Contacts of the helix formed by residues 233 - 243 (chain C) in PDB entry 1YAA
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 233 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C ILE* 4.8 17.3 - - + +
226C GLN* 2.8 70.2 + - + +
227C GLY* 4.1 0.9 - - - -
232C ASP* 1.3 71.7 - - - +
234C ASP* 1.3 63.8 + - - +
236C ASP* 3.5 1.0 + - - -
237C ALA* 3.2 12.6 + - - +
241C ARG* 4.9 0.4 - - - -
259C ASN* 4.6 1.1 - - - +
319C TRP* 3.5 36.1 - - + -
320C HIS* 3.9 17.9 - - + +
323C MET* 3.7 24.2 - - + +
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Residues in contact with ASP 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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86C ILE 4.8 0.7 - - - +
232C ASP* 3.3 10.8 + - - +
233C LEU* 1.3 79.9 - - - +
235C LYS* 1.3 66.8 + - + +
237C ALA* 3.4 11.4 + - - +
238C TYR* 3.7 8.0 + - - +
241C ARG* 3.0 38.4 + - - +
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Residues in contact with LYS 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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230C THR* 3.5 18.8 - - + +
232C ASP* 3.2 33.7 + - - +
234C ASP* 1.3 79.1 - - - +
236C ASP* 1.3 61.5 + - - +
237C ALA 3.4 0.7 + - - -
238C TYR* 3.4 21.0 + - + +
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Residues in contact with ASP 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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190C SER* 4.2 12.5 - - - +
191C CYS* 3.7 29.0 - - - +
223C THR* 5.4 0.2 - - - +
226C GLN* 3.9 11.8 - - + +
227C GLY* 2.8 33.2 + - - +
229C ALA* 3.0 33.7 + - - +
230C THR* 2.8 34.6 + - - +
232C ASP 3.3 7.9 + - - +
233C LEU 4.0 0.2 - - - +
234C ASP 3.3 0.8 - - - -
235C LYS* 1.3 76.7 - - - +
237C ALA* 1.3 58.7 + - - +
238C TYR 3.4 0.8 + - - -
239C ALA 4.9 0.9 + - - -
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Residues in contact with ALA 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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87C ILE* 3.4 24.9 - - + +
226C GLN* 3.5 15.7 - - - +
233C LEU 3.2 16.3 + - - +
234C ASP 3.4 2.2 + - - +
235C LYS 3.2 0.6 - - - -
236C ASP* 1.3 76.8 - - - +
238C TYR* 1.3 63.8 + - - +
239C ALA 3.4 2.2 - - - -
240C VAL* 3.2 11.3 + - - +
241C ARG* 3.0 40.2 + - - +
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Residues in contact with TYR 238 (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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202C SER* 3.5 44.9 + - - -
205C TRP* 4.1 11.7 - + + -
206C VAL* 3.6 9.4 - - - +
234C ASP 3.7 5.1 + - - +
235C LYS* 3.4 19.2 + - + +
236C ASP 3.4 2.0 - - - -
237C ALA* 1.3 78.0 - - - +
239C ALA* 1.3 62.8 + - - +
241C ARG* 3.4 7.7 + - + +
242C LEU* 2.9 61.2 + - + +
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Residues in contact with ALA 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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190C SER 3.7 13.9 + - - +
205C TRP* 3.4 49.1 - - + +
209C VAL* 4.8 1.9 - - - +
221C PHE* 3.3 17.6 - - + -
236C ASP 4.9 1.0 + - - -
237C ALA 3.4 0.8 - - - -
238C TYR* 1.3 84.7 - - - +
240C VAL* 1.3 59.1 + - + +
242C LEU* 3.0 27.7 + - - +
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Residues in contact with VAL 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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87C ILE* 4.1 24.2 - - + +
88C PHE* 4.5 7.6 - - + -
190C SER* 3.2 33.2 - - - +
221C PHE* 3.7 21.8 - - + -
223C THR* 4.0 6.3 - - + +
236C ASP 5.5 0.2 - - - +
237C ALA* 3.2 10.9 + - - +
239C ALA* 1.3 76.2 - - - +
241C ARG* 1.3 59.0 + - - +
242C VAL* 2.9 39.6 + - - +
252C VAL* 3.9 25.8 - - + -
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Residues in contact with ARG 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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85C LYS 4.7 0.4 + - - -
86C ILE 3.2 24.7 + - - -
87C ILE 3.0 19.4 + - - +
88C PHE* 3.6 19.1 + - - +
89C GLY* 3.8 19.2 - - - -
234C ASP* 3.0 40.3 + - - +
237C ALA* 3.0 29.6 + - - +
238C TYR* 3.8 6.5 - - + +
240C VAL* 1.3 73.2 - - - +
242C LEU* 1.3 96.5 + - - +
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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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205C TRP* 3.9 10.3 - - + +
206C VAL* 3.9 25.8 - - + +
209C VAL* 4.1 12.8 - - + -
238C TYR* 2.9 56.2 + - + +
239C ALA* 3.6 5.4 - - - +
240C VAL 3.2 0.2 - - - -
241C ARG* 1.3 74.6 - - - +
242C GLY* 1.3 78.1 + - - +
243C LYS* 3.0 57.8 + - + +
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Residues in contact with GLY 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 VAL* 4.0 16.3 - - - +
221C PHE* 4.1 15.3 - - - -
239C ALA 3.0 15.0 + - - -
240C VAL 3.2 3.1 + - - -
242C LEU* 1.3 129.0 - - - +
243C LYS 3.3 0.3 + - - -
244C LEU* 2.8 46.9 + - - +
250C VAL* 4.4 2.2 - - - -
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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