Contacts of the helix formed by residues 194 - 207 (chain B) in PDB entry 4OL0
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 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ALA* 5.1 5.6 - - + -
192B GLY 3.1 5.0 - - - +
193B THR* 1.3 82.1 - - - +
195B GLU* 1.3 69.7 + - - +
196B LYS* 3.5 18.8 + - - +
197B MET* 3.1 28.0 + - + +
198B LEU* 3.2 14.4 + - - +
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Residues in contact with GLU 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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193B THR 4.2 1.0 + - - -
194B ASP* 1.3 74.6 + - - +
196B LYS* 1.3 58.4 + - - +
197B MET 3.0 0.6 + - - -
198B LEU* 3.1 10.4 + - + +
199B MET* 2.8 44.7 + - - +
237B THR* 5.1 1.2 - - - -
238B SER* 2.6 42.6 + - - -
240B ASN* 5.3 3.3 + - - +
241B LEU* 4.1 24.6 + - + +
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Residues in contact with LYS 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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113A GLU* 6.0 2.2 - - - -
194B ASP* 3.3 15.4 + - - +
195B GLU* 1.3 78.1 - - - +
197B MET* 1.3 58.6 + - - +
199B MET* 4.1 18.6 - - + +
200B LYS* 3.4 34.5 + - - +
203B ARG* 5.6 2.1 + - - +
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Residues in contact with MET 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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140B LEU* 3.9 31.6 - - + -
141B PRO* 5.2 8.3 - - - -
144B LEU* 3.6 28.7 - - + -
187B CYS* 3.8 31.4 - - + +
191B ALA* 4.0 22.4 - - + -
192B GLY* 4.4 4.0 - - - +
194B ASP* 3.1 25.0 + - + +
195B GLU 3.0 0.6 - - - -
196B LYS* 1.3 77.2 - - - +
198B LEU* 1.3 60.3 + - + +
199B MET 3.2 1.1 - - - -
200B LYS* 3.1 11.4 + - - +
201B VAL* 2.8 33.1 + - + +
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Residues in contact with LEU 198 (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 VAL* 3.9 28.3 - - + -
192B GLY* 3.5 34.1 - - - +
194B ASP 3.2 7.8 + - - +
195B GLU* 3.1 10.6 + - + +
197B MET* 1.3 79.4 - - + +
199B MET* 1.3 57.2 + - - +
201B VAL* 3.4 7.0 - - + +
202B PHE* 2.8 43.4 + - + -
227B LEU* 4.4 14.8 - - + -
231B VAL* 5.1 10.5 - - + -
241B LEU* 3.8 27.4 - - + -
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Residues in contact with MET 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 2.8 31.8 + - - +
196B LYS* 4.1 18.2 - - + +
198B LEU* 1.3 77.2 - - - +
200B LYS* 1.3 57.3 + - - +
202B PHE* 3.3 1.7 + - - +
203B ARG* 2.8 67.9 + - - +
240B ASN* 3.8 36.8 - - + +
241B LEU* 3.7 20.2 - - + -
244B ALA* 3.9 18.9 - - + +
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 3.2 46.5 + - + +
144B LEU* 3.9 18.1 - - + +
145B GLU* 3.2 29.3 + - - +
148B THR* 4.4 2.6 + - - -
196B LYS* 3.4 21.0 + - - +
197B MET* 3.1 12.4 + - - +
199B MET* 1.3 76.0 - - - +
201B VAL* 1.3 59.1 + - - +
203B ARG* 3.3 21.6 + - - +
204B CYS* 2.9 31.9 + - - +
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Residues in contact with VAL 201 (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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144B LEU* 4.1 9.9 - - + -
184B LEU* 4.0 29.3 - - + +
187B CYS* 4.0 26.5 - - + +
188B VAL* 4.4 14.4 - - + -
197B MET* 2.8 24.5 + - + +
198B LEU* 3.4 12.8 - - + +
200B LYS* 1.3 76.5 - - - +
202B PHE* 1.3 66.2 + - + +
204B CYS* 3.5 1.9 + - - +
205B LEU* 2.8 28.4 + - + +
224B LEU* 4.2 18.2 - - + -
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Residues in contact with PHE 202 (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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198B LEU* 2.8 31.1 + - + +
199B MET 3.7 3.8 - - - +
201B VAL* 1.3 80.6 - - + +
203B ARG* 1.3 59.9 + - - +
205B LEU* 4.2 9.0 - - + -
206B GLY* 2.8 25.8 + - - -
224B LEU* 4.8 4.9 - - + -
227B LEU* 4.6 14.4 - - + -
228B LEU* 3.5 39.3 - - + -
231B VAL* 4.0 22.9 - - + -
241B LEU* 3.6 30.5 - - + -
244B ALA* 4.3 17.3 - - + +
245B ALA* 4.0 21.1 - - + -
248B CYS* 3.5 16.3 - - + +
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Residues in contact with ARG 203 (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 THR* 4.0 15.1 - - + +
196B LYS* 5.6 1.8 + - - +
199B MET* 2.8 58.5 + - - +
200B LYS* 3.6 21.2 - - - +
202B PHE* 1.3 75.9 - - - +
204B CYS* 1.3 57.4 + - - +
206B GLY* 3.1 2.4 + - - -
207B SER* 2.9 31.0 + - - -
244B ALA* 5.2 9.6 - - + +
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Residues in contact with CYS 204 (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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144B LEU* 4.1 7.9 - - + +
147B LEU* 3.9 19.1 - - - -
148B THR* 3.2 24.1 + - - +
180B VAL* 4.2 7.0 - - - -
184B LEU* 4.1 20.0 - - + -
200B LYS 2.9 16.1 + - - +
201B VAL 3.7 4.3 - - - +
203B ARG* 1.3 75.1 - - - +
205B LEU* 1.3 64.4 + - - +
207B SER* 3.1 10.4 + - - -
208B TRP* 3.1 45.3 + - - -
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Residues in contact with LEU 205 (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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181B VAL* 5.0 11.4 - - + -
184B LEU* 3.9 20.8 - - + +
201B VAL* 2.8 19.8 + - + +
202B PHE* 3.7 12.1 - - + +
204B CYS* 1.3 75.8 - - - +
206B GLY* 1.3 62.6 + - - +
208B TRP* 3.3 14.5 + - + +
209B PHE* 3.1 40.5 + - + -
224B LEU* 3.9 37.7 - - + +
225B LEU* 4.9 4.5 - - + -
228B LEU* 4.6 9.0 - - + -
248B CYS* 3.8 16.8 - - - -
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Residues in contact with GLY 206 (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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202B PHE 2.8 21.9 + - - -
203B ARG* 3.5 2.7 - - - -
205B LEU* 1.3 74.9 - - - +
207B SER* 1.3 56.0 + - - +
208B TRP 3.1 3.9 + - - -
209B PHE* 3.5 18.2 + - - +
210B ASN* 5.0 4.3 - - - +
248B CYS* 3.8 15.2 - - - -
251B SER* 3.9 23.6 - - - -
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Residues in contact with SER 207 (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 THR* 3.1 36.1 + - - +
151B PRO* 3.4 21.5 - - - +
152B GLU* 3.7 20.9 - - - +
203B ARG 2.9 14.1 + - - -
204B CYS 3.1 10.7 + - - -
206B GLY* 1.3 73.6 - - - +
208B TRP* 1.3 60.0 + - - +
209B PHE 3.6 0.7 - - - -
210B ASN* 5.1 10.4 + - - +
211B LEU* 5.3 0.3 - - - +
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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