Contacts of the helix formed by residues 191 - 208 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A HIS 4.0 0.6 + - - -
190A ALA* 1.3 72.9 - - - +
192A SER* 1.3 67.4 + - - +
193A ALA* 3.2 28.8 + - - +
194A CYS* 3.0 18.7 + - + +
195A LEU* 3.0 20.1 + - - +
321A GLY 4.3 4.6 + - - +
14C ARG* 5.9 1.5 + - - +
177C THR* 4.5 1.2 + - - +
178C PRO 3.8 4.7 - - - +
179C PRO* 4.0 6.8 - - - +
180C VAL* 2.9 37.3 + - - +
181C ASN* 4.0 4.2 + - - +
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Residues in contact with SER 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA 3.2 5.9 + - - -
191A ASP* 1.3 72.3 + - - +
193A ALA* 1.3 59.0 + - - +
195A LEU* 3.4 8.6 + - - +
196A LYS* 2.9 29.7 + - - +
180C VAL* 3.3 21.3 - - - +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASP* 3.2 13.3 + - - +
192A SER* 1.3 81.9 + - - +
194A CYS* 1.3 62.3 - - - +
196A LYS* 3.3 8.6 + - - +
197A ALA* 3.1 21.8 + - - +
177C THR* 3.7 16.0 + - - +
178C PRO* 3.9 6.1 - - + +
180C VAL* 3.5 15.3 - - + -
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Residues in contact with CYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASP* 3.0 24.6 + - + +
193A ALA* 1.3 75.3 - - - +
195A LEU* 1.3 67.8 + - - +
197A ALA* 3.2 3.8 + - - +
198A PHE* 3.0 20.8 + - - +
319A PHE* 4.1 13.3 - - - -
320A THR 3.2 27.4 - - - -
321A GLY 5.0 1.8 - - - +
322A ILE* 3.8 17.7 - - + -
146C CYS* 6.3 1.1 - - - -
177C THR* 3.8 25.1 + - + +
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ALA* 4.5 6.7 - - + +
191A ASP 3.0 11.7 + - - +
192A SER* 3.7 12.1 - - - +
194A CYS* 1.3 76.6 - - - +
196A LYS* 1.3 57.2 + - - +
198A PHE* 3.3 12.3 + - + +
199A ARG* 2.8 28.7 + - + +
322A ILE* 4.1 29.5 - - + +
326A GLN* 3.6 36.1 - - + +
330A THR* 3.5 26.0 - - + +
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Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER 2.9 17.5 + - - +
193A ALA* 3.4 9.6 - - - +
195A LEU* 1.3 74.5 - - - +
197A ALA* 1.3 60.6 + - - +
199A ARG* 3.1 13.3 + - + +
200A ASP* 2.8 73.4 + - - +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA 3.1 9.9 + - - +
194A CYS 3.2 8.0 + - - +
196A LYS* 1.3 78.5 - - - +
198A PHE* 1.3 63.6 + - - +
200A ASP* 3.5 8.3 + - - +
201A ALA* 3.1 23.7 + - - +
319A PHE* 3.6 20.9 - - + -
177C THR* 4.2 15.5 - - + -
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A CYS 3.0 6.2 + - - +
195A LEU* 3.5 22.9 - - + +
197A ALA* 1.3 76.2 - - - +
199A ARG* 1.3 66.7 + - - +
201A ALA* 3.2 2.4 + - - +
202A ALA* 2.9 22.5 + - + +
305A ILE* 4.3 7.6 - - + -
307A VAL* 4.8 0.7 - - + -
312A ALA* 3.6 22.7 - - + -
313A ARG 4.6 0.9 - - - -
314A VAL* 3.6 26.9 - - + -
319A PHE* 3.8 22.8 - + + -
322A ILE* 3.5 24.9 - - + -
327A ALA* 3.8 29.2 - - + -
330A THR* 4.2 11.4 - - + -
331A LEU* 3.9 28.3 - - + -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 2.8 17.7 + - + +
196A LYS* 3.1 15.5 + - - +
198A PHE* 1.3 78.1 - - - +
200A ASP* 1.3 62.7 + - - +
202A ALA* 3.2 1.7 + - - -
203A GLU* 2.9 36.4 + - - +
330A THR* 3.5 37.1 + - + +
