Contacts of the helix formed by residues 226 - 240 (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 ASP 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A GLU* 3.5 14.5 - - - +
192A LYS* 2.9 53.6 + - - +
193A TRP* 4.6 4.3 + - - -
225A ARG* 1.3 100.0 + - + +
227A ASP* 1.3 60.8 + - - +
230A THR* 2.7 43.7 + - - +
358A ASN* 5.7 1.0 - - - +
369A GLU* 3.2 23.6 + - - +
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Residues in contact with ASP 227 (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 HIS* 2.9 26.7 + - - -
221A ASN* 3.4 21.0 - - - +
225A ARG 3.2 7.4 + - - +
226A ASP* 1.3 76.8 - - - +
228A ALA* 1.3 62.7 + - - +
230A THR* 4.1 1.4 - - - -
231A ASP* 3.2 28.2 + - - +
254A LYS* 5.1 0.3 - - - -
369A GLU* 3.0 19.2 + - - +
370A THR 3.7 3.9 - - - +
371A MET* 3.0 38.2 - - - +
372A PRO* 3.1 15.7 - - + +
374A TYR* 4.5 3.1 - - + -
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Residues in contact with ALA 228 (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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227A ASP* 1.3 75.4 - - - +
229A GLY* 1.3 66.5 + - - +
231A ASP* 3.2 4.7 + - - +
232A SER* 3.0 24.6 + - - -
361A TYR* 3.5 36.1 - - + -
365A TYR* 4.8 0.9 + - - -
366A SER* 4.1 5.6 - - - -
369A GLU* 3.0 18.0 + - + +
374A TYR* 3.7 27.8 + - + -
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Residues in contact with GLY 229 (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* 3.7 28.7 - - - -
228A ALA* 1.3 72.5 - - - +
230A THR* 1.3 57.0 + - - +
232A SER* 3.3 1.6 + - - -
233A ILE* 2.9 34.8 + - - +
354A ILE* 5.1 2.9 - - - -
361A TYR* 3.4 16.7 - - - -
369A GLU* 2.8 14.6 + - - -
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Residues in contact with THR 230 (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 HIS* 3.5 31.2 - - + -
191A GLU* 3.1 26.5 + - - -
192A LYS* 4.4 0.4 - - - +
195A TRP* 3.8 26.9 - - + +
219A THR* 3.7 16.8 - - + -
226A ASP* 2.7 25.1 + - - +
227A ASP 4.1 0.9 - - - -
229A GLY* 1.3 73.7 - - - +
231A ASP* 1.3 65.7 + - - +
233A ILE* 4.8 5.4 - - - -
234A VAL* 2.9 25.4 + - + +
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A HIS* 6.0 0.2 + - - -
219A THR* 3.5 24.3 + - - +
227A ASP 3.2 11.1 + - - +
228A ALA 3.2 3.7 + - - +
230A THR* 1.3 76.2 - - - +
232A SER* 1.3 60.6 + - - +
235A SER* 2.8 31.9 + - - -
246A TRP* 4.2 11.0 - - - -
289A ASN* 4.4 9.3 + - - +
290A VAL* 5.2 3.9 - - - +
372A PRO 5.3 0.5 - - - +
374A TYR* 2.4 39.1 + - - +
381A ILE* 3.8 19.1 - - + +
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ALA 3.0 8.6 + - - -
229A GLY 3.6 4.0 - - - -
230A THR 3.2 0.2 - - - -
231A ASP* 1.3 79.4 - - - +
233A ILE* 1.3 56.5 + - - +
235A SER* 3.7 1.6 + - - -
236A GLY* 2.9 20.8 + - - -
361A TYR* 2.9 27.2 + - - -
365A TYR* 3.4 12.3 + - - -
381A ILE* 3.7 10.1 - - - +
382A LEU 2.6 24.2 + - - -
383A PRO* 4.0 0.3 - - - +
384A VAL* 3.1 24.8 + - - -
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Residues in contact with ILE 233 (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* 3.5 37.5 - - + +
195A TRP* 3.8 13.7 - - + -
196A GLU* 4.3 5.8 - - + +
229A GLY 2.9 21.8 + - - +
230A THR* 4.1 3.6 - - - +
232A SER* 1.3 74.9 - - - +
234A VAL* 1.3 61.3 + - - +
236A GLY* 3.2 1.9 + - - -
237A PHE* 2.9 58.0 + - + -
349A ASN* 5.2 1.6 - - - +
354A ILE* 3.6 17.7 - - + -
384A VAL* 3.7 29.2 - - + +
386A HIS* 5.5 4.7 - - + -
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Residues in contact with VAL 234 (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* 3.4 45.3 - - + +
