Contacts of the helix formed by residues 210 - 228 (chain B) in PDB entry 1YSD
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 TRP 210 (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* 3.2 10.1 + - - +
209B LYS* 1.3 118.6 - - + +
211B ASP* 1.3 59.6 + - - +
212B GLN 3.3 2.9 - - - -
213B LYS* 3.2 35.0 + - + +
214B GLY* 2.9 25.1 + - - -
238B ILE* 4.0 15.3 - - + +
239B ASN 4.6 2.5 - - - -
240B ASN* 4.0 20.9 + - - +
242B ASP* 3.7 14.7 - - - +
243B GLY* 3.3 34.4 - - - +
285B TYR* 3.4 12.5 + - - +
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Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ALA* 4.1 3.5 - - - +
208B SER* 3.0 28.8 + - - +
210B TRP* 1.3 74.2 - - - +
212B GLN* 1.3 64.1 + - - +
215B MET* 3.1 25.8 + - - +
285B TYR* 2.6 36.5 + - + -
305B ARG* 2.9 37.6 + - - -
307B VAL* 4.0 14.8 - - + +
330B VAL* 5.3 4.3 - - - +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B SER 4.8 0.8 + - - -
209B LYS 4.6 6.6 + - - +
210B TRP* 3.3 0.8 - - - +
211B ASP* 1.3 78.4 - - - +
213B LYS* 1.3 64.4 + - - +
215B MET* 4.1 4.5 - - - +
216B ASP* 3.2 45.4 + - - +
336B ARG* 5.3 3.0 - - - +
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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
----------------------------------------------------------
209B LYS 5.3 0.8 + - - +
210B TRP* 3.2 37.3 + - + +
212B GLN* 1.3 80.4 - - - +
214B GLY* 1.3 63.4 + - - +
216B ASP* 3.2 9.0 + - - +
217B ILE* 3.1 37.4 + - + +
238B ILE* 4.4 7.9 - - + -
243B GLY 3.0 24.4 + - - -
244B SER* 5.1 0.2 - - - +
245B VAL* 3.7 25.2 - - - +
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Residues in contact with GLY 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 TRP 2.9 12.7 + - - -
212B GLN 3.3 0.4 - - - -
213B LYS* 1.3 78.0 - - - +
215B MET* 1.3 56.3 + - - +
217B ILE 3.3 1.6 + - - -
218B ALA* 3.0 25.5 + - - +
236B CYS* 3.4 12.0 - - - -
238B ILE* 3.6 17.9 - - - +
285B TYR* 3.6 25.0 - - - +
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Residues in contact with MET 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 ASP 3.1 16.3 + - - +
212B GLN* 4.2 4.9 - - - +
214B GLY* 1.3 72.6 - - - +
216B ASP* 1.3 60.7 + - - +
218B ALA* 3.7 10.2 - - - +
219B TYR* 2.9 28.8 + - - +
285B TYR* 3.8 6.3 - - + -
286B THR 3.7 9.9 - - - +
307B VAL* 3.6 36.3 - - + +
308B VAL 3.8 1.3 - - - -
309B GLY* 3.5 34.5 - - - +
332B VAL* 4.2 10.8 - - + -
334B ASP* 3.6 25.8 - - - +
336B ARG* 3.9 3.5 + - - +
337B CYS* 4.3 9.2 - - - -
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Residues in contact with ASP 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 GLN* 3.2 34.4 + - - +
213B LYS* 3.5 11.8 - - - +
214B GLY 3.2 0.2 - - - -
215B MET* 1.3 78.4 - - - +
217B ILE* 1.3 60.5 + - + +
219B TYR* 3.3 4.2 + - - +
220B GLU* 2.9 29.7 + - - +
336B ARG* 3.0 33.6 + - - +
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Residues in contact with ILE 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 28.5 + - + +
214B GLY 3.6 6.7 - - - +
216B ASP* 1.3 78.3 - - + +
218B ALA* 1.3 56.8 + - - +
220B GLU* 3.1 14.2 + - - +
221B GLU* 2.8 28.5 + - + +
236B CYS* 3.6 28.7 - - + -
238B ILE* 5.7 0.2 - - + -
245B VAL* 5.1 12.8 - - + -
248B ARG* 3.5 47.3 - - + +
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Residues in contact with ALA 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 GLY 3.0 16.3 + - - +
215B MET* 3.7 14.6 - - - +
216B ASP 3.3 0.2 - - - -
217B ILE* 1.3 77.4 - - - +
219B TYR* 1.3 56.7 + - - +
221B GLU* 3.1 4.2 + - - +
222B ALA 2.9 23.0 + - - -
234B GLY* 3.5 8.6 - - - +
235B GLY* 3.6 32.5 - - - +
236B CYS* 4.6 0.2 - - - -
285B TYR* 4.3 7.2 - - + +
287B THR* 3.4 17.5 - - + +
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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 MET 2.9 18.1 + - - +
