Contacts of the helix formed by residues 235 - 246 (chain C) in PDB entry 3UGV
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 ASN 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C MET* 3.7 28.1 - - - +
231C VAL* 4.4 9.3 - - + +
232C VAL* 3.1 30.1 + - + +
233C TYR 3.3 1.2 - - - -
234C ASP* 1.3 77.8 + - - +
236C PHE* 1.3 59.0 + - - +
237C ASP* 3.6 8.0 + - - +
238C GLY* 2.9 17.8 + - - -
239C TYR* 3.1 24.7 + - - -
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Residues in contact with PHE 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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233C TYR* 3.7 20.4 - + - -
234C ASP* 3.0 18.5 + - + +
235C ASN* 1.3 70.8 - - - +
237C ASP* 1.3 67.6 + - - +
239C TYR* 3.8 7.4 - + - +
240C ALA* 3.0 25.1 + - - +
252C ILE* 4.6 5.6 - - + -
256C PHE* 4.3 15.3 - + - -
261C GLU* 4.5 15.0 - - + -
264C GLN* 4.4 10.5 - - + -
265C ALA* 3.8 38.4 - - + -
268C ALA* 4.2 20.2 - - + +
270C ALA* 4.2 14.7 - - + +
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Residues in contact with ASP 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ASN* 3.3 6.6 + - - +
236C PHE* 1.3 80.4 - - - +
238C GLY* 1.3 61.5 + - - +
240C ALA* 3.5 5.7 + - - +
241C GLN* 3.3 24.7 + - - +
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Residues in contact with GLY 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C MET* 3.6 30.7 - - - +
231C VAL* 5.3 0.4 - - - -
235C ASN* 2.9 20.7 + - - -
237C ASP* 1.3 72.1 - - - +
239C TYR* 1.3 66.0 + - - +
241C GLN* 3.1 7.6 + - - +
242C LEU* 3.0 26.2 + - - +
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Residues in contact with TYR 239 (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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229C GLU* 3.4 20.6 - - - +
230C PRO* 3.7 23.8 - - + -
231C VAL* 2.5 38.1 + - + +
232C VAL 3.7 16.7 + - - -
233C TYR* 3.7 16.7 - - - -
235C ASN 3.1 25.0 + - - +
236C PHE* 3.8 12.6 - + - +
238C GLY* 1.3 75.1 - - - +
240C ALA* 1.3 57.0 + - - +
242C LEU* 3.1 7.3 + - + -
243C ARG* 2.8 31.9 + - - +
250C LEU* 3.4 18.1 - - + +
252C ILE* 3.7 26.5 - - + -
270C ALA* 3.3 21.5 - - + +
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Residues in contact with ALA 240 (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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236C PHE 3.0 17.0 + - - +
237C ASP* 3.7 7.6 - - - +
238C GLY 3.2 0.2 - - - -
239C TYR* 1.3 74.7 - - - +
241C GLN* 1.3 64.9 + - - +
243C ARG* 3.8 2.9 - - - +
244C HIS* 3.2 23.2 + - - +
268C ALA 3.6 22.0 - - - +
269C GLY* 3.5 15.9 - - - +
270C ALA* 4.1 1.0 - - - +
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Residues in contact with GLN 241 (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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209C MET* 4.5 12.3 - - + -
213C MET* 6.3 1.6 - - + -
237C ASP 3.3 13.9 + - - +
238C GLY* 3.1 10.2 + - - +
240C ALA* 1.3 77.9 - - - +
242C LEU* 1.3 60.7 + - + +
244C HIS* 3.3 10.4 + - - +
245C ASP* 3.0 42.7 + - - +
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Residues in contact with LEU 242 (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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209C MET* 4.0 28.3 - - + -
212C ALA* 4.1 17.5 - - + +
213C MET* 4.2 13.5 - - + -
216C THR* 4.0 19.7 - - + +
230C PRO* 3.7 28.3 - - + -
231C VAL* 4.5 3.1 - - + -
238C GLY 3.0 18.8 + - - +
239C TYR* 3.7 15.5 - - + +
241C GLN* 1.3 73.0 - - - +
243C ARG* 1.3 57.4 + - - +
245C ASP* 3.3 6.2 + - + +
246C LEU* 2.8 47.5 + - + +
250C LEU* 4.0 8.3 - - + -
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Residues in contact with ARG 243 (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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241B GLN* 3.5 46.8 + - - +
245B ASP* 5.5 1.4 - - - +
239C TYR 2.8 17.5 + - - +
240C ALA 3.8 4.0 - - - +
242C LEU* 1.3 75.9 - - - +
244C HIS* 1.3 59.4 + - - +
246C LEU* 2.9 24.7 - - - +
250C LEU* 3.5 16.5 - - + +
266C LEU* 6.2 0.2 - - - +
269C GLY* 3.1 38.6 + - - +
270C ALA 4.3 0.7 - - - +
271C CYS* 3.1 26.9 + - - +
272C ASP* 3.0 36.7 + - - +
299C ILE* 5.1 9.1 - - - +
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Residues in contact with HIS 244 (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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244A HIS* 4.6 6.8 + - - -
244B HIS* 3.2 45.1 + + - -
245B ASP* 4.9 3.0 - - - +
240C ALA 3.2 14.5 + - - +
241C GLN* 3.7 10.7 + - - +
242C LEU 3.2 0.4 - - - -
243C ARG* 1.3 84.3 - - - +
245C ASP* 1.3 76.7 + - - +
246C LEU 4.1 2.6 - - - +
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Residues in contact with ASP 245 (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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213C MET* 4.4 21.3 - - - +
220C ASP* 4.3 3.6 - - - +
241C GLN* 3.0 30.4 + - - +
242C LEU* 3.8 7.8 - - + +
244C HIS* 1.3 91.8 + - - +
246C LEU* 1.3 63.0 + - + +
247C LYS* 3.8 4.7 + - - +
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Residues in contact with LEU 246 (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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213B MET* 6.1 0.2 - - - +
245B ASP* 5.0 6.2 - - - +
216C THR* 3.3 55.6 - - + +
217C ARG* 4.2 3.4 - - + +
220C ASP* 3.3 23.1 - - + +
227C ILE* 4.1 14.4 - - + -
242C LEU* 2.8 29.9 + - + +
243C ARG* 2.9 18.1 - - - +
244C HIS 4.1 2.0 - - - +
245C ASP* 1.3 77.9 - - + +
247C LYS* 1.3 62.3 + - - +
248C THR 3.8 14.8 - - - +
250C LEU* 4.4 18.2 - - + -
272C ASP* 5.5 0.7 - - - +
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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