Contacts of the helix formed by residues 212 - 217 (chain C) in PDB entry 1KYZ
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 GLY 212 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C GLY 3.6 4.7 + - - -
210C GLY 3.2 3.0 - - - -
211C THR* 1.3 80.3 - - - +
213C ALA* 1.3 50.3 + - - +
214C VAL 2.5 16.3 + - - -
215C ILE* 2.6 4.7 + - - +
216C ASN* 2.3 40.6 + - - -
229C ASN* 2.9 23.3 - - - +
247C HIS* 4.3 2.5 - - - -
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Residues in contact with ALA 213 (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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181C SER* 6.0 1.6 - - - +
184C SER* 5.5 5.4 - - - +
185C THR* 5.6 6.3 - - - +
209C GLY 4.9 0.4 + - - +
211C THR* 3.6 6.9 - - + +
212C GLY* 1.3 71.9 - - - +
214C VAL* 1.3 66.8 + - + +
216C ASN* 3.1 20.5 - - - +
217C THR* 5.0 0.6 - - - +
218C ILE* 2.9 31.3 - - + +
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C SER* 4.2 17.7 - - - +
188C MET* 3.6 16.9 - - - +
206C ASP* 3.8 19.3 - - - +
209C GLY 4.1 13.2 - - - +
212C GLY 2.5 4.4 + - - +
213C ALA* 1.3 73.2 - - + +
215C ILE* 1.3 57.9 + - - +
218C ILE* 3.1 23.2 - - - +
219C VAL* 3.0 18.8 - - + +
263C PHE* 3.4 37.2 - - + -
265C LYS* 4.4 11.0 - - + +
1699C SAH 4.4 11.7 - - - +
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Residues in contact with ILE 215 (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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204C LEU* 3.3 44.9 - - + +
206C ASP* 4.1 21.5 - - + -
212C GLY 2.6 10.3 + - - +
214C VAL* 1.3 76.1 - - + +
216C ASN* 1.3 59.4 + - - +
217C THR* 2.4 23.3 + - - -
219C VAL* 3.8 19.7 - - + -
220C SER* 3.2 22.4 + - - +
225C ILE* 6.2 0.9 - - + -
227C GLY* 3.3 22.0 - - - -
228C ILE 3.5 2.7 - - - +
229C ASN* 4.0 30.5 - - + +
245C VAL* 4.2 7.4 - - + -
263C PHE* 6.4 0.2 - - + -
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Residues in contact with ASN 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C THR* 3.5 17.0 + - - +
212C GLY* 2.3 37.0 + - - +
213C ALA* 3.1 15.7 - - - +
215C ILE* 1.3 68.8 - - - +
217C THR* 1.3 63.3 + - + +
240C PRO* 3.4 33.0 + - - +
242C TYR* 2.6 49.3 - - - +
243C PRO 4.3 0.3 - - - +
245C VAL* 3.0 25.7 - - - +
247C HIS* 4.5 1.3 + - - -
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Residues in contact with THR 217 (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 ALA 5.0 0.2 - - - +
215C ILE 2.4 6.9 + - - -
216C ASN* 1.3 88.9 - - + +
218C ILE* 1.3 73.6 + - + +
219C VAL 3.4 1.6 - - - -
220C SER* 3.0 9.9 + - - -
221C LYS* 2.8 50.3 + - - +
242C TYR* 4.2 17.7 - - + -
243C PRO* 4.4 12.8 - - - +
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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