Contacts of the helix formed by residues 205 - 219 (chain B) in PDB entry 1KOH
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 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B LEU* 1.3 73.8 - - - +
206B PRO* 1.3 62.6 - - + +
207B GLU* 2.9 48.8 + - + +
208B GLN* 2.5 43.0 - - + +
209B VAL* 2.5 36.1 + - - +
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Residues in contact with PRO 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LEU 4.6 1.8 - - - +
205B LYS* 1.3 82.2 - - + +
207B GLU* 1.3 52.7 + - + +
208B GLN 2.7 5.6 + - - -
209B VAL* 2.5 16.8 + - + +
210B GLU* 2.3 37.7 + - - +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LYS* 2.9 28.0 + - + +
206B PRO* 1.3 78.5 - - + +
208B GLN* 1.3 55.1 + - - +
210B GLU* 2.7 39.8 - - - +
211B GLN* 4.1 1.6 + - - +
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.0 24.4 - - + +
205B LYS* 2.5 70.0 + - + +
206B PRO 2.7 0.8 + - - -
207B GLU* 1.3 78.1 - - - +
209B VAL* 1.3 50.1 + - - +
210B GLU 3.0 1.3 - - - -
211B GLN* 2.6 24.7 + - - +
212B LEU* 2.7 18.6 + - - +
242B ASN 5.7 0.2 - - - +
243B ILE* 3.2 39.8 - - + +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LEU* 4.9 13.2 - - + +
205B LYS 2.5 24.2 + - - +
206B PRO* 2.5 20.5 + - + +
208B GLN* 1.3 66.0 - - - +
210B GLU* 1.3 55.7 + - - +
211B GLN 2.6 15.1 + - - -
212B LEU* 4.1 11.0 - - + +
213B LYS* 2.9 28.0 + - + +
255B ALA* 5.7 11.0 - - + -
259B ILE* 4.7 16.2 - - + -
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B PRO 2.3 30.3 + - - +
207B GLU* 2.7 38.6 - - - +
209B VAL* 1.3 67.5 - - - +
211B GLN* 1.3 71.7 + - - +
213B LYS* 4.8 2.3 - - - +
214B LEU* 3.0 39.5 + - + +
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLU 4.4 0.9 - - - +
208B GLN* 2.6 24.2 + - - +
210B GLU* 1.3 92.1 - - - +
212B LEU* 1.3 52.6 + - - +
213B LYS 2.9 1.8 - - - -
214B LEU* 2.5 50.2 + - - +
215B ILE* 2.2 43.1 + - + +
237B ASP 5.0 0.7 - - - +
238B LEU* 4.2 16.8 - - + -
241B GLN* 2.8 39.6 + - + +
243B ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LEU* 4.6 19.7 - - + -
208B GLN 2.7 16.5 + - - +
209B VAL* 3.1 11.0 + - + +
211B GLN* 1.3 70.0 - - - +
213B LYS* 1.3 60.3 + - - +
215B ILE* 2.7 25.3 - - + +
216B MET* 2.9 25.0 + - + +
232B LEU* 3.9 13.9 - - + -
238B LEU* 5.1 2.8 - - - +
243B ILE* 5.4 0.8 - - - +
245B VAL* 3.6 38.1 - - + -
252B SER 4.1 4.3 - - - +
255B ALA* 4.4 4.0 - - + -
256B THR* 2.8 43.5 - - + +
259B ILE* 4.1 6.7 - - + -
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Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B VAL* 2.9 17.2 + - + +
210B GLU* 4.8 2.9 - - - +
211B GLN 2.9 0.4 - - - -
212B LEU* 1.3 78.7 - - - +
214B LEU* 1.3 57.3 + - - +
216B MET* 3.4 5.2 + - - +
217B SER* 3.1 25.3 + - - -
258B ARG 5.6 0.2 + - - -
259B ILE* 3.4 44.4 + - + +
262B GLU* 2.9 36.6 + - - +
263B ASN* 4.2 14.6 - - - +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLU* 3.0 35.6 + - + +
211B GLN* 2.5 25.6 + - - +
213B LYS* 1.3 76.7 - - - +
215B ILE* 1.3 57.8 + - - +
217B SER* 3.5 24.0 - - - +
218B LYS* 4.4 2.6 + - - +
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLN* 2.2 31.0 + - - +
212B LEU* 2.7 41.1 - - + +
214B LEU* 1.3 69.3 - - - +
216B MET* 1.3 72.3 + - + +
218B LYS* 3.9 5.9 + - - +
219B ARG* 3.2 27.2 + - - +
232B LEU* 4.9 5.6 - - + -
235B ASP* 3.0 32.5 - - + +
237B ASP* 5.0 6.7 - - + +
238B LEU* 3.5 41.7 - - + -
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Residues in contact with MET 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LEU* 2.9 30.2 + - + +
213B LYS* 3.6 3.1 - - - +
215B ILE* 1.3 85.4 - - + +
217B SER* 1.3 57.9 + - - +
219B ARG* 2.3 49.8 + - - +
227B LEU* 4.2 10.8 - - + -
229B LEU* 3.9 21.3 - - + -
232B LEU* 5.3 1.8 - - + -
256B THR* 3.9 26.0 - - + +
259B ILE* 3.1 50.7 - - + -
260B ILE* 4.5 14.6 - - - -
263B ASN* 5.3 4.5 - - - +
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LYS 3.1 11.1 + - - -
214B LEU* 3.5 30.7 - - - +
216B MET* 1.3 80.6 - - - +
218B LYS* 1.3 71.4 + - - +
219B ARG 3.3 5.4 - - - +
220B TYR* 3.5 13.9 - - - +
263B ASN* 5.1 7.9 + - - -
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Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU 4.4 2.8 + - - +
215B ILE 3.9 9.0 + - - +
216B MET 2.7 2.0 + - - -
217B SER* 1.3 84.0 + - - +
219B ARG* 1.3 58.5 + - + +
220B TYR* 2.6 22.9 + - - +
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Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ILE* 3.2 35.2 - - + +
216B MET* 2.3 31.8 + - - +
218B LYS* 1.3 74.5 - - + +
220B TYR* 1.3 65.9 + - - +
227B LEU* 3.4 9.9 - - - +
228B ASP* 2.8 58.4 + - + +
229B LEU* 4.7 6.3 - - + -
230B LYS* 4.0 18.9 - - - +
231B GLY 3.3 26.8 + - - -
232B LEU* 4.3 5.7 - - - +
235B ASP* 3.4 24.0 + - - +
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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