Contacts of the helix formed by residues 205 - 223 (chain B) in PDB entry 2Y0N
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 ASN 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B CYS* 3.8 11.2 + - - +
203B GLN 4.0 1.2 + - - -
204B THR* 1.3 72.5 - - - +
206B ILE* 1.3 60.5 + - - +
207B ILE* 3.8 5.9 - - - +
208B THR* 3.0 30.8 + - - +
209B ILE* 3.0 28.7 + - - +
448B SER 3.7 3.5 + - - +
449B TYR* 3.3 50.9 + - - +
450B ILE 4.7 1.3 - - - -
451B TYR 3.3 16.2 - - - +
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Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASN* 1.3 73.3 - - - +
207B ILE* 1.3 66.3 + - - +
209B ILE* 3.7 6.3 - - + +
210B LEU* 3.0 44.1 + - + +
262B ARG* 5.1 3.1 - - + -
265B PHE* 3.3 49.1 - - + -
448B SER* 3.4 19.0 + - - +
451B TYR 2.9 14.4 + - - +
452B GLY 3.3 28.7 - - - +
456B LEU* 3.8 25.8 - - + -
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASN* 3.3 9.4 - - - +
206B ILE* 1.3 79.2 - - - +
208B THR* 1.3 59.7 + - + +
210B LEU* 3.5 2.3 + - - +
211B GLU* 3.0 50.5 + - - +
262B ARG* 3.8 25.6 - - + -
448B SER* 3.6 33.2 - - - +
449B TYR* 3.7 42.2 - - + +
440D GLU* 4.2 12.1 - - + +
441D PHE* 3.8 12.1 - - + -
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Residues in contact with THR 208 (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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203B GLN 6.0 0.7 - - - +
204B THR* 3.5 13.7 + - - -
205B ASN* 3.0 39.0 + - - +
207B ILE* 1.3 76.8 - - + +
209B ILE* 1.3 65.2 + - - +
211B GLU* 3.3 20.3 + - - +
212B SER* 2.9 24.7 + - - -
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Residues in contact with ILE 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 THR* 4.0 15.7 + - - +
205B ASN 3.0 21.1 + - - +
206B ILE* 3.7 10.3 - - - +
208B THR* 1.3 75.1 + - - +
210B LEU* 1.3 62.7 + - - +
212B SER* 3.2 9.1 + - - -
213B TYR* 3.1 19.9 + - - +
452B GLY 3.9 4.9 - - - -
453B ALA* 3.4 42.8 - - + +
456B LEU* 4.1 19.7 - - + -
487B PHE* 4.5 6.7 - - + -
490B PHE* 4.6 2.1 - - + -
491B LEU* 4.4 15.3 - - + -
498B PHE* 4.2 25.8 - - + -
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 3.0 31.7 + - + +
207B ILE* 5.0 0.4 - - - -
209B ILE* 1.3 75.1 - - - +
211B GLU* 1.3 65.2 + - - +
213B TYR* 3.3 5.7 + - - +
214B VAL* 3.2 26.5 + - - +
258B VAL* 3.2 42.8 - - + +
261B LEU* 4.4 14.4 - - + -
262B ARG* 3.8 24.0 - - + +
456B LEU* 4.4 8.3 - - + -
487B PHE* 3.8 30.7 - - + -
441D PHE* 3.6 15.7 - - + -
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Residues in contact with GLU 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 ILE* 3.0 36.6 + - - +
208B THR* 3.5 22.7 - - - +
210B LEU* 1.3 75.4 - - - +
212B SER* 1.3 61.1 + - - +
214B VAL* 3.6 5.4 + - - +
215B LYS* 3.4 36.6 + - - +
440D GLU* 3.6 19.8 - - - +
441D PHE* 3.4 23.3 - - + -
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Residues in contact with SER 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 THR 2.9 12.9 + - - -
209B ILE* 3.3 12.8 - - - -
210B LEU 3.2 0.2 - - - -
211B GLU* 1.3 74.2 - - - +
213B TYR* 1.3 65.3 + - - +
215B LYS* 3.3 13.1 + - - +
216B HIS* 2.9 44.9 + - - -
490B PHE* 4.3 8.1 - - - -
498B PHE* 4.7 9.1 - - - -
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Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE 3.1 7.2 + - - +
210B LEU* 3.3 7.4 + - - +
212B SER* 1.3 78.7 - - - +
214B VAL* 1.3 54.4 + - - +
216B HIS* 3.0 4.1 + - + +
217B PHE* 2.7 59.9 + + + +
254B CYS* 3.4 27.6 - - - -
257B MET* 4.2 8.7 - - + -
258B VAL* 4.3 9.6 - - + -
483B HIS* 4.0 5.5 + + - -
