Contacts of the helix formed by residues 204 - 213 (chain C) in PDB entry 1KKQ
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 LYS 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C THR* 3.3 28.0 - - - +
201C ALA 4.7 1.8 - - - -
202C ASP 2.8 2.6 - - - +
203C LEU* 1.3 84.4 - - - +
205C SER* 1.3 61.8 + - - +
206C LEU* 3.2 2.4 + - - -
207C ALA* 4.1 17.2 + - - +
208C LYS* 4.6 4.7 + - - +
407C VAL* 5.6 1.8 - - + -
410C LEU* 5.1 15.8 - - - +
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Residues in contact with SER 205 (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 ALA 5.3 0.4 - - - -
202C ASP* 3.0 34.2 + - - +
204C LYS* 1.3 77.4 - - - +
206C LEU* 1.3 67.5 + - - +
208C LYS* 3.3 7.9 + - - +
209C ARG* 2.9 35.1 + - - +
295C PRO* 5.7 1.0 - - - +
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Residues in contact with LEU 206 (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 ASP 3.4 6.8 + - - +
203C LEU* 3.8 25.8 - - + +
205C SER* 1.3 85.0 + - - +
207C ALA* 1.3 66.5 + - - +
208C LYS 3.0 0.3 + - - -
209C ARG* 3.1 11.0 + - - -
210C ILE* 3.1 28.2 + - + +
294C ILE* 5.7 0.2 - - + -
295C PRO* 3.5 38.8 - - + +
377C LEU* 6.0 0.2 - - + -
400C MET 5.5 0.2 - - - +
403C GLY* 2.9 37.7 - - - +
404C ILE* 4.0 13.7 - - + +
407C VAL* 4.0 5.2 - - + -
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Residues in contact with ALA 207 (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 LYS* 4.1 14.9 + - - +
205C SER 3.5 0.2 - - - -
206C LEU* 1.3 79.2 - - - +
208C LYS* 1.3 60.7 + - + +
210C ILE 4.0 0.2 + - - -
211C TYR* 3.6 19.2 + - - +
377C LEU* 4.1 18.7 - - + +
407C VAL* 3.2 32.5 - - + +
411C HIS* 5.2 12.8 - - + -
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Residues in contact with LYS 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 LYS 4.6 3.6 + - - +
205C SER* 3.3 9.6 + - - +
206C LEU 3.2 0.6 - - - -
207C ALA* 1.3 77.1 - - + +
209C ARG* 1.3 61.2 + - + +
210C ILE 3.1 4.9 - - - -
211C TYR* 3.5 8.9 + - + +
212C GLU* 3.0 48.1 + - + +
700G TRP* 5.5 1.8 - - + -
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Residues in contact with ARG 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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205C SER* 2.9 31.7 + - - +
206C LEU 4.1 1.1 - - - +
208C LYS* 1.3 74.6 - - + +
210C ILE* 1.3 57.4 + - - +
212C GLU* 3.9 12.8 - - - +
213C ALA* 3.6 22.4 + - - +
293C ALA* 2.4 57.8 + - - +
294C ILE* 3.4 1.0 - - - +
295C PRO* 3.3 33.0 - - + +
700G TRP* 4.4 34.5 + - + -
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Residues in contact with ILE 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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206C LEU* 3.1 32.0 + - + +
207C ALA 4.2 2.5 - - - +
209C ARG* 1.3 78.6 - - - +
211C TYR* 1.3 64.8 + - - +
212C GLU 3.1 1.1 - - - -
213C ALA* 3.2 11.5 + - - +
214C TYR* 3.3 8.5 + - - +
290C PHE* 3.5 15.3 - - + -
294C ILE* 3.8 27.8 - - + -
295C PRO* 3.4 24.7 - - + -
376C SER* 4.0 21.3 - - - +
377C LEU* 3.9 22.9 - - + -
380C ALA* 4.1 14.8 - - + -
404C ILE* 4.5 7.9 - - + -
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Residues in contact with TYR 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 ALA 3.6 15.5 + - - +
208C LYS* 3.5 10.5 + - + +
210C ILE* 1.3 79.7 - - - +
212C GLU* 1.3 65.6 + - + +
214C TYR* 3.0 18.8 + - + +
215C LEU* 3.1 40.7 + - + +
223C VAL* 5.9 1.6 - - - +
371C ASP* 5.2 1.6 + - - -
372C ASP* 3.6 22.3 - - + +
373C SER* 3.4 43.8 + - - +
376C SER* 3.6 14.8 - - - +
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Residues in contact with GLU 212 (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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208C LYS* 3.0 52.9 + - + +
209C ARG 3.9 6.1 - - - +
210C ILE 3.1 0.2 - - - -
211C TYR* 1.3 78.1 - - + +
213C ALA* 1.3 55.8 + - - +
214C TYR 3.0 5.2 - - - -
215C LEU* 3.5 11.7 + - + +
216C LYS* 2.9 29.0 + - - +
700G TRP* 2.9 51.7 - - + -
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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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209C ARG* 3.6 16.2 + - - +
210C ILE* 3.2 12.0 + - - +
212C GLU* 1.3 78.8 - - - +
214C TYR* 1.3 55.9 + - - +
216C LYS* 3.8 4.3 - - - -
217C ASN* 3.0 37.0 + - - +
290C PHE* 3.5 14.5 - - + +
293C ALA* 3.5 32.3 - - + -
294C ILE 5.0 0.4 - - - +
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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