216B ASP 3.6 4.7 - - - +
218B ALA* 1.3 73.3 - - - +
220B GLU* 1.3 61.9 + - - +
222B ALA* 3.0 4.2 + - + +
223B LEU* 2.9 69.3 + - + +
287B THR* 3.7 8.0 - - - +
336B ARG* 3.5 74.8 + - + +
337B CYS* 4.1 16.8 - - - -
339B LYS* 5.4 1.6 + - - -
340B LEU* 4.1 15.2 - - + +
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Residues in contact with GLU 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 ASP 2.9 13.1 + - - +
217B ILE* 3.4 18.5 - - - +
219B TYR* 1.3 78.0 - - - +
221B GLU* 1.3 58.1 + - - +
223B LEU* 3.4 12.1 + - - +
224B LEU* 3.0 30.7 + - + +
248B ARG* 2.8 29.0 + - - +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE 2.8 15.8 + - - +
218B ALA 3.1 8.5 + - - +
220B GLU* 1.3 78.1 - - - +
222B ALA* 1.3 56.6 + - - +
224B LEU* 3.2 16.4 + - - +
225B GLY 2.9 23.9 + - - -
234B GLY* 3.8 2.7 - - - -
235B GLY 3.8 7.4 - - - +
248B ARG* 2.8 36.4 + - + +
249B GLY* 3.2 42.3 - - - +
250B HIS* 2.8 42.2 + - - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ALA 2.9 12.9 + - - +
219B TYR* 3.4 9.6 - - + +
221B GLU* 1.3 73.9 - - - +
223B LEU* 1.3 60.0 + - - +
225B GLY 3.2 1.3 + - - +
226B TYR* 2.9 27.9 + - - +
232B PRO* 3.5 32.5 - - - +
233B ILE 4.2 1.3 - - - +
234B GLY* 3.7 14.0 - - - +
250B HIS* 4.8 0.4 - - - -
287B THR* 4.1 10.3 - - + +
340B LEU* 3.8 13.5 - - + -
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Residues in contact with LEU 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* 2.9 61.8 + - + +
220B GLU* 3.7 9.0 - - - +
222B ALA* 1.3 73.3 - - - +
224B LEU* 1.3 61.9 + - - +
226B TYR* 3.2 9.3 + - + +
227B LYS* 2.9 29.3 + - - +
340B LEU* 3.9 23.6 - - + -
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Residues in contact with LEU 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 GLU* 3.0 16.2 + - + +
221B GLU* 3.3 24.0 - - - +
222B ALA 3.2 0.2 - - - -
223B LEU* 1.3 77.3 - - - +
225B GLY* 1.3 63.4 + - - +
227B LYS* 3.2 26.1 + - - +
228B GLU* 2.8 50.5 + - + +
250B HIS* 3.8 17.0 - - + +
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Residues in contact with GLY 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 GLU 2.9 12.6 + - - -
222B ALA 3.2 2.9 + - - -
224B LEU* 1.3 76.8 - - - +
226B TYR* 1.3 59.1 + - - +
228B GLU* 3.1 8.8 + - - +
230B GLY* 2.9 30.7 + - - -
231B VAL 4.7 5.8 - - - -
250B HIS* 3.4 28.9 - - - -
255B GLN* 3.9 4.5 - - - -
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Residues in contact with TYR 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 ALA 2.9 13.8 + - - +
223B LEU* 3.2 15.2 + - + +
225B GLY* 1.3 75.8 - - - +
227B LYS* 1.3 59.5 + - - +
229B GLY* 3.0 19.6 + - - -
230B GLY 3.9 11.6 + - - -
232B PRO* 4.0 20.3 - - + +
340B LEU* 3.8 22.2 - - + -
343B GLN* 3.5 17.9 + - + -
344B PHE* 4.5 18.4 - + + -
347B GLU* 2.6 36.2 + - - -
348B ARG* 6.0 2.9 - - - -
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Residues in contact with LYS 227 (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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223B LEU 2.9 13.0 + - - +
224B LEU* 3.2 31.2 + - - +
226B TYR* 1.3 79.9 - - - +
228B GLU* 1.3 64.0 + - + +
229B GLY 3.1 3.7 + - - -
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Residues in contact with GLU 228 (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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224B LEU* 2.8 37.0 + - + +
225B GLY 3.1 6.9 + - - +
227B LYS* 1.3 83.4 + - + +
229B GLY* 1.3 61.4 + - - +
230B GLY 3.6 0.2 + - - -
250B HIS* 2.8 25.8 + - - -
252B MET* 4.6 2.5 - - - +
254B PHE* 6.0 0.3 - - - +
255B GLN* 2.9 31.0 + - + +
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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