486B LEU* 3.4 23.7 - - + +
487B PHE* 3.6 35.3 + + + -
490B PHE* 3.3 59.4 - + + -
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU 3.2 15.8 + - - +
211B GLU* 3.8 7.9 - - - +
212B SER 3.3 0.2 - - - -
213B TYR* 1.3 77.8 - - - +
215B LYS* 1.3 61.8 + - + +
217B PHE* 3.3 7.6 + - - +
218B ALA* 3.0 23.9 + - + +
251B VAL* 5.0 6.4 - - + +
254B CYS* 4.5 5.6 - - - -
255B LYS* 4.1 34.8 - - + -
258B VAL* 3.7 29.8 - - + -
441D PHE* 4.5 13.7 - - + +
442D ASP* 6.2 0.2 - - - +
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLU* 3.4 25.9 + - - +
212B SER* 3.3 13.0 + - - +
213B TYR 3.3 0.2 - - - -
214B VAL* 1.3 76.8 - - + +
216B HIS* 1.3 66.7 + - + +
218B ALA* 3.2 15.1 + - - +
219B ILE* 3.4 23.3 + - + +
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Residues in contact with HIS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER* 2.9 38.3 + - - +
213B TYR* 3.0 7.9 + - + +
215B LYS* 1.3 81.0 - - + +
217B PHE* 1.3 63.7 + - - +
219B ILE* 3.7 4.1 + - - +
220B ASN* 3.2 25.8 + - - +
490B PHE* 3.9 27.2 - + + -
494B TYR* 4.5 21.3 + + - -
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 2.7 50.4 + + + +
214B VAL 3.5 5.2 - - - +
216B HIS* 1.3 73.2 - - - +
218B ALA* 1.3 61.5 - - - +
220B ASN* 3.4 7.4 + - - +
221B ALA* 3.2 21.3 + - + +
248B GLU 3.3 26.0 - - - -
249B LYS* 4.0 7.6 - - - -
250B ASN 3.4 29.2 - - - -
251B VAL* 3.6 13.5 - - + -
254B CYS* 3.5 22.7 - - + -
483B HIS* 3.6 25.1 - + - -
486B LEU* 4.0 10.1 - - + -
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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 VAL* 3.0 17.9 + - + +
215B LYS* 3.2 7.8 + - - +
217B PHE* 1.3 77.3 - - - +
219B ILE* 1.3 64.0 + - + +
221B ALA* 3.7 5.6 + - - +
222B ALA* 3.4 21.5 + - - +
251B VAL* 4.0 23.3 - - + -
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Residues in contact with ILE 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 LYS* 3.4 19.7 + - + +
216B HIS* 4.5 3.6 - - - +
217B PHE 3.3 0.2 - - - -
218B ALA* 1.3 76.9 - - + +
220B ASN* 1.3 59.0 + - - +
221B ALA 3.0 4.9 - - - -
222B ALA* 4.6 0.9 - - - -
223B PHE* 3.0 56.3 + - + +
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Residues in contact with ASN 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 HIS 3.2 20.5 + - - +
217B PHE* 3.4 7.6 + - + +
219B ILE* 1.3 76.3 - - - +
221B ALA* 1.3 56.0 + - - +
223B PHE 3.1 14.5 - - - +
224B SER* 3.3 16.6 + - - -
249B LYS* 5.1 1.9 - - - +
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Residues in contact with ALA 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 PHE* 3.2 17.3 + - + +
218B ALA* 3.8 7.0 - - - +
219B ILE 3.0 0.6 - - - -
220B ASN* 1.3 76.7 - - - +
222B ALA* 1.3 68.7 + - - +
223B PHE 2.9 9.8 + - - -
224B SER* 3.8 5.9 + - - +
249B LYS* 3.9 45.7 + - + +
251B VAL* 5.8 3.1 - - + -
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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
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218B ALA 3.4 15.2 + - - +
219B ILE* 4.6 0.7 - - - -
221B ALA* 1.3 78.4 - - - +
223B PHE* 1.3 87.2 + - + +
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Residues in contact with PHE 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 ILE* 3.0 42.8 + - + +
220B ASN* 3.1 15.6 - - - +
222B ALA* 1.3 96.0 - - + +
224B SER* 1.3 67.6 + - - +
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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
------------------------------------------------------------
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