - - + -
349A ASN* 3.1 31.5 + - - +
353A ARG* 3.4 16.8 - - + +
354A ILE* 3.4 8.3 - - - +
355A SER* 2.7 46.6 + - - -
386A HIS* 2.9 30.6 + - + +
387A GLU* 5.0 3.1 - - - +
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Residues in contact with THR 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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163A TYR* 3.4 40.8 + - + +
193A TRP* 2.7 35.1 + - + -
194A PHE* 3.0 7.6 + - - -
196A GLU* 1.3 75.5 - - - +
198A ILE* 1.3 66.9 + - - +
200A ASN* 3.3 16.4 + - + +
201A ASP* 3.4 9.5 + - - +
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Residues in contact with ILE 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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163A TYR* 3.5 31.6 - - + +
167A LEU* 5.4 0.4 - - + -
168A ALA* 4.2 9.1 - - + +
187A TRP* 3.4 40.2 - - + -
194A PHE* 2.9 47.6 + - + +
195A TRP* 3.9 19.5 - - + +
196A GLU 3.4 0.2 - - - -
197A THR* 1.3 75.9 - - - +
199A MET* 1.3 59.5 + - + +
201A ASP* 3.2 25.5 + - - +
204A PHE* 3.7 22.8 - - + +
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Residues in contact with MET 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 TRP 3.3 4.2 + - - -
198A ILE* 1.3 77.0 - - + +
200A ASN* 1.3 59.9 + - - +
201A ASP 3.3 1.8 - - - -
204A PHE* 4.0 11.4 - - + -
205A PHE* 3.4 43.5 - - + +
208A SER* 3.6 26.0 - - - +
217A LEU* 3.7 28.9 - - + -
237A PHE* 3.7 20.9 - - + -
242A LEU* 3.7 32.5 - - + -
386A HIS* 3.5 28.0 - - + +
388A LYS* 3.7 9.5 - - - +
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Residues in contact with ASN 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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196A GLU* 3.1 24.6 + - - +
197A THR* 3.6 9.0 - - - +
198A ILE 3.2 0.2 - - - -
199A MET* 1.3 74.4 - - - +
201A ASP* 1.3 64.2 + - - +
202A PRO* 3.3 9.7 - - - +
205A PHE* 5.3 0.2 - - - -
353A ARG* 4.8 1.6 + - - -
386A HIS* 3.1 17.6 - - - -
387A GLU* 3.0 27.2 - - - +
388A LYS* 2.7 44.6 + - - +
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Residues in contact with ASP 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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163A TYR* 5.5 3.6 + - - +
165A ASN* 4.7 3.8 - - - +
168A ALA* 3.6 24.1 - - + +
169A PRO* 3.9 14.2 - - - +
197A THR 3.4 6.1 + - - +
198A ILE 3.2 16.0 + - - +
199A MET 4.0 0.3 - - - +
200A ASN* 1.3 76.7 - - - +
202A PRO* 1.3 69.3 - - - +
203A THR* 3.1 16.2 + - - -
204A PHE* 2.9 26.1 + - + +
205A PHE* 2.9 30.3 + - - +
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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