Contacts of the helix formed by residues 185 - 196 (chain G) in PDB entry 2W3S
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 THR 185 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183G PRO* 4.4 0.2 - - - +
184G GLU* 1.3 90.1 + - + +
186G SER* 1.3 67.2 + - - +
187G ASP* 4.4 9.6 - - - +
188G ALA* 3.0 33.3 + - - +
189G LEU* 3.1 12.3 + - - +
228G CYS* 3.9 4.3 - - - -
230G ASP* 3.4 14.1 - - + +
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Residues in contact with SER 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G THR* 1.3 71.2 - - - +
187G ASP* 1.3 62.8 + - - +
189G LEU* 3.2 11.4 + - - +
190G ALA* 2.8 24.1 + - - +
228G CYS* 3.8 4.7 - - - -
230G ASP* 2.8 38.1 + - - -
231G LEU* 3.8 17.9 + - - +
308G ARG* 3.8 18.7 - - - -
335G PHE* 4.5 5.6 - - - -
337G GLU* 5.3 4.3 - - - +
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Residues in contact with ASP 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G THR* 3.2 8.4 - - - +
186G SER* 1.3 75.9 - - - +
188G ALA* 1.3 64.8 + - - +
190G ALA* 2.8 5.2 + - - +
191G ASP* 2.8 29.4 + - - +
230G ASP* 5.7 1.3 - - - -
308G ARG* 3.0 28.7 + - - +
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Residues in contact with ALA 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G PHE* 3.9 15.1 - - + -
183G PRO* 5.1 0.2 - - + -
184G GLU* 4.8 4.5 - - + +
185G THR* 3.0 28.8 + - - +
187G ASP* 1.3 78.8 - - - +
189G LEU* 1.3 61.5 + - - +
191G ASP* 3.3 21.3 - - - +
192G TRP* 3.4 9.4 + - - +
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Residues in contact with LEU 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G PHE* 4.0 9.4 - - + -
183G PRO* 3.9 18.8 - - + +
185G THR 3.1 8.3 + - - +
186G SER* 3.5 7.6 - - - +
187G ASP 3.1 0.4 - - - -
188G ALA* 1.3 74.9 - - - +
190G ALA* 1.3 58.6 + - - +
192G TRP* 2.9 10.5 + - + +
193G TYR* 2.8 49.5 + - + +
201G LEU* 4.4 9.9 - - + -
223G ALA* 5.3 1.3 - - + -
225G LEU* 3.7 30.5 - - + -
228G CYS* 5.4 1.3 - - - -
231G LEU* 3.7 30.1 - - + -
335G PHE* 4.2 23.6 - - + -
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Residues in contact with ALA 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G SER 2.8 7.5 + - - +
187G ASP 2.8 8.1 + - - +
189G LEU* 1.3 74.8 - - - +
191G ASP* 1.3 63.6 + - - +
193G TYR* 4.6 0.4 - - - +
194G LEU* 3.0 28.2 + - - +
308G ARG* 3.3 31.6 - - - +
310G GLY* 3.4 21.4 + - - +
335G PHE* 3.7 21.5 - - + -
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Residues in contact with ASP 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G ASP* 2.8 15.1 + - - +
188G ALA* 3.3 16.3 - - - +
190G ALA* 1.3 79.2 - - - +
192G TRP* 1.3 61.5 + - + +
194G LEU* 3.5 12.1 - - - +
195G ALA* 3.3 19.2 + - - +
310G GLY 5.7 0.7 - - - +
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Residues in contact with TRP 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G PHE* 3.2 57.4 - + + +
188G ALA 3.9 2.9 - - - +
189G LEU* 2.9 7.0 + - + +
191G ASP* 1.3 77.3 - - - +
193G TYR* 1.3 64.7 + + + +
195G ALA* 3.0 4.8 + - - -
196G HIS* 2.7 74.1 + + + -
199G ALA* 3.4 33.0 - - + -
201G LEU* 4.4 9.2 - - + -
221G GLU* 4.2 12.1 - - + -
222G VAL 4.2 4.7 - - - -
223G ALA* 3.5 30.7 - - + -
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Residues in contact with TYR 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G LEU* 2.8 30.9 + - + +
190G ALA 4.5 1.3 - - - +
192G TRP* 1.3 77.9 - + + +
194G LEU* 1.3 60.7 + - - +
196G HIS 3.0 37.6 - - - +
197G PRO 3.1 28.9 + - - -
199G ALA 3.7 15.3 + - - -
201G LEU* 3.7 28.5 - - + -
330G ARG* 3.0 24.8 + - - -
331G ARG 5.5 0.3 + - - -
332G PRO* 5.8 0.3 - - - +
333G GLY* 3.3 34.3 + - - +
334G GLU 3.3 23.9 + - - -
335G PHE* 3.6 17.0 - + + -
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Residues in contact with LEU 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G ALA 3.0 17.7 + - - +
191G ASP* 3.5 9.9 - - - +
193G TYR* 1.3 77.1 - - - +
195G ALA* 1.3 57.3 + - - +
197G PRO* 4.6 5.4 - - - +
309G ARG* 3.7 29.2 - - + +
310G GLY* 3.5 35.9 - - - +
311G GLN 4.8 1.1 - - - +
332G PRO 5.2 0.2 - - - +
333G GLY* 4.0 11.9 + - - +
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Residues in contact with ALA 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G ASP 3.3 10.0 + - - +
192G TRP* 3.0 11.9 + - - +
194G LEU* 1.3 79.5 - - - +
196G HIS* 1.3 72.3 + - + +
197G PRO* 3.5 9.3 - - - +
198G GLU* 4.8 0.2 - - - +
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Residues in contact with HIS 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G TRP* 2.7 69.5 + + + +
193G TYR* 3.0 22.7 - - - -
195G ALA* 1.3 83.9 + - + +
197G PRO* 1.3 67.6 - - - +
198G GLU* 3.2 6.3 + - - +
199G ALA* 3.6 12.3 + - + +
221G GLU* 3.3 36.1 + - - +
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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