Contacts of the helix formed by residues 207 - 226 (chain B) in PDB entry 1KNU
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B SER* 1.3 71.1 + - - +
209B ALA* 3.1 4.6 - - - +
210B ASP* 2.8 29.1 + - + +
211B LEU* 3.2 24.8 + - + +
415B GLN* 5.1 10.9 + - - +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU* 1.3 81.9 - - - +
209B ALA* 1.3 66.1 + - - +
211B LEU* 3.1 11.7 + - - +
212B ARG* 3.1 27.4 + - - +
419B LEU* 3.8 19.4 - - - +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU* 3.1 2.1 - - - +
208B SER* 1.3 85.0 + - - +
210B ASP* 1.3 62.8 + - - +
212B ARG* 3.4 9.0 + - - +
213B ALA* 3.0 27.5 + - - +
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Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU* 2.8 20.8 + - + +
209B ALA* 1.3 79.9 - - - +
211B LEU* 1.3 60.6 + - + +
213B ALA* 3.3 8.2 + - - +
214B LEU* 3.0 27.0 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU* 3.8 20.4 - - + +
208B SER* 3.1 15.4 + - - +
210B ASP* 1.3 77.5 - - + +
212B ARG* 1.3 60.8 + - - +
214B LEU* 3.3 6.2 + - + +
215B ALA* 3.0 26.3 + - - +
412B ASN* 3.3 29.4 - - - +
415B GLN* 3.9 28.3 - - + +
416B ALA* 3.7 28.2 - - + +
419B LEU* 3.9 22.0 - - + -
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Residues in contact with ARG 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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208B SER* 3.1 19.0 + - - +
209B ALA* 3.7 9.2 - - - +
210B ASP 3.3 0.2 - - - -
211B LEU* 1.3 74.9 + - - +
213B ALA* 1.3 61.2 + - - +
215B ALA* 3.1 18.3 + - - +
216B LYS* 2.9 52.3 + - - +
416B ALA 4.8 1.0 + - - -
419B LEU* 3.8 19.7 - - + +
420B GLN* 2.7 52.3 + - - +
423B LEU* 3.8 23.6 - - + +
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Residues in contact with ALA 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 ALA 3.0 13.7 + - - +
210B ASP* 3.4 12.6 - - - +
212B ARG* 1.3 77.8 - - - +
214B LEU* 1.3 57.7 + - - +
216B LYS* 3.2 13.6 + - - +
217B HIS* 2.9 29.7 + - - +
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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 ASP 3.0 13.2 + - - +
211B LEU* 3.5 9.4 - - + +
212B ARG 3.2 0.2 - - - -
213B ALA* 1.3 75.8 - - - +
215B ALA* 1.3 57.9 + - - +
217B HIS* 3.6 5.3 - - + +
218B LEU* 3.0 53.3 + - + +
304B PRO* 3.8 32.1 - - + -
412B ASN* 3.8 30.1 - - + +
413B LEU* 3.8 21.5 - - + -
416B ALA* 3.8 14.6 - - + -
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Residues in contact with ALA 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 LEU 3.0 14.2 + - - +
212B ARG* 3.1 33.6 + - - +
214B LEU* 1.3 75.5 - - - +
216B LYS* 1.3 64.3 + - - +
218B LEU* 3.6 1.8 + - - +
219B TYR* 3.0 24.8 + - - +
382B SER* 5.3 2.3 - - - +
386B ILE* 3.8 30.5 - - + +
416B ALA* 5.0 1.3 - - + +
420B GLN* 4.2 3.8 - - + +
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Residues in contact with LYS 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 ARG* 2.9 41.6 + - - +
213B ALA* 3.6 11.8 - - - +
215B ALA* 1.3 73.4 - - - +
217B HIS* 1.3 61.7 + - - +
219B TYR* 3.2 6.3 + - - +
220B ASP* 2.8 42.7 + - - +
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Residues in contact with HIS 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 ALA 2.9 17.3 + - - +
214B LEU* 3.6 8.3 - - + +
216B LYS* 1.3 77.7 - - - +
218B LEU* 1.3 68.8 + - + +
220B ASP* 3.3 8.8 + - + +
221B SER* 3.0 26.0 + - - -
302B SER* 2.9 41.0 + - - -
304B PRO* 4.0 21.7 - - + +
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Residues in contact with LEU 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* 3.0 34.4 + - + +
215B ALA* 4.0 4.0 - - - +
217B HIS* 1.3 77.3 - - - +
219B TYR* 1.3 59.2 + - - +
221B SER* 3.3 3.2 + - - -
222B TYR* 2.8 29.6 + - - +
299B TYR* 3.3 27.2 - - + +
302B SER* 4.8 2.7 - - - +
303B ILE* 4.1 34.1 - - + -
304B PRO* 4.3 7.2 - - + -
