Contacts of the helix formed by residues 191 - 208 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B THR* 4.2 1.6 + - - +
178B PRO 3.8 5.2 - - - +
179B PRO* 3.8 6.6 - - - +
180B VAL* 2.8 37.3 + - - +
181B ASN 4.2 2.3 + - - -
189D HIS 4.0 0.6 + - - -
190D ALA* 1.3 71.9 - - - +
192D SER* 1.3 68.7 + - - +
193D ALA* 3.1 28.4 - - - +
194D CYS* 2.9 29.9 + - + +
195D LEU* 3.0 11.4 + - - +
321D GLY 4.2 4.7 + - - +
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Residues in contact with SER 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 3.4 21.4 - - - +
190D ALA 3.2 7.0 + - - -
191D ASP* 1.3 71.9 + - - +
193D ALA* 1.3 58.6 + - - +
195D LEU* 3.3 8.9 + - - +
196D LYS* 2.9 31.0 + - - +
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Residues in contact with ALA 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR* 3.4 17.0 + - - +
178B PRO* 3.9 5.6 - - + +
180B VAL* 3.7 14.1 - - + -
191D ASP* 3.1 15.5 + - - +
192D SER* 1.3 81.2 + - - +
194D CYS* 1.3 61.5 + - - +
196D LYS* 3.3 8.1 + - - +
197D ALA* 3.1 22.2 + - - +
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Residues in contact with CYS 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B CYS* 6.2 0.9 - - - -
177B THR* 3.6 26.6 + - + +
191D ASP* 2.9 22.7 + - + +
193D ALA* 1.3 79.2 - - - +
195D LEU* 1.3 63.3 + - - +
197D ALA* 3.2 3.6 + - - +
198D PHE* 3.0 21.5 + - - +
319D PHE* 4.1 13.0 - - - -
320D THR 3.4 25.8 - - - -
321D GLY 5.0 1.8 - - - +
322D ILE* 3.9 19.5 - - + -
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ALA* 4.5 7.6 - - + +
191D ASP 3.0 11.3 + - - +
192D SER* 3.6 11.2 - - - +
194D CYS* 1.3 78.3 - - - +
196D LYS* 1.3 57.5 + - - +
198D PHE* 3.3 9.9 + - + +
199D ARG* 2.9 28.3 + - + +
322D ILE* 4.0 29.3 - - + +
326D GLN* 3.7 35.0 - - + +
330D THR* 3.5 24.9 - - + +
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Residues in contact with LYS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D SER 2.9 13.5 + - - +
193D ALA* 3.4 12.8 - - - +
195D LEU* 1.3 75.5 - - - +
197D ALA* 1.3 56.7 + - - +
199D ARG* 3.0 14.7 + - + +
200D ASP* 2.8 77.2 + - - +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B THR* 4.3 14.1 - - + -
193D ALA 3.1 9.1 + - - +
194D CYS 3.5 9.4 - - - +
196D LYS* 1.3 79.3 - - - +
198D PHE* 1.3 62.4 + - - +
200D ASP* 4.0 8.1 - - - +
201D ALA* 3.1 24.1 + - - +
319D PHE* 3.7 20.3 - - + -
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D CYS 3.0 5.8 + - - +
195D LEU* 3.6 16.8 - - + +
197D ALA* 1.3 75.6 - - - +
199D ARG* 1.3 66.7 + - - +
201D ALA* 3.3 1.6 + - - +
202D ALA* 2.9 23.2 + - + +
305D ILE* 4.4 7.0 - - + -
307D VAL* 4.8 0.7 - - + -
312D ALA* 3.6 21.5 - - + -
313D ARG 4.7 0.7 - - - -
314D VAL* 3.6 27.8 - - + -
319D PHE* 3.8 22.4 - + + -
322D ILE* 3.5 31.0 - - + -
327D ALA* 3.8 30.1 - - + -
330D THR* 4.3 11.7 - - + -
331D LEU* 4.0 28.7 - - + -
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Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 2.9 16.1 + - + +
196D LYS* 3.4 17.0 - - - +
198D PHE* 1.3 77.3 - - - +
200D ASP* 1.3 64.0 + - - +
202D ALA* 3.2 2.8 + - - -
203D GLU* 2.9 36.5 + - - +
330D THR* 3.6 37.0 + - + +
333D GLU* 3.2 40.6 + - - +
334D LEU* 3.6 30.0 - - + +
337D GLN* 4.9 8.3 - - - +
