Contacts of the helix formed by residues 207 - 226 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A PRO* 1.3 102.8 - - - +
208A SER* 1.3 68.1 + - - +
209A ALA 3.1 2.7 - - - -
210A ASP* 3.1 27.5 + - + +
211A LEU* 3.2 23.4 + - + +
415A GLN* 5.4 5.8 - - - +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU 4.0 6.0 + - - -
205A ASN* 4.2 20.0 - - - -
206A PRO* 3.0 17.3 - - - +
207A GLU* 1.3 82.3 + - - +
209A ALA* 1.3 64.5 + - - +
211A LEU* 3.0 8.6 + - - +
212A ARG* 2.9 27.8 + - - +
419A LEU* 4.0 23.4 - - - +
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Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ASN* 4.5 8.1 + - + +
206A PRO 3.6 12.8 + - - +
208A SER* 1.3 79.8 - - - +
210A ASP* 1.3 64.2 + - - +
212A ARG* 3.2 8.4 + - - +
213A ALA* 3.0 23.6 + - - +
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Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PRO 5.9 0.2 - - - -
207A GLU* 3.1 21.7 + - + +
209A ALA* 1.3 79.0 - - - +
211A LEU* 1.3 66.8 + - + +
213A ALA* 3.3 8.6 + - - +
214A LEU* 3.1 22.0 + - - +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU* 3.2 20.2 + - + +
208A SER* 3.0 10.3 + - - +
210A ASP* 1.3 77.7 - - + +
212A ARG* 1.3 67.1 + - - +
214A LEU* 3.2 6.8 + - + +
215A ALA* 3.0 21.5 + - - +
412A ASN* 3.3 30.1 - - - +
415A GLN* 3.8 38.8 - - + +
416A ALA* 4.0 22.8 - - + +
419A LEU* 3.9 21.8 - - + -
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Residues in contact with ARG 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER* 2.9 21.1 + - - +
209A ALA* 3.8 8.1 - - - +
211A LEU* 1.3 75.4 + - - +
213A ALA* 1.3 58.8 + - - +
215A ALA* 3.0 18.0 + - - +
216A LYS* 2.9 63.0 + - - +
416A ALA 4.5 1.8 + - - -
419A LEU* 3.9 11.4 - - + +
420A GLN* 2.8 54.5 + - - +
423A LEU* 3.5 31.2 - - + +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA 3.0 13.1 + - - +
210A ASP* 3.3 13.2 - - - +
212A ARG* 1.3 78.7 - - - +
214A LEU* 1.3 60.9 + - - +
216A LYS* 3.5 11.1 + - - +
217A HIS* 3.1 23.4 + - - +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASP 3.1 13.6 + - - +
211A LEU* 3.6 8.5 - - + +
212A ARG 3.2 0.2 - - - -
213A ALA* 1.3 74.1 - - - +
215A ALA* 1.3 66.9 + - - +
217A HIS* 3.2 10.1 + - + +
218A LEU* 3.0 41.7 + - + +
304A PRO* 3.9 35.0 - - + -
412A ASN* 3.8 33.7 - - - +
413A LEU* 4.1 20.9 - - + -
416A ALA* 4.1 12.8 - - + -
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LEU 3.0 13.0 + - - +
212A ARG* 3.0 33.4 + - - +
214A LEU* 1.3 78.2 - - - +
216A LYS* 1.3 63.8 + - + +
218A LEU* 3.3 3.4 + - - +
219A TYR* 2.9 24.4 + - - +
382A SER 5.5 0.7 - - - +
386A ILE* 3.8 32.7 - - + +
416A ALA* 5.0 1.5 - - - +
420A GLN* 4.3 4.7 - - - +
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ARG* 2.9 52.8 + - - +
213A ALA* 3.8 8.7 - - - +
215A ALA* 1.3 76.3 - - + +
217A HIS* 1.3 58.1 + - - +
219A TYR* 3.3 8.1 + - - +
220A ASP* 2.8 32.5 + - - +
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Residues in contact with HIS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ALA 3.1 15.2 + - - +
214A LEU* 3.3 13.9 - - + +
216A LYS* 1.3 76.3 - - - +
218A LEU* 1.3 68.0 + - - +
220A ASP* 3.4 8.2 + - - +
221A SER* 2.8 42.4 + - - -
302A SER* 3.0 32.2 + - - -
