Contacts of the helix formed by residues 235 - 242 (chain C) in PDB entry 6B0Z
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 TYR 235 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C HIS* 2.7 37.1 + + - +
197C PHE* 3.6 35.7 - + + -
198C GLN* 3.7 31.2 + - + -
201C LEU* 4.1 20.2 - - + -
230C ILE* 3.5 20.0 - - + -
231C TYR* 3.2 12.5 + - + +
233C LYS 3.8 0.6 - - - -
234C GLN* 1.3 98.2 + - + +
236C LYS* 1.3 57.5 + - - +
237C SER* 3.1 3.3 - - - +
238C GLN* 2.9 15.9 + - - -
239C PHE* 2.7 49.3 + - + -
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Residues in contact with LYS 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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231C TYR* 2.9 55.4 + - + +
232C ASP* 4.4 20.9 + - - +
233C LYS 5.4 0.2 - - - -
235C TYR* 1.3 74.3 - - - +
237C SER* 1.3 61.7 + - - +
239C PHE* 3.8 0.2 - - - +
240C GLU* 3.1 52.3 + - - +
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Residues in contact with SER 237 (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 LYS 5.7 1.2 + - - -
234C GLN 6.2 0.7 - - - -
235C TYR* 3.1 1.7 - - - +
236C LYS* 1.3 81.8 - - - +
238C GLN* 1.3 66.0 + - - +
240C GLU* 3.5 8.4 + - - +
241C ALA* 3.4 17.3 + - - +
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Residues in contact with GLN 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C LEU* 4.0 26.4 - - + +
234C GLN 3.6 18.5 + - - +
235C TYR* 2.9 22.0 + - - +
237C SER* 1.3 78.5 - - - +
239C PHE* 1.3 65.4 + - + +
241C ALA* 3.2 20.2 + - - +
242C GLN* 3.6 14.6 + - - +
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Residues in contact with PHE 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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197C PHE* 3.6 43.1 - + - -
200C ALA* 3.5 29.2 - - + -
201C LEU* 4.8 8.3 - - + -
207C LEU* 4.3 3.6 - - + -
231C TYR* 3.4 24.0 - + + +
235C TYR* 2.7 34.5 + + + +
236C LYS 3.8 1.6 - - - +
238C GLN* 1.3 77.6 - - + +
240C GLU* 1.3 59.0 + - - +
241C ALA 3.4 0.5 + - - -
242C GLN 3.5 0.7 + - - -
243C LYS 3.5 2.1 + - - -
244C ILE* 3.0 47.2 + - + +
245C TRP* 3.3 44.0 - - - -
246C TYR* 3.9 7.2 - - + -
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Residues in contact with GLU 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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231C TYR* 5.0 2.5 - - - +
236C LYS* 3.1 50.4 + - + +
237C SER* 4.1 6.6 - - - +
238C GLN 3.3 0.4 - - - -
239C PHE* 1.3 75.7 - - + +
241C ALA* 1.3 64.7 + - - +
243C LYS* 3.6 15.1 + - - +
244C ILE 4.2 8.3 - - - +
245C TRP* 6.5 0.2 - - + -
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Residues in contact with ALA 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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237C SER 3.4 11.6 + - - +
238C GLN* 3.2 14.1 + - - +
240C GLU* 1.3 79.6 - - - +
242C GLN* 1.3 61.7 + - + +
243C LYS* 3.2 16.5 + - - +
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Residues in contact with GLN 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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201C LEU* 3.4 40.9 + - - +
204C GLY* 3.7 16.3 - - - +
238C GLN* 3.6 11.8 + - - +
239C PHE 3.5 2.0 + - - -
241C ALA* 1.3 78.6 - - + +
243C LYS* 1.3 70.2 + - - +
244C ILE* 3.1 26.9 + - + +
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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