Contacts of the helix formed by residues 225 - 236 (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 LEU 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220D VAL* 2.9 22.7 + - + +
223D HIS* 3.5 20.0 - - + +
224D GLY* 1.3 75.0 - - - +
226D LYS* 1.3 67.7 + - - +
227D HIS 3.4 2.0 - - - -
228D ALA* 3.4 21.3 + - + +
229D LEU* 3.1 27.0 + - + +
324D MET* 3.6 38.1 - - + -
325D ASN* 3.7 32.1 - - + +
328D ILE* 3.7 11.4 - - + -
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Residues in contact with LYS 226 (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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220D VAL* 3.9 12.4 + - - +
221D LEU* 4.4 19.1 - - + +
224D GLY* 3.5 2.9 - - - -
225D LEU* 1.3 75.3 - - - +
227D HIS* 1.3 65.0 + - + +
229D LEU* 2.8 26.9 + - - +
230D GLN* 2.9 30.3 + - - +
248D GLY 2.8 30.0 + - - -
249D ILE* 3.5 28.2 - - + +
398D ASP* 4.7 8.9 + - - +
399D VAL 3.8 20.8 + - - +
400D ASN* 5.4 1.8 - - - +
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Residues in contact with HIS 227 (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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224D GLY 5.3 1.7 + - - +
225D LEU 3.4 0.2 - - - -
226D LYS* 1.3 86.4 - - + +
228D ALA* 1.3 58.0 + - - +
230D GLN* 3.7 22.5 - - - +
231D LYS* 2.9 34.9 + - - +
398D ASP* 5.5 4.6 + - - -
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Residues in contact with ALA 228 (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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225D LEU* 3.4 34.4 + - + +
226D LYS 3.1 0.6 - - - -
227D HIS* 1.3 79.3 - - - +
229D LEU* 1.3 61.3 + - + +
231D LYS* 3.6 6.8 + - - +
232D TRP* 2.9 27.8 + - - +
328D ILE* 4.8 10.7 - - + +
332D VAL* 5.3 2.3 - - - +
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Residues in contact with LEU 229 (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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214D LEU* 4.7 5.6 - - + +
216D ALA* 3.2 34.5 - - + -
220D VAL* 4.0 14.4 - - + -
225D LEU* 3.1 19.4 + - + +
226D LYS* 2.8 14.6 + - - +
228D ALA* 1.3 75.9 - - + +
230D GLN* 1.3 64.8 + - - +
232D TRP* 3.1 17.3 + - + +
233D VAL* 3.0 24.9 + - - +
249D ILE* 3.5 15.9 - - + -
250D PHE* 3.7 16.6 - - + -
283D VAL* 4.6 5.8 - - + -
328D ILE* 3.8 34.3 - - + -
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Residues in contact with GLN 230 (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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226D LYS* 2.9 33.7 + - - +
227D HIS* 3.7 26.3 - - - +
229D LEU* 1.3 75.2 - - - +
231D LYS* 1.3 63.9 + - - +
233D VAL* 3.1 13.0 - - - +
234D LYS* 3.0 24.8 + - - +
249D ILE 3.1 30.1 + - - +
250D PHE* 4.4 6.2 - - + -
251D ASP* 4.4 13.9 - - - +
397D ALA* 5.9 2.0 - - - +
398D ASP* 5.4 10.3 + - - +
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D HIS 2.9 18.4 + - - +
228D ALA* 3.7 6.5 - - - +
230D GLN* 1.3 78.0 - - - +
232D TRP* 1.3 62.3 + - - +
234D LYS* 3.2 10.6 + - + +
235D GLU* 3.0 54.3 + - + +
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Residues in contact with TRP 232 (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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214D LEU* 3.9 23.8 - - + -
228D ALA 2.9 16.3 + - - +
229D LEU* 3.3 18.4 - - + +
231D LYS* 1.3 77.7 - - - +
233D VAL* 1.3 59.7 + - - +
235D GLU* 3.1 3.1 + - - +
236D VAL* 2.8 33.0 + - + -
238D MET* 3.2 25.7 - - + +
281D LEU* 3.4 36.8 - - + -
283D VAL* 4.3 13.9 - - + -
328D ILE* 3.9 23.1 - - + -
331D LEU* 3.7 24.7 - - + -
332D VAL* 3.5 37.1 - - + +
335D CYS* 3.7 20.4 - - - +
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Residues in contact with VAL 233 (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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214D LEU* 5.0 3.6 - - + +
229D LEU 3.0 10.9 + - - +
230D GLN* 3.1 19.3 - - - +
232D TRP* 1.3 82.2 - - - +
234D LYS* 1.3 63.3 + - + +
236D VAL 3.3 21.3 - - - +
237D PRO* 3.6 6.8 - - - +
238D MET* 4.3 10.1 - - + +
240D HIS* 3.2 47.3 - - + +
250D PHE* 3.8 24.0 - - + -
254D GLN* 6.5 0.9 - - + -
255D ALA 4.8 2.6 - - - +
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Residues in contact with LYS 234 (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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230D GLN 3.0 18.8 + - - +
231D LYS* 3.5 10.5 - - + +
233D VAL* 1.3 82.5 - - + +
235D GLU* 1.3 64.6 + - + +
237D PRO* 3.9 11.4 - - - +
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Residues in contact with GLU 235 (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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231D LYS* 3.0 57.9 + - + +
232D TRP* 3.8 4.3 - - - +
234D LYS* 1.3 83.0 - - + +
236D VAL* 1.3 60.9 + - + +
237D PRO* 3.2 9.1 - - - +
332D VAL* 5.0 2.1 - - + +
336D LYS* 2.8 42.4 + - - +
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Residues in contact with VAL 236 (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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232D TRP* 2.8 24.4 + - + +
233D VAL* 3.3 12.6 - - - +
235D GLU* 1.3 80.3 - - + +
237D PRO* 1.3 68.8 - - + +
238D MET* 3.3 35.3 + - + +
332D VAL* 4.7 0.9 - - + +
335D CYS* 4.0 20.0 - - + +
336D LYS* 3.6 38.6 - - + +
339D VAL* 5.4 9.0 - - + -
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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