Contacts of the helix formed by residues 191 - 208 (chain B) in PDB entry 1OVM
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 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B HIS 4.0 0.6 + - - -
190B ALA* 1.3 72.4 - - - +
192B SER* 1.3 67.3 + - - +
193B ALA* 3.1 29.3 - - - +
194B CYS* 2.9 29.4 + - + +
195B LEU* 3.0 11.6 + - - +
321B GLY 4.2 4.2 + - - +
14D ARG* 5.8 1.2 + - - +
177D THR* 4.2 1.1 + - - +
178D PRO 3.6 5.9 - - - +
179D PRO* 3.6 8.1 - - - +
180D VAL* 2.6 36.3 + - - +
181D ASN* 4.0 2.8 + - - +
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ALA 3.2 6.5 + - - -
191B ASP* 1.3 71.9 + - - +
193B ALA* 1.3 63.0 + - - +
195B LEU* 3.4 8.0 + - - +
196B LYS* 3.0 24.4 + - - +
180D VAL* 3.2 23.1 - - - +
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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
----------------------------------------------------------
191B ASP* 3.1 15.7 + - - +
192B SER* 1.3 80.5 + - - +
194B CYS* 1.3 60.5 + - - +
196B LYS* 3.2 8.5 + - - +
197B ALA* 3.1 21.7 + - - +
177D THR* 3.5 15.3 + - - +
178D PRO* 3.7 7.0 - - + +
180D VAL* 3.5 13.5 - - + -
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Residues in contact with CYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASP* 2.9 26.3 + - + +
193B ALA* 1.3 73.8 - - - +
195B LEU* 1.3 66.6 + - - +
197B ALA* 3.2 3.8 + - - +
198B PHE* 3.0 21.0 + - - +
319B PHE* 4.0 13.8 - - - -
320B THR 3.4 25.4 - - - +
321B GLY 5.0 1.3 - - - +
322B ILE* 3.8 19.3 - - + -
146D CYS* 6.1 1.6 - - - -
177D THR* 3.6 27.7 + - + +
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ALA* 4.6 7.9 - - + +
191B ASP 3.0 11.7 + - - +
192B SER* 3.7 11.4 - - - +
194B CYS* 1.3 77.2 - - - +
196B LYS* 1.3 52.7 + - - +
198B PHE* 3.2 12.3 + - + +
199B ARG* 2.8 33.9 + - + +
322B ILE* 4.1 30.0 - - + +
326B GLN* 3.8 35.2 - - + +
330B THR* 3.5 26.5 - - + +
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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
----------------------------------------------------------
192B SER 3.0 13.9 + - - +
193B ALA* 3.3 13.5 - - - +
195B LEU* 1.3 74.4 - - - +
197B ALA* 1.3 60.9 + - - +
199B ARG* 3.0 14.2 + - + +
200B ASP* 2.8 73.5 + - - +
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ALA 3.1 10.0 + - - +
194B CYS 3.5 7.9 - - - +
196B LYS* 1.3 78.0 - - - +
198B PHE* 1.3 63.0 + - - +
200B ASP* 3.5 8.0 + - - +
201B ALA* 3.1 24.8 + - - +
319B PHE* 3.7 20.1 - - + -
177D THR* 4.2 15.5 - - + -
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Residues in contact with PHE 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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194B CYS 3.0 6.4 + - - +
195B LEU* 3.5 22.2 - - + +
197B ALA* 1.3 77.0 - - - +
199B ARG* 1.3 65.2 + - - +
201B ALA* 3.2 2.3 + - - +
202B ALA* 2.9 24.4 + - + +
305B ILE* 4.3 7.0 - - + -
307B VAL* 4.8 0.7 - - + -
312B ALA* 3.6 24.2 - - + -
313B ARG 4.6 0.4 - - - -
314B VAL* 3.6 27.4 - - + -
319B PHE* 3.7 23.3 - + + -
322B ILE* 3.5 25.1 - - + -
327B ALA* 3.8 28.7 - - + -
330B THR* 4.2 12.3 - - + -
331B LEU* 3.9 29.4 - - + -
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Residues in contact with ARG 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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195B LEU* 2.8 20.4 + - + +
196B LYS* 3.0 16.8 + - - +
198B PHE* 1.3 75.2 - - - +
200B ASP* 1.3 63.8 + - - +
202B ALA* 3.2 2.0 + - - -
203B GLU* 2.9 34.2 + - - +