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Residues in contact with ASP 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D LYS* 2.8 61.9 + - - +
197D ALA* 4.0 6.9 - - - +
199D ARG* 1.3 78.2 - - - +
201D ALA* 1.3 63.0 + - - +
203D GLU* 3.7 12.5 - - - +
204D ASN* 3.1 33.5 + - - +
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Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ALA 3.1 16.4 + - - +
198D PHE 3.7 2.7 - - - +
200D ASP* 1.3 79.5 - - - +
202D ALA* 1.3 63.4 + - - +
204D ASN* 3.6 5.8 + - - +
205D LYS* 3.3 21.5 + - - +
314D VAL* 3.3 31.9 - - + +
319D PHE* 3.8 9.6 - - + -
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D PHE* 2.9 22.8 + - + +
199D ARG* 3.6 4.5 - - - +
201D ALA* 1.3 75.7 - - - +
203D GLU* 1.3 57.6 + - - +
205D LYS* 3.1 2.8 + - - +
206D LEU* 2.8 34.4 + - + +
305D ILE* 4.2 17.0 - - + -
314D VAL* 4.1 7.5 - - + +
331D LEU* 4.0 20.6 - - + -
334D LEU* 3.7 15.5 - - + -
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Residues in contact with GLU 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ARG* 2.9 22.3 + - - +
200D ASP* 3.7 14.5 - - - +
202D ALA* 1.3 75.6 - - - +
204D ASN* 1.3 59.3 + - - +
205D LYS 3.1 0.3 + - - -
206D LEU* 3.1 4.0 + - - +
207D ALA* 2.6 39.3 + - + +
334D LEU* 3.6 22.0 - - + +
337D GLN* 2.5 38.5 + - - +
338D HIS* 4.1 10.9 - - + +
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Residues in contact with ASN 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D ASP* 3.1 18.9 + - - +
201D ALA* 3.8 6.7 - - - +
202D ALA 3.4 0.2 - - - -
203D GLU* 1.3 81.2 - - - +
205D LYS* 1.3 58.7 + - - +
207D ALA* 3.7 6.4 + - - +
208D MET* 3.0 33.8 - - - +
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Residues in contact with LYS 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ALA 3.3 10.8 + - - +
202D ALA 3.1 8.7 + - - +
203D GLU 3.1 0.4 - - - -
204D ASN* 1.3 80.4 - - - +
206D LEU* 1.3 65.5 + - + +
207D ALA 3.4 0.3 + - - -
208D MET* 3.5 12.1 + - - +
209D SER* 3.5 11.1 + - - -
278D ASP 3.3 18.8 + - - -
279D THR* 3.1 28.3 - - - +
302D ALA* 2.8 31.2 + - - +
303D GLN* 3.8 5.8 - - - +
304D THR 4.8 2.9 - - - +
305D ILE* 3.9 23.8 - - + -
314D VAL* 5.5 3.4 - - + -
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ALA 2.8 23.6 + - - +
203D GLU* 3.9 3.8 - - - +
205D LYS* 1.3 75.2 - - + +
207D ALA* 1.3 63.9 + - - +
209D SER* 3.2 21.7 + - - +
212D THR* 4.7 11.8 + - + +
279D THR* 4.5 9.0 - - - +
281D LEU* 4.5 7.9 - - + -
305D ILE* 3.3 27.4 - - + -
331D LEU* 4.7 11.9 - - + -
334D LEU* 4.1 26.5 - - + -
335D CYS* 4.1 26.0 - - - +
338D HIS* 4.1 21.9 - - + +
340D HIS* 4.7 1.6 - - - -
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Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D GLU* 2.6 25.2 + - + +
204D ASN* 3.8 9.2 - - - +
205D LYS 3.2 0.2 - - - -
206D LEU* 1.3 74.3 - - - +
208D MET* 1.3 60.3 + - + +
209D SER 3.4 1.3 - - - +
338D HIS* 3.4 30.2 - - + +
340D HIS* 5.7 2.6 + - - -
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Residues in contact with MET 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D ASN* 3.0 23.1 - - - +
205D LYS* 3.5 5.3 + - - +
206D LEU 3.2 0.4 - - - -
207D ALA* 1.3 80.4 - - + +
209D SER* 1.3 62.4 + - - +
210D LYS* 3.6 15.3 + - - +
278D 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