Contacts of the helix formed by residues 185 - 196 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183E PRO* 3.5 1.4 - - - +
184E GLU* 1.3 91.7 - - + +
186E SER* 1.3 69.7 + - - +
187E ASP* 3.8 12.2 - - - +
188E ALA* 2.8 27.2 + - - +
189E LEU* 3.0 11.9 + - - +
228E CYS* 4.0 5.4 - - - -
230E ASP* 3.4 26.2 - - - +
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Residues in contact with SER 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E THR* 1.3 68.2 - - - +
187E ASP* 1.3 61.9 + - - +
189E LEU* 2.8 15.5 + - - +
190E ALA* 2.6 35.3 + - - +
228E CYS* 4.1 2.5 - - - -
230E ASP* 3.1 21.2 + - - -
231E LEU* 3.8 20.6 - - - +
308E ARG* 3.4 23.8 - - - -
335E PHE* 4.7 7.4 - - - -
337E GLU* 4.0 9.9 + - - -
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Residues in contact with ASP 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E THR* 3.8 9.5 - - - +
186E SER* 1.3 79.1 + - - +
188E ALA* 1.3 62.7 + - - +
190E ALA* 3.1 2.3 + - - +
191E ASP* 3.0 29.7 + - - +
230E ASP* 3.6 19.8 - - - +
308E ARG* 3.4 20.2 + - - +
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Residues in contact with ALA 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E PHE* 4.2 7.5 - - + -
183E PRO* 4.6 3.6 - - + -
184E GLU* 4.4 11.4 - - + +
185E THR* 2.8 32.8 + - - +
187E ASP* 1.3 76.2 - - - +
189E LEU* 1.3 63.3 + - - +
191E ASP* 3.2 21.0 - - - +
192E TRP* 3.3 8.3 + - - +
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Residues in contact with LEU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E PHE* 4.1 9.6 - - + -
183E PRO* 3.7 26.6 - - + +
185E THR 3.0 6.9 + - - +
186E SER* 2.8 13.8 + - - +
188E ALA* 1.3 69.4 - - - +
190E ALA* 1.3 55.2 + - - +
192E TRP* 2.7 25.0 + - + +
193E TYR* 2.8 32.6 + - + +
201E LEU* 4.4 11.9 - - + -
223E ALA* 5.0 2.5 - - + -
225E LEU* 4.0 28.9 - - + -
228E CYS* 6.0 1.6 - - - -
231E LEU* 4.0 21.5 - - + -
335E PHE* 3.9 32.3 - - + -
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Residues in contact with ALA 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E SER 2.6 19.5 + - - +
187E ASP 3.4 2.2 - - - +
189E LEU* 1.3 72.3 - - - +
191E ASP* 1.3 57.6 + - - +
193E TYR* 4.6 1.1 - - - +
194E LEU* 3.1 27.5 + - - +
308E ARG* 3.4 19.7 - - - +
310E GLY* 3.3 30.3 + - - +
333E GLY 5.2 0.3 - - - +
335E PHE* 3.6 28.0 - - + -
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Residues in contact with ASP 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ASP* 3.0 24.9 + - - +
188E ALA* 3.2 11.5 - - - +
189E LEU 2.9 0.4 + - - -
190E ALA* 1.3 76.2 - - - +
192E TRP* 1.3 64.3 + - - +
194E LEU* 3.0 27.3 - - - +
195E ALA* 3.1 8.4 + - - +
310E GLY 4.6 6.8 - - - +
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Residues in contact with TRP 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E PHE* 3.2 63.6 - + + +
188E ALA 3.3 2.4 + - - +
189E LEU* 2.7 9.5 + - + +
191E ASP* 1.3 76.7 - - + +
193E TYR* 1.3 68.7 + + + +
195E ALA* 3.1 6.2 + - - +
196E HIS* 2.8 56.7 + + + -
199E ALA* 3.4 35.2 - - + -
201E LEU* 4.6 1.6 - - + -
221E GLU* 3.6 25.6 - - + -
222E VAL 4.3 7.6 - - - -
223E ALA* 3.9 22.2 - - + -
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Residues in contact with TYR 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E LEU* 2.8 27.6 + - + +
190E ALA 4.6 1.3 - - - +
192E TRP* 1.3 79.1 - - + +
194E LEU* 1.3 66.8 + - - +
195E ALA 3.0 1.6 - - - -
196E HIS 2.9 21.1 + - - -
197E PRO* 3.2 43.1 + - + +
199E ALA* 4.1 14.3 + - + -
201E LEU* 3.7 28.3 - - + -
330E ARG* 3.1 20.9 + - - -
331E ARG 5.4 0.5 + - - -
333E GLY* 3.3 21.4 + - - +
334E GLU 2.9 27.1 + - - -
335E PHE* 3.8 23.3 - + + -
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Residues in contact with LEU 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ALA 3.1 12.4 + - - +
191E ASP* 3.0 19.3 - - - +
193E TYR* 1.3 77.1 - - - +
195E ALA* 1.3 58.8 + - - +
197E PRO* 4.0 9.2 - - - +
309E ARG* 3.5 34.3 - - - +
310E GLY* 3.9 22.4 - - - +
311E GLN* 6.1 0.9 - - + -
312E GLU* 5.4 0.9 - - - +
333E GLY* 4.3 11.0 + - - -
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Residues in contact with ALA 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E ASP 3.1 10.6 + - - +
192E TRP* 3.2 14.6 - - - +
193E TYR 3.0 0.2 - - - -
194E LEU* 1.3 78.6 - - - +
196E HIS* 1.3 73.9 + - + +
197E PRO* 3.2 9.6 - - - +
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Residues in contact with HIS 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E TRP* 2.8 58.9 + + + +
193E TYR* 2.9 13.5 + - - +
195E ALA* 1.3 86.7 + - + +
197E PRO* 1.3 51.3 - - - +
198E GLU* 2.7 25.9 + - - +
199E ALA* 2.9 18.4 + - - +
221E GLU* 2.9 40.2 + - + +
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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