385B ALA* 4.0 7.0 - - + -
386B ILE* 4.5 18.8 - - + -
389B ALA* 4.4 8.5 - - + -
413B LEU* 3.7 26.7 - - + -
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Residues in contact with TYR 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 ALA 3.0 19.3 + - - +
216B LYS* 3.4 7.2 - - - +
217B HIS 3.2 0.2 - - - -
218B LEU* 1.3 77.7 - - - +
220B ASP* 1.3 78.1 - - - +
222B TYR* 2.9 14.7 + + - +
223B ILE* 3.0 42.9 + - + +
381B ASP* 3.9 16.2 + - + +
382B SER* 3.5 44.2 - - - -
385B ALA* 4.0 8.0 - - - +
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Residues in contact with ASP 220 (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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216B LYS* 2.8 33.7 + - - +
217B HIS* 3.8 6.6 + - + +
219B TYR* 1.3 87.5 - - - +
221B SER* 1.3 60.8 + - - +
223B ILE* 3.5 7.1 + - - +
224B LYS* 3.4 26.3 + - - +
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Residues in contact with SER 221 (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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217B HIS* 3.0 21.4 + - - -
218B LEU* 3.5 5.8 - - - -
220B ASP* 1.3 77.7 - - - +
222B TYR* 1.3 63.5 + - - +
224B LYS* 3.3 8.4 + - - +
225B SER* 3.1 27.9 + - - -
299B TYR* 3.5 10.2 + - - -
302B SER* 2.6 37.3 + - - -
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Residues in contact with TYR 222 (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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218B LEU 2.8 14.2 + - - +
219B TYR* 3.2 9.2 - + - +
221B SER* 1.3 72.7 - - - +
223B ILE* 1.3 75.4 + - + +
224B LYS 3.0 2.0 - - - -
225B SER 3.1 0.3 + - - -
226B PHE* 2.9 62.3 + + + +
229B THR* 4.6 7.6 - - + -
230B LYS* 4.4 4.7 + - - +
299B TYR* 3.5 15.0 - + + -
329B MET* 3.9 21.3 - - + +
332B SER* 5.0 1.9 + - - -
381B ASP* 2.9 48.2 + - + -
384B LEU* 4.1 14.8 - - + +
385B ALA* 3.8 26.2 - - + -
388B ILE* 3.9 13.9 - - + -
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Residues in contact with ILE 223 (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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219B TYR* 3.0 58.7 + - + +
220B ASP* 3.8 7.9 - - - +
222B TYR* 1.3 84.4 - - + +
224B LYS* 1.3 58.8 + - - +
226B PHE 4.1 11.9 - - - +
227B PRO* 5.3 1.4 - - - +
229B THR* 3.6 28.3 - - + +
381B ASP* 4.8 2.9 - - + +
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Residues in contact with LYS 224 (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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220B ASP* 3.4 16.6 + - - +
221B SER* 3.3 9.6 + - - +
222B TYR 3.0 0.8 - - - -
223B ILE* 1.3 81.2 - - + +
225B SER* 1.3 59.6 + - - +
226B PHE 5.2 0.4 - - - -
227B PRO* 5.5 0.3 - - - +
298B GLU* 3.9 11.6 - - - +
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Residues in contact with SER 225 (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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221B SER* 3.1 16.5 + - - -
222B TYR 3.1 3.4 + - - -
224B LYS* 1.3 80.1 - - - +
226B PHE* 1.3 62.5 + - - +
227B PRO* 3.4 9.8 - - - +
295B GLU* 3.5 37.0 - - - +
298B GLU* 3.2 29.8 + - - +
299B TYR* 3.6 19.1 + - - -
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Residues in contact with PHE 226 (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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222B TYR* 2.9 49.4 + + + +
223B ILE 4.1 9.0 - - - +
224B LYS 5.2 0.2 - - - -
225B SER* 1.3 81.4 - - - +
227B PRO* 1.3 69.5 - - - +
228B LEU 3.3 8.8 + - - +
229B THR* 3.7 16.6 - - + +
288B ARG* 5.7 0.2 - - - -
295B GLU* 3.5 33.7 - - + -
296B ILE* 3.8 28.0 - - + -
299B TYR* 3.9 29.2 - + + -
325B ILE* 5.3 0.9 - - + -
329B MET* 3.5 39.7 - - + -
388B ILE* 4.8 2.7 - - + -
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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