Contacts of the helix formed by residues 205 - 223 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C CYS* 3.8 11.2 + - - +
203C GLN 3.9 1.0 + - - -
204C THR* 1.3 73.7 - - - +
206C ILE* 1.3 63.6 + - - +
207C ILE* 3.8 6.3 - - - +
208C THR* 3.0 30.9 + - - +
209C ILE* 3.0 25.1 + - - +
448C SER 3.7 3.5 + - - +
449C TYR* 3.3 49.7 + - - +
450C ILE 4.7 1.3 - - - -
451C TYR 3.3 16.4 - - - +
452C GLY* 4.2 0.4 - - - -
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Residues in contact with ILE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ASN* 1.3 73.7 - - - +
207C ILE* 1.3 66.8 + - - +
209C ILE* 3.3 5.9 + - - +
210C LEU* 2.9 44.8 + - + +
261C LEU 6.1 0.2 - - - -
262C ARG* 5.1 3.4 - - + -
265C PHE* 3.3 44.9 - - + -
448C SER* 3.4 20.4 + - - +
451C TYR 2.9 13.9 + - - +
452C GLY 3.4 29.6 - - - +
456C LEU* 3.7 28.7 - - + -
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Residues in contact with ILE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLU* 4.1 7.6 - - + +
441A PHE* 4.4 7.6 - - + -
205C ASN* 3.3 8.9 + - - +
206C ILE* 1.3 78.2 - - - +
208C THR* 1.3 60.5 + - + +
210C LEU* 3.8 5.1 - - - +
211C GLU* 3.0 48.2 + - + +
262C ARG* 3.8 24.0 - - + -
448C SER* 3.5 32.5 + - - +
449C TYR* 3.6 46.4 - - + +
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Residues in contact with THR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLN 6.0 0.9 - - - +
204C THR* 3.6 12.7 + - - -
205C ASN* 3.0 38.8 + - - +
207C ILE* 1.3 78.6 - - + +
209C ILE* 1.3 64.3 + - - +
211C GLU* 3.2 16.0 + - - +
212C SER* 2.9 24.7 + - - -
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Residues in contact with ILE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 4.0 16.8 - - - +
205C ASN 3.0 22.2 + - - +
206C ILE* 3.6 12.3 - - + +
208C THR* 1.3 75.0 + - - +
210C LEU* 1.3 63.4 + - - +
212C SER* 3.2 9.0 + - - -
213C TYR* 3.1 20.1 + - - +
452C GLY 3.9 4.3 - - - -
453C ALA* 3.4 43.1 - - + +
456C LEU* 4.1 17.9 - - + -
487C PHE* 4.5 5.8 - - + -
490C PHE* 4.6 2.1 - - + -
491C LEU* 4.4 15.7 - - + -
498C PHE* 4.3 24.9 - - + -
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Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A PHE* 3.5 20.4 - - + -
206C ILE* 2.9 31.4 + - + +
207C ILE* 3.8 0.7 - - - +
209C ILE* 1.3 77.7 - - - +
211C GLU* 1.3 61.8 + - - +
213C TYR* 3.3 6.1 + - - +
214C VAL* 3.3 26.2 + - - +
258C VAL* 3.2 43.2 - - + +
261C LEU* 4.4 14.6 - - + -
262C ARG* 3.8 17.9 - - + +
456C LEU* 4.4 9.0 - - + -
487C PHE* 3.8 30.3 - - + -
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Residues in contact with GLU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A GLU* 3.1 28.5 - - - +
441A PHE* 4.2 11.3 - - + -
207C ILE* 3.0 36.5 + - - +
208C THR* 3.2 15.7 + - - +
210C LEU* 1.3 74.2 - - - +
212C SER* 1.3 62.7 + - - +
214C VAL* 3.8 7.7 + - - +
215C LYS* 3.5 35.5 + - - +
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Residues in contact with SER 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C THR 2.9 12.7 + - - -
209C ILE* 3.3 13.5 - - - -
211C GLU* 1.3 76.7 - - - +
213C TYR* 1.3 64.0 + - - +
215C LYS* 3.4 14.0 + - - +
216C HIS* 3.0 22.2 + - - +
490C PHE* 4.4 11.6 - - - -
498C PHE* 4.8 8.5 - - - -
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Residues in contact with TYR 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ILE 3.1 7.4 + - - +
210C LEU* 3.3 7.2 + - - +
212C SER* 1.3 79.7 - - - +
214C VAL* 1.3 55.4 + - - +
216C HIS* 3.2 6.5 + + - +
217C PHE* 2.7 55.4 + + + +