333A GLU* 3.3 36.9 + - - +
334A LEU* 3.6 21.3 - - + +
337A GLN* 3.8 23.8 - - - +
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Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS* 2.8 61.3 + - - +
197A ALA* 4.0 6.9 - - - +
199A ARG* 1.3 78.6 - - - +
201A ALA* 1.3 63.2 + - - +
203A GLU* 3.7 12.4 - - - +
204A ASN* 3.0 33.6 + - - +
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ALA 3.1 19.0 + - - +
198A PHE 3.7 2.9 - - - +
200A ASP* 1.3 75.8 - - - +
202A ALA* 1.3 63.4 + - - +
204A ASN* 3.5 7.0 + - - +
205A LYS* 3.3 21.3 + - - +
314A VAL* 3.3 31.4 - - + +
319A PHE* 3.8 9.4 - - + -
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PHE* 2.9 21.0 + - + +
199A ARG* 3.6 5.4 - - - +
201A ALA* 1.3 77.8 - - - +
203A GLU* 1.3 57.4 + - - +
205A LYS* 3.2 3.3 + - - +
206A LEU* 2.8 33.2 + - + +
305A ILE* 4.3 8.7 - - + -
314A VAL* 4.0 16.0 - - + +
331A LEU* 4.0 21.1 - - + -
334A LEU* 3.8 14.6 - - + -
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ARG* 2.9 22.5 + - - +
200A ASP* 3.7 14.1 - - - +
202A ALA* 1.3 74.2 - - - +
204A ASN* 1.3 62.5 + - - +
206A LEU* 3.9 3.8 - - - +
207A ALA* 2.6 40.6 + - + +
334A LEU* 3.5 21.9 - - + +
337A GLN* 2.9 26.3 + - - +
338A HIS* 4.4 12.4 + - + +
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Residues in contact with ASN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASP* 3.0 24.1 + - - +
201A ALA* 3.8 7.2 - - - +
203A GLU* 1.3 80.9 - - - +
205A LYS* 1.3 58.5 + - - +
207A ALA* 3.7 5.9 + - - +
208A MET* 3.0 33.4 - - - +
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ALA 3.3 10.8 + - - +
202A ALA 3.2 8.5 + - - +
203A GLU 3.1 0.4 - - - -
204A ASN* 1.3 79.7 - - - +
206A LEU* 1.3 64.9 + - + +
208A MET* 3.4 13.4 + - - +
209A SER* 3.5 10.4 + - - -
278A ASP 3.4 18.0 + - - -
279A THR* 3.1 29.0 - - - +
302A ALA* 2.7 30.3 + - - +
303A GLN* 3.8 4.0 - - - +
304A THR 4.9 1.1 - - - +
305A ILE* 3.8 26.7 - - + -
314A VAL* 5.5 3.8 - - + -
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA 2.8 21.5 + - - +
203A GLU* 3.9 3.4 - - - +
205A LYS* 1.3 74.5 - - + +
207A ALA* 1.3 64.8 + - - +
209A SER* 3.1 23.7 + - - +
212A THR* 4.8 8.5 + - + +
279A THR* 4.3 14.1 - - - +
281A LEU* 4.5 8.1 - - + -
305A ILE* 3.5 27.8 - - + -
331A LEU* 4.5 13.2 - - + -
334A LEU* 3.9 35.2 - - + -
335A CYS* 4.7 15.5 - - - -
338A HIS* 3.7 23.9 - - + +
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLU* 2.6 27.1 + - + +
204A ASN* 3.8 9.0 - - - +
205A LYS 3.2 0.2 - - - -
206A LEU* 1.3 73.4 - - - +
208A MET* 1.3 59.9 + - + +
209A SER 3.9 1.2 + - - +
338A HIS* 3.3 25.1 - - + +
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Residues in contact with MET 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASN* 3.0 22.9 - - - +
205A LYS* 3.4 6.2 + - - +
206A LEU 3.1 0.4 - - - -
207A ALA* 1.3 79.6 - - + +
209A SER* 1.3 62.6 + - - +
210A LYS* 3.6 14.6 + - - +
278A ASP* 4.2 1.6 - - - +
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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