Contacts of the helix formed by residues 205 - 223 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A CYS* 3.8 11.5 + - - +
203A GLN 4.0 1.0 + - - -
204A THR* 1.3 73.1 - - - +
206A ILE* 1.3 59.9 + - - +
207A ILE* 3.6 6.3 - - - +
208A THR* 3.0 31.8 + - - +
209A ILE* 3.0 28.7 + - - +
448A SER 3.7 3.8 + - - +
449A TYR* 3.3 50.3 + - - +
450A ILE 4.7 1.3 - - - -
451A TYR 3.3 15.9 - - - +
452A GLY* 4.3 0.4 - - - -
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Residues in contact with ILE 206 (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* 1.3 73.3 - - - +
207A ILE* 1.3 67.0 + - - +
209A ILE* 3.6 5.7 - - + +
210A LEU* 2.9 44.8 + - + +
262A ARG* 5.1 2.7 - - + -
265A PHE* 3.4 47.8 - - + -
448A SER* 3.4 20.1 + - - +
451A TYR 3.0 14.8 + - - +
452A GLY 3.3 28.9 - - - +
456A LEU* 3.8 25.4 - - + -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ASN* 3.4 9.1 - - - +
206A ILE* 1.3 78.6 - - - +
208A THR* 1.3 60.3 + - + +
210A LEU* 3.5 2.6 + - - +
211A GLU* 3.0 51.0 + - + +
262A ARG* 3.8 23.3 - - + -
448A SER* 3.6 33.7 - - - +
449A TYR* 3.7 43.3 - - + +
440C GLU* 4.2 13.0 - - + +
441C PHE* 3.8 11.4 - - + -
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Residues in contact with THR 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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203A GLN 6.0 0.7 - - - +
204A THR* 3.5 13.3 + - - -
205A ASN* 3.0 38.5 + - - +
207A ILE* 1.3 76.4 - - + +
209A ILE* 1.3 64.6 + - - +
211A GLU* 3.3 20.9 + - - +
212A SER* 3.0 24.3 + - - -
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Residues in contact with ILE 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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204A THR* 4.0 15.5 - - - +
205A ASN 3.0 21.1 + - - +
206A ILE* 3.6 12.1 - - + +
208A THR* 1.3 75.5 + - - +
210A LEU* 1.3 63.0 + - - +
212A SER* 3.2 8.8 + - - -
213A TYR* 3.1 20.4 + - - +
452A GLY 3.9 4.9 - - - -
453A ALA* 3.4 42.8 - - + +
456A LEU* 4.1 17.7 - - + -
487A PHE* 4.5 6.3 - - + -
490A PHE* 4.6 2.2 - - + -
491A LEU* 4.4 13.2 - - + -
498A PHE* 4.2 27.6 - - + -
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Residues in contact with LEU 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 ILE* 2.9 31.7 + - + +
207A ILE* 5.1 0.4 - - - -
209A ILE* 1.3 74.9 - - - +
211A GLU* 1.3 64.8 + - - +
213A TYR* 3.2 6.5 + - - +
214A VAL* 3.2 26.0 + - - +
258A VAL* 3.2 43.3 - - + +
261A LEU* 4.4 13.9 - - + -
262A ARG* 3.8 23.3 - - + +
456A LEU* 4.4 9.0 - - + -
487A PHE* 3.8 30.5 - - + -
441C PHE* 3.6 16.4 - - + -
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Residues in contact with GLU 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 ILE* 3.0 38.8 + - - +
208A THR* 3.4 23.6 - - - +
210A LEU* 1.3 74.5 - - - +
212A SER* 1.3 61.3 + - - +
214A VAL* 3.4 6.0 + - - +
215A LYS* 3.3 37.9 + - - +
440C GLU* 3.9 17.1 - - - +
441C PHE* 3.4 23.2 - - + -
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Residues in contact with SER 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 THR 3.0 12.9 + - - -
209A ILE* 3.3 12.6 - - - -
210A LEU 3.2 0.2 - - - -
211A GLU* 1.3 74.9 - - - +
213A TYR* 1.3 64.8 + - - +
215A LYS* 3.4 13.9 + - - +
216A HIS* 3.0 44.6 + - - -
490A PHE* 4.4 6.4 - - - -
498A PHE* 4.8 8.8 - - - -
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Residues in contact with TYR 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 ILE 3.1 7.0 + - - +
210A LEU* 3.2 7.6 + - - +
212A SER* 1.3 79.3 - - - +
214A VAL* 1.3 53.6 + - - +
216A HIS* 3.0 4.2 + - + +
217A PHE* 2.6 59.0 + + + +
254A CYS* 3.5 26.9 - - - -
257A MET* 4.3 9.4 - - + -
258A VAL* 4.3 10.3 - - + -
483A HIS* 4.0 5.3 + + - -
486A LEU* 3.4 24.7 - - + +