254C CYS* 3.5 27.4 - - - -
257C MET* 4.2 9.4 - - + -
258C VAL* 4.3 10.5 - - + -
483C HIS* 4.0 5.2 + + - -
486C LEU* 3.4 26.7 - - + +
487C PHE* 3.5 35.3 + + + -
490C PHE* 3.3 56.0 - + + -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A PHE* 4.6 11.7 - - + +
442A ASP* 5.7 2.0 - - - +
210C LEU 3.3 16.3 + - - +
211C GLU* 4.0 6.5 - - - +
212C SER 3.3 0.2 - - - -
213C TYR* 1.3 77.3 - - - +
215C LYS* 1.3 63.4 + - + +
217C PHE* 3.4 7.9 + - - +
218C ALA* 3.0 23.0 + - + +
251C VAL* 5.0 6.4 - - + +
254C CYS* 4.6 5.8 - - - -
255C LYS* 4.1 35.0 - - + -
258C VAL* 3.7 29.8 - - + -
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C GLU* 3.5 24.4 + - - +
212C SER* 3.4 11.1 + - - +
213C TYR 3.3 0.2 - - - -
214C VAL* 1.3 76.5 - - + +
216C HIS* 1.3 64.5 + - - +
218C ALA* 3.0 9.1 + - - +
219C ILE* 2.9 36.1 + - + +
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Residues in contact with HIS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C SER* 3.0 11.4 + - - +
213C TYR* 3.3 11.4 - + - +
215C LYS* 1.3 78.1 - - - +
217C PHE* 1.3 53.9 + - - +
219C ILE* 3.2 16.2 + - + +
220C ASN* 2.8 49.0 + - + +
490C PHE* 3.2 37.8 - + + -
493C GLU* 4.6 6.6 + - - -
494C TYR* 3.2 32.5 + + - -
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Residues in contact with PHE 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C TYR* 2.7 48.9 + + + +
214C VAL 3.4 5.2 - - - +
216C HIS* 1.3 74.0 - - - +
218C ALA* 1.3 54.2 + - - +
220C ASN* 3.3 10.1 + - - +
221C ALA* 2.7 39.7 + - + +
248C GLU 2.9 29.2 - - - -
249C LYS* 4.3 6.3 - - - -
250C ASN 3.7 3.8 - - - -
251C VAL* 3.6 37.5 - - + -
254C CYS* 3.6 30.1 - - + -
483C HIS* 3.9 12.1 - - - -
486C LEU* 4.1 12.6 - - + -
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Residues in contact with ALA 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C VAL* 3.0 14.1 + - + +
215C LYS* 3.0 11.0 + - - +
217C PHE* 1.3 77.2 - - - +
219C ILE* 1.3 64.3 + - + +
221C ALA* 3.6 7.9 + - - +
222C ALA* 3.5 20.4 + - - +
251C VAL* 4.3 17.3 - - + -
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Residues in contact with ILE 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LYS* 2.9 28.6 + - + +
216C HIS* 3.6 13.9 - - + +
218C ALA* 1.3 74.4 - - + +
220C ASN* 1.3 62.9 + - - +
222C ALA* 3.5 14.5 + - - +
223C PHE* 3.5 42.5 + - + -
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Residues in contact with ASN 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C HIS* 2.8 34.3 + - + +
217C PHE* 3.5 11.4 - - - +
219C ILE* 1.3 72.4 - - - +
221C ALA* 1.3 56.7 + - - +
223C PHE* 2.8 46.2 - - + +
249C LYS* 3.8 5.8 + - - -
486C LEU* 6.4 0.2 - - - +
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Residues in contact with ALA 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C PHE* 2.7 29.8 + - + +
218C ALA* 3.7 10.1 - - - +
219C ILE 3.3 0.4 - - - -
220C ASN* 1.3 74.2 - - - +
222C ALA* 1.3 62.2 + - - +
249C LYS* 3.2 49.4 + - + +
251C VAL* 5.5 4.7 - - + -
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ALA 3.5 9.3 + - - +
219C ILE* 3.7 10.1 - - - +
220C ASN 3.3 0.6 - - - -
221C ALA* 1.3 80.9 - - - +
223C PHE* 1.3 63.1 + - + +
249C LYS* 4.9 1.0 + - - -
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Residues in contact with PHE 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ILE* 3.5 39.9 + - + -
220C ASN* 2.8 32.7 + - - +
222C ALA* 1.3 81.6 - - + +
249C LYS* 3.0 20.3 + - - -
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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