Contacts of the helix formed by residues 186 - 200 (chain B) in PDB entry 4OGB
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 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B PHE* 1.3 75.8 - - - +
187B ASP* 1.3 60.9 + - - +
188B LEU* 3.4 9.3 + - - +
189B GLU* 2.9 41.3 + - - +
190B ILE* 2.8 27.5 + - - +
306B ARG* 4.0 7.4 - - - +
508B EDO 4.0 24.2 - - - +
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Residues in contact with ASP 187 (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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129B ARG 5.6 2.3 - - - +
131B LEU* 4.2 9.0 - - + +
134B THR* 3.7 23.1 + - + +
135B PHE* 3.3 27.4 - - + -
185B PHE 5.3 0.3 - - - +
186B THR* 1.3 72.5 - - - +
188B LEU* 1.3 60.2 + - - +
190B ILE* 3.7 20.8 - - - +
191B LEU* 3.0 20.8 + - - +
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Residues in contact with LEU 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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135B PHE* 3.5 29.2 - - + -
186B THR* 3.2 8.1 + - - +
187B ASP* 1.3 76.7 - - - +
189B GLU* 1.3 60.9 + - + +
191B LEU* 3.0 15.8 + - + +
192B ALA* 2.8 29.1 + - - +
252B LEU* 4.3 7.4 - - + -
256B GLN* 3.6 41.5 - - + +
259B SER* 4.4 7.9 - - - -
260B LEU* 4.3 13.7 - - + +
263B MET* 4.1 19.3 - - + -
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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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185B PHE* 3.4 15.5 - - + -
186B THR* 2.9 42.9 + - - +
188B LEU* 1.3 75.1 - - + +
190B ILE* 1.3 62.6 + - - +
192B ALA* 3.7 1.8 - - - +
193B ALA* 3.1 24.6 + - - +
263B MET* 3.5 31.8 - - + +
303B TYR* 6.0 2.1 - - - -
306B ARG* 2.9 41.3 + - - +
310B LEU* 4.0 20.8 - - + +
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Residues in contact with ILE 190 (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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129B ARG* 3.4 37.9 - - - +
131B LEU* 4.7 8.3 - - + -
176B LEU* 3.9 25.2 - - + +
185B PHE* 4.2 15.7 - - + +
186B THR 2.8 20.7 + - - +
187B ASP* 3.7 22.7 - - - +
188B LEU 3.2 0.2 - - - -
189B GLU* 1.3 77.2 - - - +
191B LEU* 1.3 63.1 + - - +
194B ILE* 3.2 39.7 + - + +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 3.7 35.0 - - + -
131B LEU* 4.9 9.2 - - + -
135B PHE* 4.1 18.8 - - + -
137B ILE* 5.4 2.2 - - + -
187B ASP 3.0 15.9 + - - +
188B LEU* 3.0 13.9 + - + +
190B ILE* 1.3 75.8 - - - +
192B ALA* 1.3 60.3 + - - +
194B ILE* 3.2 4.4 + - + -
195B PHE* 2.8 34.2 + - + +
249B PHE* 3.5 35.2 - - + -
252B LEU* 4.1 13.2 - - + -
260B LEU* 3.7 15.7 - - + -
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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 LEU 2.8 18.8 + - - +
189B GLU* 3.7 5.4 - - - +
191B LEU* 1.3 73.0 - - - +
193B ALA* 1.3 56.4 + - - +
195B PHE* 4.5 0.4 - - - -
196B ALA* 2.9 33.4 + - - +
260B LEU* 3.6 20.6 - - + +
263B MET* 3.9 33.7 - - + -
264B VAL* 3.8 8.7 - - + +
267B ILE* 4.1 5.6 - - + +
310B LEU* 5.6 0.7 - - + -
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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
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172B THR* 4.2 16.6 - - + -
176B LEU* 4.3 13.9 - - + -
189B GLU 3.1 16.2 + - - +
190B ILE 4.0 3.4 - - - +
192B ALA* 1.3 76.4 - - - +
194B ILE* 1.3 53.7 + - - +
196B ALA* 3.9 0.2 - - - +
197B SER* 2.6 37.2 + - - -
267B ILE* 3.7 19.3 - - + +
310B LEU* 4.6 9.0 - - + -
313B MET* 5.3 1.1 - - - -
314B VAL* 3.8 9.3 - - + +
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET* 3.9 22.4 - - - -
125B ILE* 4.0 15.3 - - + -
126B PHE* 3.9 14.4 - - + -
