Contacts of the helix formed by residues 207 - 218 (chain C) in PDB entry 1KOO
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 GLU 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C GLU* 4.0 0.3 - - - +
156C ASN* 3.4 29.6 + - + +
158C ARG* 2.7 38.8 + - - +
205C LYS* 2.5 39.5 + - - +
206C PRO* 1.3 76.9 - - - +
208C GLN* 1.3 55.0 + - + +
209C VAL 3.0 2.0 - - - +
210C GLU* 2.8 14.4 + - + +
211C GLN* 2.6 38.2 + - - +
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Residues in contact with GLN 208 (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* 2.6 47.1 - - + +
205C LYS* 2.5 49.8 + - + +
207C GLU* 1.3 72.5 - - + +
209C VAL* 1.3 54.6 + - - +
211C GLN* 3.7 6.3 + - - +
212C LEU* 2.9 29.5 + - - +
243C ILE* 6.0 0.2 - - - +
244C ASP* 6.0 0.4 + - - -
245C VAL* 5.0 8.7 - - + +
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Residues in contact with VAL 209 (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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203C GLU 4.9 0.7 - - - +
204C LEU* 3.6 33.4 - - + +
205C LYS 3.3 2.7 + - - +
206C PRO* 5.1 1.8 - - + -
207C GLU 3.0 0.4 - - - -
208C GLN* 1.3 76.0 - - - +
210C GLU* 1.3 73.1 + - - +
212C LEU* 3.0 6.8 + - - +
213C LYS* 2.7 41.9 + - + +
255C ALA* 4.7 12.1 - - + -
259C ILE* 4.8 16.4 - - + -
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Residues in contact with GLU 210 (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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335B SER* 4.9 15.3 + - - -
360B ILE* 4.4 7.0 - - - +
206C PRO* 3.4 17.4 - - - +
207C GLU* 2.8 25.3 + - + +
209C VAL* 1.3 95.3 - - - +
211C GLN* 1.3 63.4 + - - +
212C LEU 3.2 0.2 + - - -
213C LYS* 3.4 20.3 + - - +
214C LEU* 3.4 11.6 + - - +
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Residues in contact with GLN 211 (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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207C GLU 2.6 19.2 + - - +
208C GLN* 3.9 6.7 - - - +
210C GLU* 1.3 73.1 - - - +
212C LEU* 1.3 62.1 + - - +
214C LEU* 3.1 37.9 - - - +
215C ILE* 3.4 14.5 - - + +
218C LYS* 5.9 0.8 - - - +
237C ASP* 5.8 1.4 + - - -
241C GLN* 5.7 3.5 - - - +
243C ILE* 3.3 40.3 - - + +
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.9 6.5 - - + -
208C GLN 2.9 21.0 + - - +
209C VAL* 3.5 4.7 - - - +
211C GLN* 1.3 72.4 - - - +
213C LYS* 1.3 55.5 + - - +
214C LEU 2.6 17.4 + - - -
215C ILE* 2.9 32.7 + - + -
216C MET* 3.0 42.1 + - + +
229C LEU* 5.7 1.8 - - + -
232C LEU* 5.8 3.1 - - + -
245C VAL* 3.6 37.5 - - + -
247C LEU* 5.7 0.9 - - + -
252C SER 4.6 1.6 - - - +
255C ALA* 4.2 24.7 - - + -
256C THR* 4.3 7.9 - - - +
259C ILE* 4.0 3.4 - - + -
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Residues in contact with LYS 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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339B SER* 4.6 12.7 + - - -
360B ILE* 4.8 18.2 - - + +
362B PHE* 2.8 49.4 - - + -
209C VAL* 2.7 27.1 + - + +
210C GLU* 3.7 14.5 + - - +
212C LEU* 1.3 71.0 - - - +
214C LEU* 1.3 57.2 + - - +
216C MET* 3.2 3.4 - - - +
259C ILE* 3.4 26.3 - - + +
262C GLU* 3.0 26.9 + - - -
263C ASN* 3.4 29.4 + - - +
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Residues in contact with LEU 214 (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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360B ILE* 3.8 27.1 - - + +
210C GLU 3.4 7.9 + - - +
211C GLN* 3.1 31.0 - - - +
212C LEU 2.6 5.1 + - - -
213C LYS* 1.3 72.5 - - - +
215C ILE* 1.3 53.6 + - + +
216C MET 2.6 4.6 + - - -
217C SER* 2.4 48.5 + - - +
218C LYS* 3.0 31.4 + - + +
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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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211C GLN* 3.4 23.1 - - + +
212C LEU* 2.9 24.4 + - + +
214C LEU* 1.3 74.5 - - + +
216C MET* 1.3 58.4 - - + +
218C LYS* 2.6 44.9 - - + +
219C ARG* 3.5 13.4 - - + +
237C ASP* 5.1 14.1 - - + +
238C LEU* 5.9 5.4 - - + -
241C GLN* 3.4 24.9 - - + +
243C ILE* 4.0 13.7 - - + -
245C VAL* 5.5 2.7 - - + -
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Residues in contact with MET 216 (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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362B PHE* 3.4 9.6 - - + -
212C LEU* 3.0 48.9 + - + +
213C LYS 3.2 14.1 - - - +
214C LEU 2.6 4.6 + - - -
215C ILE* 1.3 71.9 - - - +
217C SER* 1.3 68.2 + - - +
220C TYR* 3.3 20.6 + - - +
227C LEU* 3.3 37.9 - - + +
229C LEU* 4.0 21.1 - - + -
256C THR* 4.1 22.2 - - - +
259C ILE* 3.3 38.1 - - + -
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Residues in contact with SER 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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360B ILE* 3.8 8.8 - - - +
361B ALA 3.6 24.2 - - - -
362B PHE* 3.1 26.9 - - - +
214C LEU* 2.4 45.0 + - - +
216C MET* 1.3 73.7 - - - +
218C LYS* 1.3 55.0 + - - +
219C ARG 2.5 17.8 + - - -
220C TYR* 2.7 21.6 + - - +
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Residues in contact with LYS 218 (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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211C GLN* 5.9 0.6 - - - +
214C LEU* 3.0 34.7 + - + +
215C ILE* 2.6 32.0 - - + +
217C SER* 1.3 81.2 + - - +
219C ARG* 1.3 69.3 + - - +
237C ASP* 5.2 10.1 + - - +
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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