487A PHE* 3.6 34.9 + + + -
490A PHE* 3.3 57.6 - + + -
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Residues in contact with VAL 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 LEU 3.2 15.6 + - - +
211A GLU* 3.7 7.9 - - - +
212A SER 3.3 0.2 - - - -
213A TYR* 1.3 77.2 - - - +
215A LYS* 1.3 62.6 + - + +
217A PHE* 3.3 7.6 + - - +
218A ALA* 3.0 23.9 + - + +
251A VAL* 5.0 6.4 - - + +
254A CYS* 4.5 5.8 - - - -
255A LYS* 4.1 34.8 - - + -
258A VAL* 3.7 29.8 - - + -
441C PHE* 4.5 13.7 - - + +
442C ASP* 6.2 0.2 - - - +
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Residues in contact with LYS 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 GLU* 3.3 27.1 + - - +
212A SER* 3.6 12.6 - - - +
213A TYR 3.3 0.2 - - - -
214A VAL* 1.3 76.4 - - + +
216A HIS* 1.3 65.7 + - + +
218A ALA* 3.2 6.9 + - - +
219A ILE* 3.2 34.2 + - + +
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Residues in contact with HIS 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 SER* 3.0 35.4 + - - +
213A TYR* 3.0 8.2 + - + +
215A LYS* 1.3 83.2 - - + +
217A PHE* 1.3 61.0 + - - +
219A ILE* 3.7 5.4 + - - +
220A ASN* 3.2 26.0 + - - +
490A PHE* 3.8 27.8 - + + -
494A TYR* 4.6 21.7 + + - -
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Residues in contact with PHE 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 TYR* 2.6 49.6 + + + +
214A VAL 3.5 4.9 - - - +
216A HIS* 1.3 73.2 - - - +
218A ALA* 1.3 56.9 + - - +
220A ASN* 3.3 6.4 + - + +
221A ALA* 3.0 27.8 + - + +
248A GLU 3.1 28.7 - - - -
249A LYS* 3.8 7.2 - - - -
250A ASN 3.6 20.2 - - - -
251A VAL* 3.7 17.5 - - + -
254A CYS* 3.5 24.0 - - + -
483A HIS* 3.6 26.9 - + - -
486A LEU* 4.0 9.4 - - + -
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Residues in contact with ALA 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 VAL* 3.0 17.6 + - + +
215A LYS* 3.2 6.0 + - - +
217A PHE* 1.3 75.6 - - - +
219A ILE* 1.3 66.9 + - + +
221A ALA* 3.7 4.5 + - - +
222A ALA* 3.4 22.0 + - - +
251A VAL* 3.9 24.2 - - + -
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Residues in contact with ILE 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 LYS* 3.2 24.0 + - + +
216A HIS* 4.3 4.5 - - - +
218A ALA* 1.3 80.1 - - + +
220A ASN* 1.3 59.8 + - - +
222A ALA* 4.6 0.7 - - - -
223A PHE* 3.0 50.9 + - + +
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Residues in contact with ASN 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 HIS 3.2 20.5 + - - +
217A PHE* 3.5 6.9 - - - +
218A ALA 3.2 0.6 - - - -
219A ILE* 1.3 76.4 - - - +
221A ALA* 1.3 65.8 + - - +
223A PHE 2.8 26.8 - - - +
224A SER* 3.2 22.3 + - - -
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Residues in contact with ALA 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 PHE* 3.0 19.7 + - + +
218A ALA* 4.1 5.8 - - - +
219A ILE 3.5 0.2 - - - -
220A ASN* 1.3 76.7 - - - +
222A ALA* 1.3 63.8 + - - +
224A SER* 4.6 3.1 + - - -
249A LYS* 3.5 58.6 + - + +
251A VAL* 5.6 2.7 - - + -
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Residues in contact with ALA 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 ALA 3.4 15.4 + - - +
219A ILE* 3.9 0.7 - - - +
220A ASN 3.3 0.6 - - - -
221A ALA* 1.3 81.2 - - - +
223A PHE* 1.3 87.0 + - + +
224A SER 3.9 2.1 + - - +
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Residues in contact with PHE 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 ILE* 3.0 44.2 + - + +
220A ASN* 2.8 18.9 - - - +
222A ALA* 1.3 91.4 - - + +
224A SER* 1.3 60.6 + - - +
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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
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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