129B ARG* 3.8 33.4 - - - +
131B LEU* 4.6 5.8 - - + -
169B VAL* 4.1 12.3 - - + +
172B THR* 4.6 5.6 - - + -
173B HIS* 4.6 6.5 - - + +
176B LEU* 3.7 15.0 - - + -
190B ILE* 3.2 23.7 + - + +
191B LEU* 3.2 4.6 + - + +
193B ALA* 1.3 75.6 - - - +
195B PHE* 1.3 59.3 + - - +
197B SER* 3.3 8.2 + - - -
198B ALA* 3.0 25.8 + - - +
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Residues in contact with PHE 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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122B MET* 4.7 9.8 - - + +
126B PHE* 5.6 1.1 - + + -
145B TYR* 3.3 35.2 - + - -
191B LEU* 2.8 23.7 + - + +
192B ALA* 3.9 2.9 - - - +
194B ILE* 1.3 74.0 - - - +
196B ALA* 1.3 65.1 + - - +
198B ALA* 2.9 18.0 + - + +
199B ILE* 3.1 29.5 + - + +
237B GLY 4.2 7.6 - - - -
238B PHE* 3.8 31.4 - + - -
241B LEU* 4.4 2.7 - - + -
248B ILE* 4.3 7.9 - - + -
249B PHE* 3.6 41.5 - + + -
260B LEU* 5.2 0.7 - - + -
264B VAL* 3.4 25.4 - - + -
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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 22.7 + - - +
193B ALA 3.9 2.7 - - - +
195B PHE* 1.3 73.8 - - - +
197B SER* 1.3 53.7 + - - +
199B ILE* 3.3 9.4 + - - +
200B HIS* 2.8 39.9 + - - +
264B VAL* 4.3 9.2 - - + +
267B ILE* 3.6 36.3 - - + -
268B VAL* 3.8 10.7 - - + +
314B VAL* 5.3 0.2 - - - -
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Residues in contact with SER 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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165B ALA* 3.9 7.8 - - - +
168B VAL* 4.1 5.3 - - - +
169B VAL* 3.8 25.1 - - - -
172B THR* 2.9 22.4 + - - +
193B ALA 2.6 22.1 + - - -
194B ILE* 3.3 7.6 - - - -
195B PHE 3.1 0.6 - - - -
196B ALA* 1.3 78.0 - - - +
198B ALA* 1.3 59.7 - - - +
200B HIS* 2.7 32.0 + - - -
314B VAL* 3.7 11.2 - - - +
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Residues in contact with ALA 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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118B LEU* 4.1 6.1 - - + +
122B MET* 3.5 32.8 - - + -
149B LEU* 3.6 20.3 - - + +
153B TYR* 2.8 29.6 + - - -
165B ALA* 3.9 5.0 - - - +
169B VAL* 3.4 14.8 - - + -
194B ILE 3.0 5.8 + - - +
195B PHE* 2.9 10.7 + - + +
197B SER* 1.3 78.6 - - - +
199B ILE* 1.3 54.2 + - + +
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Residues in contact with ILE 199 (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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145B TYR* 3.5 25.1 - - - +
149B LEU* 3.7 21.3 - - + -
153B TYR* 3.5 3.4 - - - -
195B PHE* 3.5 39.0 - - + +
196B ALA* 3.4 10.8 - - - +
198B ALA* 1.3 79.8 - - + +
200B HIS* 1.3 66.7 + - - +
201B ASP 3.0 5.0 + - - -
202B VAL* 3.2 17.5 + - - +
233B HIS* 3.6 10.3 - - - +
234B LEU* 4.3 16.8 - - + +
237B GLY* 4.0 21.5 - - - -
238B PHE* 4.7 1.1 - - + -
264B VAL* 3.9 15.7 - - + -
268B VAL* 4.3 1.8 - - + -
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Residues in contact with HIS 200 (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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153B TYR* 4.5 0.8 + - - -
164B HIS* 3.6 12.3 - + - -
165B ALA* 4.5 5.6 - - - -
168B VAL* 3.8 20.6 - - + -
196B ALA 2.8 17.8 + - - +
197B SER* 2.7 26.8 + - - -
198B ALA 3.6 0.2 - - - -
199B ILE* 1.3 75.4 - - - +
201B ASP* 1.3 70.9 + - + +
233B HIS* 3.0 22.1 - - - +
268B VAL* 4.0 25.5 - - + +
271B THR* 4.1 25.8 + - + -
314B VAL* 5.4 2.5 - - + -
318B ASP* 3.3 9.7 + - - -
502B ZN 2.4 34.0 - - - -
503B ZN 4.2 3.1 - - - -
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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