Contacts of the helix formed by residues 187 - 197 (chain B) in PDB entry 1WOI
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 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B THR* 3.2 37.6 + - - +
150B ASP 4.6 1.0 + - - -
151B THR 5.1 0.3 - - - +
186B PHE* 1.3 71.7 - - - +
188B PRO* 1.3 64.3 - - - +
189B GLU* 2.8 24.9 + - - +
190B ALA* 3.1 20.3 + - + +
191B VAL* 2.9 31.4 + - - +
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Residues in contact with PRO 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR* 4.6 21.1 - - + -
71A GLY* 5.6 6.1 - - - +
186B PHE* 3.2 11.5 - - + +
187B ASP* 1.3 88.4 - - - +
189B GLU* 1.3 58.0 + - + +
191B VAL* 3.9 7.0 - - + +
192B ALA* 3.0 30.1 + - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASP* 4.0 13.0 + - - +
164B ARG* 2.9 44.3 + - - -
187B ASP* 2.8 13.0 + - - +
188B PRO* 1.3 80.6 - - + +
190B ALA* 1.3 60.6 + - - +
192B ALA* 3.5 4.6 + - - +
193B ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.8 11.6 - - + +
148B PHE* 3.3 39.0 - - - +
149B THR* 3.8 4.9 - - - +
164B ARG* 4.2 1.1 - - - +
187B ASP* 3.1 28.6 + - + +
189B GLU* 1.3 80.3 + - - +
191B VAL* 1.3 64.0 - - - +
193B ALA 3.3 0.5 + - - -
194B ALA* 3.0 24.9 + - - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.9 41.3 - - + +
146B LEU* 3.7 17.9 - - + -
186B PHE* 4.2 13.9 - - + -
187B ASP 2.9 23.7 + - - +
188B PRO* 3.9 7.6 - - + +
190B ALA* 1.3 76.0 - - - +
192B ALA* 1.3 62.6 + - - +
194B ALA* 3.2 3.8 + - - +
195B ARG* 3.1 44.2 + - - +
201B ILE* 4.2 4.9 - - + +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PRO 3.0 19.9 + - - +
189B GLU* 3.9 4.9 - - - +
191B VAL* 1.3 76.5 - - - +
193B ALA* 1.3 57.8 + - - +
195B ARG* 3.3 8.0 + - - +
196B ALA* 2.9 31.5 + - - +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PHE* 3.7 7.6 - - + -
164B ARG* 3.8 31.2 - - - +
189B GLU* 2.9 21.9 + - - +
190B ALA 3.7 4.5 - - - +
192B ALA* 1.3 77.0 - - - +
194B ALA* 1.3 61.8 + - - +
196B ALA* 3.6 6.8 + - - +
197B ARG* 3.2 29.7 + - + +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU* 4.2 17.3 - - + -
148B PHE* 3.7 19.0 - - + -
190B ALA 3.0 16.2 + - - +
191B VAL 3.6 4.7 - - - +
192B ALA 3.2 0.2 - - - -
193B ALA* 1.3 74.6 - - - +
195B ARG* 1.3 63.7 + - - +
197B ARG* 3.2 6.8 + - - -
199B HIS* 2.9 47.1 + - + +
201B ILE* 4.4 9.0 - - + -
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 4.6 16.6 + - - +
191B VAL* 3.1 28.5 + - - +
192B ALA* 3.9 6.5 - - - +
194B ALA* 1.3 73.9 - - - +
196B ALA* 1.3 58.8 + - - +
198B GLY* 2.6 25.8 + - - +
199B HIS 4.4 11.3 + - - +
201B ILE* 4.0 43.8 + - + +
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ALA 2.9 18.6 + - - +
193B ALA* 3.6 10.1 - - - +
195B ARG* 1.3 77.7 - - - +
197B ARG* 1.3 62.3 + - + +
198B GLY* 3.4 1.2 + - - -
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Residues in contact with ARG 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 3.7 23.6 - - - -
164B ARG* 5.3 2.2 + - - +
167B CYS* 3.2 49.7 + - - +
168B GLU* 4.1 6.3 - - - +
170B LEU 5.1 1.2 + - - -
171B PRO* 5.6 4.2 + - - +
173B LEU 4.4 10.3 + - - -
174B VAL 4.5 8.8 - - - +
175B HIS* 5.4 0.2 - - - -
193B ALA* 3.2 13.2 - - - +
194B ALA 3.2 7.3 + - - +
195B ARG 3.1 1.0 - - - -
196B ALA* 1.3 78.9 - - + +
198B GLY* 1.3 60.7 + - - +
199B HIS* 3.4 19.3 + - + +
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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