Contacts of the helix formed by residues 230 - 242 (chain D) in PDB entry 2OVL
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 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255C TYR* 5.8 3.6 - - + -
258C HIS* 5.7 5.9 + - - -
204D VAL* 3.5 15.8 - - - +
226D THR* 4.9 2.0 + - + +
227D ILE* 3.6 23.0 + - + +
228D PRO 3.2 2.7 - - - -
229D ASP* 1.3 74.9 - - - +
231D LEU* 1.3 62.7 + - - +
232D VAL* 3.5 6.4 + - - +
233D GLY* 2.9 35.1 + - - -
234D ASN* 2.6 32.8 + - - +
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Residues in contact with LEU 231 (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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231C LEU* 4.9 5.6 - - + -
259C ASN* 3.9 31.1 + - - +
228D PRO 4.7 10.1 - - - +
229D ASP 3.2 8.9 + - - +
230D ASP* 1.3 73.0 + - - +
232D VAL* 1.3 61.3 + - + +
235D ALA* 2.9 30.0 + - - +
256D ASP 5.3 0.9 - - - +
259D ASN* 4.0 25.8 - - + +
260D ALA* 3.9 22.0 - - + +
263D ALA* 4.3 14.2 - - + +
265D SER* 3.4 25.3 - - - +
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Residues in contact with VAL 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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258C HIS* 5.3 6.5 - - + +
262C ARG* 3.3 47.3 - - - +
230D ASP* 3.4 5.7 + - - +
231D LEU* 1.3 77.2 - - + +
233D GLY* 1.3 68.2 + - - +
235D ALA* 3.2 7.6 + - - +
236D ARG* 3.0 22.1 + - + +
239D ARG* 4.9 2.7 + - - +
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Residues in contact with GLY 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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204D VAL* 3.6 21.4 - - - +
230D ASP* 2.9 29.4 + - - -
232D VAL* 1.3 75.6 - - - +
234D ASN* 1.3 58.2 + - - +
236D ARG* 3.1 8.0 + - - +
237D ILE* 2.9 30.5 + - - +
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Residues in contact with ASN 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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204D VAL* 4.8 0.2 - - - +
225D PRO* 4.2 11.6 - - - +
226D THR* 3.5 20.7 + - - +
227D ILE 2.9 26.5 + - - +
228D PRO* 4.1 9.0 + - - +
230D ASP* 2.6 30.8 + - - +
233D GLY* 1.3 76.0 - - - +
235D ALA* 1.3 57.3 + - - +
237D ILE* 3.1 11.9 + - - +
238D VAL* 2.9 31.9 + - - +
245D ILE* 5.3 2.4 - - - +
265D SER* 3.3 28.5 - - - +
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Residues in contact with ALA 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 LEU 2.9 18.6 + - - +
232D VAL* 3.4 8.7 - - - +
233D GLY 3.2 0.2 - - - -
234D ASN* 1.3 76.7 - - - +
236D ARG* 1.3 57.3 + - - +
238D VAL* 3.3 3.1 + - - +
239D ARG* 3.0 46.4 + - + +
263D ALA* 3.6 24.0 - - + +
264D GLY 3.6 14.3 - - - +
265D SER* 3.7 1.0 - - - +
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Residues in contact with ARG 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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204D VAL* 3.4 19.6 - - + +
205D ASP* 2.7 31.1 + - - +
208D ILE* 4.0 14.1 - - + +
232D VAL* 3.0 13.5 + - + +
233D GLY* 3.1 12.8 + - - +
235D ALA* 1.3 76.2 - - - +
237D ILE* 1.3 64.6 + - - +
239D ARG* 3.2 27.8 + - - +
240D GLU* 3.0 49.4 + - - +
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Residues in contact with ILE 237 (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 VAL* 3.9 24.9 - - + +
207D ALA* 3.8 24.5 - - + -
208D ILE* 4.1 11.0 - - + +
225D PRO* 3.9 18.2 - - + -
226D THR* 3.6 30.5 - - + -
233D GLY 2.9 18.4 + - - +
234D ASN* 3.1 10.5 + - - +
236D ARG* 1.3 76.0 - - - +
238D VAL* 1.3 56.6 + - - +
241D SER* 2.8 45.1 + - - -
245D ILE* 3.9 23.3 - - + -
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Residues in contact with VAL 238 (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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234D ASN 2.9 17.5 + - - +
235D ALA 3.4 8.7 - - - +
237D ILE* 1.3 79.2 - - - +
239D ARG* 1.3 67.1 + - + +
240D GLU 3.4 0.2 + - - -
241D SER* 3.9 7.4 + - - -
242D GLY 4.5 3.5 + - - -
243D HIS 5.0 3.2 - - - +
245D ILE* 3.9 22.2 - - + -
264D GLY 3.5 22.0 - - - +
265D SER 3.6 17.3 - - - +
266D LEU* 3.7 9.4 - - - +
267D THR* 3.8 21.3 - - + -
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Residues in contact with ARG 239 (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 VAL* 4.9 2.2 + - - +
235D ALA* 3.0 39.4 + - - +
236D ARG* 3.2 32.4 + - - +
238D VAL* 1.3 82.8 - - + +
240D GLU* 1.3 64.4 + - + +
264D GLY 6.1 0.2 - - - +
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Residues in contact with GLU 240 (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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208D ILE* 3.8 39.4 - - + +
212D ARG* 5.3 4.5 + - - +
236D ARG* 3.0 46.0 + - + +
239D ARG* 1.3 83.9 + - + +
241D SER* 1.3 61.9 + - - +
242D GLY 3.5 3.3 + - - -
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Residues in contact with SER 241 (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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208D ILE* 5.0 4.4 - - - +
211D ALA* 3.6 28.1 - - - +
215D ALA* 5.8 0.3 - - - +
222D ILE* 5.2 0.4 - - - -
237D ILE* 2.8 37.6 + - - -
238D VAL 3.9 2.4 + - - -
239D ARG 3.8 0.4 - - - -
240D GLU* 1.3 75.0 - - - +
242D GLY* 1.3 59.8 + - - +
243D HIS* 2.8 36.4 + - - -
245D ILE* 3.4 20.7 - - - +
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Residues in contact with GLY 242 (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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238D VAL 4.5 4.6 + - - -
239D ARG 5.1 1.0 + - - -
240D GLU 3.5 3.8 + - - -
241D SER* 1.3 78.7 + - - +
243D HIS* 1.3 63.4 + - - +
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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