304A PRO* 4.3 15.6 - - + +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.0 30.1 + - + +
215A ALA* 3.8 3.8 - - - +
217A HIS* 1.3 83.3 - - - +
219A TYR* 1.3 66.2 + - - +
221A SER* 3.2 2.5 + - - -
222A TYR* 2.9 25.6 + - - +
299A TYR* 3.5 28.7 - - + +
302A SER* 4.9 1.8 - - - +
303A ILE* 4.4 20.2 - - + -
304A PRO* 4.4 12.1 - - + -
385A ALA* 3.9 7.2 - - + -
386A ILE* 4.2 27.1 - - + +
389A ALA* 4.4 4.5 - - + -
413A LEU* 3.8 24.7 - - + -
416A ALA* 5.7 0.2 - - + -
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Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ALA 2.9 17.6 + - - +
216A LYS* 3.6 8.5 - - - +
218A LEU* 1.3 75.7 - - - +
220A ASP* 1.3 63.7 + - - +
222A TYR* 3.3 5.1 + + - +
223A ILE* 3.1 50.4 + - + +
381A ASP* 3.6 22.4 + - + +
382A SER* 3.5 48.9 + - - +
385A ALA* 3.8 7.7 - - + +
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Residues in contact with ASP 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LYS 2.8 18.2 + - - +
217A HIS* 3.4 8.8 - - - +
219A TYR* 1.3 78.3 - - - +
221A SER* 1.3 63.5 + - - +
223A ILE* 3.2 9.8 + - - +
224A LYS* 2.8 64.0 + - - +
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Residues in contact with SER 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A HIS* 2.8 25.6 + - - -
218A LEU* 3.2 5.2 + - - -
220A ASP* 1.3 74.4 + - - +
222A TYR* 1.3 55.7 + - - +
224A LYS* 3.3 10.9 + - - +
225A SER* 2.7 42.9 + - - -
299A TYR* 3.9 7.2 - - - -
302A SER* 3.0 37.2 + - - -
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU 2.9 17.8 + - - +
219A TYR* 3.3 6.7 - + - +
221A SER* 1.3 74.8 - - - +
223A ILE* 1.3 74.9 + - + +
226A PHE* 3.0 48.5 + + + +
229A THR* 4.2 12.9 - - + -
230A LYS 4.5 2.1 + - - -
299A TYR* 3.6 13.0 - + + -
329A MET* 3.6 30.3 - - + +
332A SER* 5.1 1.2 + - - -
381A ASP* 2.6 50.6 + - + -
384A LEU* 3.6 17.1 - - + +
385A ALA* 3.8 27.8 - - + -
388A ILE* 4.1 13.0 - - + -
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TYR* 3.1 49.1 + - + +
220A ASP* 3.6 9.0 - - - +
222A TYR* 1.3 79.9 - - + +
224A LYS* 1.3 65.1 + - + +
225A SER 3.4 0.2 + - - -
226A PHE 3.7 15.9 + - - +
227A PRO* 5.2 0.7 - - - +
229A THR* 4.2 22.2 - - + -
381A ASP* 5.2 1.1 - - + +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ASP* 2.8 47.7 + - - +
221A SER* 3.7 10.5 - - - +
222A TYR 3.2 0.2 - - - -
223A ILE* 1.3 81.7 - - + +
225A SER* 1.3 59.7 + - - +
298A GLU* 4.1 8.8 - - - +
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A SER* 2.7 25.6 + - - -
222A TYR 3.1 2.0 + - - -
224A LYS* 1.3 78.5 - - - +
226A PHE* 1.3 64.6 + - - +
227A PRO* 3.7 4.3 - - - +
295A GLU* 3.0 36.3 - - - +
298A GLU* 4.0 18.7 + - - +
299A TYR* 3.7 34.6 + - - -
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A TYR* 3.0 58.8 + + + +
223A ILE 3.7 12.6 - - - +
224A LYS 3.7 0.8 - - - -
225A SER* 1.3 81.1 - - - +
227A PRO* 1.3 69.4 - - + +
228A LEU 3.2 9.8 + - - +
229A THR* 3.9 12.9 - - + +
288A ARG* 5.9 0.4 - - - -
292A ALA* 6.2 0.4 - - - -
295A GLU* 3.8 34.3 - - + +
296A ILE* 4.1 12.6 - - + -
299A TYR* 3.9 36.1 - + + -
329A MET* 3.7 37.2 - - + -
388A ILE* 5.0 3.1 - - + -
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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