Contacts of the helix formed by residues 225 - 236 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C VAL* 2.9 24.0 + - + +
223C HIS* 3.5 26.0 - - + +
224C GLY* 1.3 74.8 - - - +
226C LYS* 1.3 64.3 + - - +
227C HIS 3.4 2.2 - - - -
228C ALA* 3.4 19.4 + - + +
229C LEU* 3.2 24.9 + - - +
324C MET* 3.7 32.5 - - + -
325C ASN* 3.8 31.6 - - + +
328C ILE* 3.7 16.4 - - + -
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Residues in contact with LYS 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C VAL* 3.9 11.8 + - - +
221C LEU* 4.1 20.1 - - + +
224C GLY* 3.5 4.2 - - - -
225C LEU* 1.3 75.6 - - - +
227C HIS* 1.3 71.8 + - + +
229C LEU* 3.1 6.0 + - - +
230C GLN* 3.0 38.1 + - - +
248C GLY 2.9 29.8 + - - -
249C ILE* 3.7 25.1 - - + +
398C ASP* 5.2 6.0 - - - +
399C VAL 3.6 21.0 + - - +
400C ASN* 4.8 6.7 - - - +
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Residues in contact with HIS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLY 5.2 1.5 + - - +
225C LEU 3.4 0.4 - - - -
226C LYS* 1.3 86.4 - - + +
228C ALA* 1.3 57.3 + - - +
230C GLN* 3.7 21.8 - - - +
231C LYS* 2.9 34.2 + - - +
398C ASP* 5.5 4.8 + - - -
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LEU* 3.4 32.8 + - + +
226C LYS 3.2 0.8 - - - -
227C HIS* 1.3 77.6 - - - +
229C LEU* 1.3 62.8 + - + +
231C LYS* 3.8 7.9 - - - +
232C TRP* 3.0 26.9 + - - +
328C ILE* 4.7 11.5 - - + +
332C VAL* 5.2 2.1 - - - +
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Residues in contact with LEU 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LEU* 4.7 4.7 - - + +
216C ALA* 3.2 35.7 - - + -
220C VAL* 4.1 13.5 - - + -
225C LEU* 3.2 15.3 + - + +
226C LYS 3.1 8.5 + - - +
228C ALA* 1.3 80.5 - - - +
230C GLN* 1.3 65.6 + - - +
232C TRP* 3.2 16.1 + - + +
233C VAL* 3.0 26.0 + - - +
249C ILE* 3.5 14.6 - - + -
250C PHE* 3.7 16.8 - - + -
283C VAL* 4.5 7.2 - - + -
328C ILE* 3.9 34.3 - - + -
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Residues in contact with GLN 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C LYS* 3.0 33.6 + - - +
227C HIS* 3.7 22.5 - - - +
229C LEU* 1.3 75.6 - - - +
231C LYS* 1.3 63.2 + - - +
233C VAL* 3.0 25.8 - - - +
234C LYS* 3.0 12.0 + - - +
248C GLY 5.0 0.4 + - - -
249C ILE 2.9 31.1 + - - +
250C PHE* 4.3 10.7 - - + +
251C ASP* 4.5 7.8 - - - +
397C ALA* 6.1 2.0 - - - +
398C ASP* 5.4 9.6 + - - +
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C HIS 2.9 18.7 + - - +
228C ALA* 3.8 7.2 - - - +
230C GLN* 1.3 77.8 - - - +
232C TRP* 1.3 61.6 + - - +
234C LYS* 3.2 10.3 + - + +
235C GLU* 2.9 54.2 + - + +
336C LYS* 6.0 0.4 - - - +
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Residues in contact with TRP 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LEU* 3.9 24.5 - - + -
228C ALA 3.0 17.0 + - - +
229C LEU* 3.3 18.4 - - + +
231C LYS* 1.3 77.6 - - - +
233C VAL* 1.3 60.6 + - - +
235C GLU* 3.1 4.0 + - - +
236C VAL* 2.8 33.0 + - + -
238C MET* 3.3 24.7 - - + +
281C LEU* 3.5 35.7 - - + -
283C VAL* 4.3 14.4 - - + -
328C ILE* 4.1 22.7 - - + -
331C LEU* 3.7 26.7 - - + -
332C VAL* 3.5 36.2 - - + +
335C CYS* 3.9 21.1 - - - +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LEU* 4.9 5.2 - - + -
229C LEU 3.0 11.5 + - - +
230C GLN* 3.0 22.4 - - - +
232C TRP* 1.3 81.0 - - - +
234C LYS* 1.3 62.6 + - + +
236C VAL 3.3 20.6 - - - +
237C PRO* 3.6 6.8 - - + +
238C MET* 4.2 10.5 - - + +
240C HIS* 3.1 48.2 - - + +
250C PHE* 3.8 22.2 - - + -
255C ALA 4.9 1.7 - - - +
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C GLN 3.0 18.0 + - - +
231C LYS* 3.5 10.5 - - + +
232C TRP 3.1 0.2 - - - -
233C VAL* 1.3 80.1 - - + +
235C GLU* 1.3 63.1 + - + +
237C PRO* 4.0 10.9 - - - +
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Residues in contact with GLU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LYS* 2.9 55.8 + - + +
232C TRP* 3.7 4.0 - - - +
234C LYS* 1.3 83.3 - - + +
236C VAL* 1.3 61.4 + - + +
237C PRO* 3.3 8.9 - - - +
332C VAL* 5.1 2.0 - - + +
336C LYS* 2.6 48.3 + - + +
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C TRP* 2.8 17.7 + - + +
233C VAL* 3.3 11.2 - - - +
235C GLU* 1.3 84.1 - - + +
237C PRO* 1.3 69.1 - - + +
238C MET* 3.4 35.9 + - + +
332C VAL 4.7 0.7 - - - +
335C CYS* 4.0 20.0 - - + +
336C LYS* 3.7 38.8 - - + +
338C HIS 5.8 1.6 - - - +
339C VAL* 5.7 8.7 - - + -
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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