330B THR* 3.6 36.1 + - + +
333B GLU* 3.3 36.7 + - - +
334B LEU* 3.5 28.5 - - + +
337B GLN* 4.0 14.8 - - - +
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Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LYS* 2.8 63.7 + - - +
197B ALA* 4.0 6.8 - - - +
199B ARG* 1.3 77.6 - - - +
201B ALA* 1.3 62.9 + - - +
203B GLU* 3.4 13.3 + - - +
204B ASN* 3.0 34.3 + - - +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA 3.1 18.6 + - - +
198B PHE 3.7 3.1 - - - +
200B ASP* 1.3 78.6 - - - +
202B ALA* 1.3 62.1 + - - +
204B ASN* 3.6 5.9 + - - +
205B LYS* 3.3 21.5 + - - +
314B VAL* 3.3 31.5 - - + +
319B PHE* 3.8 10.8 - - + -
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PHE* 2.9 20.8 + - + +
199B ARG* 3.6 5.8 - - - +
201B ALA* 1.3 77.9 - - - +
203B GLU* 1.3 57.2 + - - +
205B LYS* 3.1 7.6 + - - +
206B LEU* 2.8 32.4 + - + +
305B ILE* 4.6 5.2 - - + -
314B VAL* 4.1 16.3 - - + +
331B LEU* 4.0 21.8 - - + -
334B LEU* 3.6 14.8 - - + -
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 2.9 21.2 + - - +
200B ASP* 3.6 15.0 - - - +
202B ALA* 1.3 74.6 - - - +
204B ASN* 1.3 62.3 + - - +
206B LEU* 3.2 3.7 + - - +
207B ALA* 2.6 42.1 + - + +
334B LEU* 3.4 26.1 - - + +
337B GLN* 3.2 23.0 - - - +
338B HIS* 4.4 11.6 + - + -
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Residues in contact with ASN 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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200B ASP* 3.0 21.4 + - - +
201B ALA* 3.9 6.7 - - - +
203B GLU* 1.3 81.0 - - - +
205B LYS* 1.3 59.6 + - - +
207B ALA* 3.7 6.7 + - - +
208B MET* 3.0 33.2 - - - +
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Residues in contact with LYS 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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201B ALA 3.3 11.0 + - - +
202B ALA 3.1 8.5 + - - +
203B GLU 3.1 0.4 - - - -
204B ASN* 1.3 77.3 - - - +
206B LEU* 1.3 64.5 + - + +
208B MET* 3.4 12.6 + - - +
209B SER* 3.5 11.1 + - - -
278B ASP* 3.3 19.8 + - - +
279B THR* 3.1 28.3 - - + +
302B ALA* 2.8 29.6 + - - +
303B GLN* 3.8 6.3 - - - +
304B THR 4.9 0.9 - - - +
305B ILE* 3.8 26.5 - - + -
314B VAL* 5.5 4.5 - - + -
315B GLY 6.2 1.6 - - - +
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Residues in contact with LEU 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 ALA 2.8 20.2 + - - +
203B GLU* 3.9 3.6 - - - +
205B LYS* 1.3 73.0 - - + +
207B ALA* 1.3 65.8 + - - +
209B SER* 3.0 21.9 + - - +
212B THR* 4.4 9.8 + - + +
279B THR* 3.8 20.0 - - - +
281B LEU* 4.5 8.7 - - + -
305B ILE* 3.7 23.6 - - + -
331B LEU* 4.6 12.8 - - + -
334B LEU* 4.0 29.6 - - + +
335B CYS* 4.4 21.1 - - - -
338B HIS* 3.5 26.3 - - + +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU* 2.6 27.8 + - + +
204B ASN* 3.7 9.0 - - - +
205B LYS 3.3 0.2 - - - -
206B LEU* 1.3 73.0 - - - +
208B MET* 1.3 59.7 + - + +
209B SER 3.4 1.3 + - - +
338B HIS* 3.0 26.5 + - - +
340B HIS* 6.1 0.7 - - - -
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Residues in contact with MET 208 (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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204B ASN* 3.0 23.1 - - - +
205B LYS* 3.4 6.0 + - - +
206B LEU 3.1 0.8 - - - -
207B ALA* 1.3 80.7 - - + +
209B SER* 1.3 63.1 + - - +
210B LYS* 3.6 14.5 + - - +
278B ASP* 4.2 1.4 - - - +
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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