Contacts of the helix formed by residues 236 - 245 (chain H) in PDB entry 6V3O
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 THR 236 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234H GLN 3.6 2.8 + - - -
235H PRO* 1.3 74.9 - - - +
237H PRO* 1.3 68.8 - - - +
238H GLN* 2.6 31.2 + - + +
239H ASP* 3.1 38.3 + - - +
240H GLU* 2.9 26.1 + - - +
242H ARG* 5.1 0.9 - - - +
298H ARG* 4.3 4.0 - - - +
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Residues in contact with PRO 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H PRO 4.5 1.6 - - - +
236H THR* 1.3 92.0 - - - +
238H GLN* 1.3 59.0 + - - +
240H GLU* 3.5 16.0 + - + +
241H MET* 3.0 27.9 + - - +
289H MET* 5.1 0.2 - - - +
290H GLY* 4.9 10.4 + - - +
296H ASN* 6.2 0.2 - - - +
298H ARG* 4.1 37.2 - - + +
299H VAL* 4.5 14.8 - - + -
303H VAL* 3.8 24.0 - - + -
307H VAL* 4.4 4.0 - - - +
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Residues in contact with GLN 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H THR* 2.6 32.8 + - + +
237H PRO* 1.3 77.3 - - - +
239H ASP* 1.3 59.8 + - - +
241H MET* 3.3 5.5 + - - +
242H ARG* 3.0 47.2 + - - +
302H GLU* 5.2 2.2 + - - -
303H VAL* 3.6 26.2 - - - +
306H ASP* 3.1 40.0 + - + +
307H VAL* 4.4 11.7 - - + -
310H LEU* 4.4 12.6 - - + -
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Residues in contact with ASP 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H PRO* 4.3 5.9 - - + +
236H THR* 3.1 31.7 + - + +
238H GLN* 1.3 73.5 - - - +
240H GLU* 1.3 66.3 + - - +
242H ARG* 2.6 39.5 + - - +
243H TYR* 2.9 52.3 + - + -
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Residues in contact with GLU 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ALA* 3.7 29.9 - - + +
177H HIS 5.2 2.8 - - - +
181H SER* 5.6 2.2 - - - +
235H PRO* 4.3 23.4 - - + +
236H THR 2.9 14.1 + - - +
237H PRO* 3.5 16.4 - - + +
238H GLN 3.4 0.2 - - - -
239H ASP* 1.3 76.5 - - - +
241H MET* 1.3 61.9 + - - +
243H TYR* 3.5 8.5 + - - +
244H GLY* 3.1 18.7 + - - -
289H MET* 4.0 18.4 - - + +
758H SER* 4.0 22.5 + - - -
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Residues in contact with MET 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237H PRO 3.0 14.4 + - - +
238H GLN 3.5 7.6 - - - +
239H ASP 3.1 0.2 - - - -
240H GLU* 1.3 73.8 - - - +
242H ARG* 1.3 65.4 + - + +
244H GLY* 3.1 10.6 + - - +
245H MET* 3.1 24.8 + - + +
287H SER* 5.2 2.0 - - - +
289H MET* 4.0 29.3 - - + +
307H VAL* 3.5 47.3 - - + +
310H LEU* 3.5 32.8 - - + -
311H ALA* 4.4 4.5 - - - +
314H MET* 3.7 20.0 - - + -
451H VAL* 6.5 0.7 - - + -
453H LEU* 6.2 0.4 - - + -
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Residues in contact with ARG 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364G GLN* 5.2 9.2 + - - -
184H ARG* 3.7 20.7 + - - +
236H THR* 5.1 0.8 - - - +
238H GLN* 3.0 35.0 + - - +
239H ASP* 2.6 41.7 + - - +
241H MET* 1.3 79.0 - - + +
243H TYR* 1.3 73.7 + - + +
245H MET* 3.2 9.9 + - - +
246H SER 3.5 7.3 + - - -
310H LEU* 4.2 30.0 - - + +
314H MET* 4.2 22.9 - - + -
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Residues in contact with TYR 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H SER* 3.1 34.8 - - - +
182H ALA* 3.3 29.7 - - + +
183H ARG* 4.0 18.4 - - + -
184H ARG* 5.3 3.6 - - - -
235H PRO* 4.8 6.1 - - + -
239H ASP* 2.9 44.4 + - + +
240H GLU* 4.0 5.6 - - - +
242H ARG* 1.3 87.4 - - + +
244H GLY* 1.3 57.6 + - - +
246H SER* 2.3 27.2 + - - -
247H TYR* 4.5 2.1 - - - -
1002H SO4 3.9 22.7 + - - -
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Residues in contact with GLY 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H PHE* 5.2 9.0 - - - -
240H GLU 3.1 11.8 + - - -
241H MET 3.1 7.7 + - - -
243H TYR* 1.3 76.8 - - - +
245H MET* 1.3 67.5 + - - +
246H SER 3.2 2.9 + - - -
247H TYR* 4.0 13.0 + - - +
248H ILE* 4.6 5.4 + - - +
289H MET* 4.2 17.2 - - - +
677H ILE* 5.2 5.5 - - - +
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Residues in contact with MET 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H PHE* 5.0 3.1 - - + -
184H ARG* 3.9 3.6 + - - +
241H MET* 3.1 26.1 + - + +
242H ARG 3.2 6.9 + - - +
244H GLY* 1.3 79.9 - - - +
246H SER* 1.3 64.4 + - - +
247H TYR 3.3 0.9 - - - -
248H ILE* 3.2 28.5 + - + +
249H HIS* 3.1 21.3 + - - +
287H SER* 4.5 3.6 - - - +
289H MET* 4.3 16.8 - - + -
311H ALA* 5.8 4.0 - - - -
314H MET* 3.6 30.5 - - - +
450H LEU* 4.3 19.3 - - + +
451H VAL* 3.7 33.4 - - + -
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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