217A LEU* 3.3 37.0 - - + +
218A ALA* 3.9 5.2 - - - +
219A THR* 4.4 7.4 - - + -
230A THR* 2.9 24.4 + - + +
231A ASP 4.6 0.2 - - - +
233A ILE* 1.3 74.3 - - - +
235A SER* 1.3 64.3 + - - +
237A PHE* 3.1 20.0 + - + +
238A TRP* 3.4 10.2 + - - +
243A CYS* 4.7 0.5 - - - -
246A TRP* 3.8 19.1 - - + +
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASP 2.8 24.8 + - - -
232A SER 3.7 1.9 + - - -
234A VAL* 1.3 77.2 - - - +
236A GLY* 1.3 57.8 + - - +
238A TRP* 3.2 7.8 + - - +
239A LEU* 3.0 37.3 + - - +
246A TRP* 3.5 40.6 - - - +
293A GLY 4.4 5.4 - - - -
381A ILE* 3.6 17.3 - - - +
383A PRO* 5.0 2.1 - - - +
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Residues in contact with GLY 236 (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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232A SER 2.9 22.1 + - - -
233A ILE 3.2 3.1 + - - -
234A VAL 3.1 0.4 - - - -
235A SER* 1.3 75.3 + - - +
237A PHE* 1.3 56.9 + - - +
239A LEU* 3.3 11.1 + - - +
240A SER* 2.7 39.8 + - - -
383A PRO* 4.7 2.0 - - - -
384A VAL 3.5 13.2 - - - -
385A ILE* 4.4 6.1 - - - -
386A HIS 6.1 0.4 - - - -
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Residues in contact with PHE 237 (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* 3.6 45.8 - + + -
199A MET* 3.7 25.6 - - + -
217A LEU* 3.4 32.8 - - + -
233A ILE* 2.9 40.8 + - + -
234A VAL* 3.1 14.8 + - + +
236A GLY* 1.3 75.9 - - - +
238A TRP* 1.3 61.5 + - - +
240A SER* 3.3 9.3 + - - -
241A GLY 3.3 0.2 + - - -
242A LEU* 3.0 45.5 + - + +
243A CYS* 4.0 4.9 - - - -
384A VAL 6.0 0.4 - - - -
386A HIS* 3.9 22.0 - + + -
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Residues in contact with TRP 238 (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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234A VAL 3.4 2.8 + - - +
235A SER 3.2 15.6 + - - +
237A PHE* 1.3 79.8 - - - +
239A LEU* 1.3 84.5 + - + +
241A GLY* 3.1 11.3 + - - -
243A CYS* 3.3 29.9 - - - +
244A ASP* 3.2 31.1 + - - -
245A ASN* 3.7 6.3 + - - +
246A TRP* 3.5 29.2 - + + -
293A GLY 3.5 18.8 - - - -
294A GLY* 3.7 28.0 - - - -
296A THR* 6.2 0.2 - - + -
334A PRO 4.1 1.3 - - - -
335A SER* 4.0 1.1 - - - -
336A LYS* 3.5 57.0 - - + +
339A VAL* 4.0 9.4 - - + -
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Residues in contact with LEU 239 (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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235A SER* 3.0 23.7 + - - +
236A GLY* 3.7 7.4 - - - +
238A TRP* 1.3 92.0 - - + +
240A SER* 1.3 59.9 + - - +
241A GLY 3.3 0.4 - - - -
336A LYS* 3.5 23.8 + - + +
339A VAL* 3.7 31.9 - - + -
340A VAL* 3.8 24.2 - - + +
383A PRO* 3.6 36.6 - - + -
385A ILE* 5.1 0.7 - - + -
397A ILE* 3.7 19.9 - - - +
398A PHE* 3.9 18.2 - - + -
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Residues in contact with SER 240 (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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236A GLY 2.7 23.8 + - - -
237A PHE* 3.6 8.9 - - - -
238A TRP 3.2 0.2 - - - -
239A LEU* 1.3 75.3 - - - +
241A GLY* 1.3 60.9 + - - +
242A LEU* 3.6 9.4 + - - +
336A LYS* 5.0 0.2 - - - -
385A ILE* 3.6 28.9 - - - +
386A HIS* 5.0 1.0 + - - +
389A ILE* 4.0 27.4 - - - +
393A LYS* 5.4 4.7 - - - +
397A ILE* 4.1 18.7 - - - +
398A PHE* 6.0 0.2 - - - -
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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