Contacts of the helix formed by residues 209 - 223 (chain B) in PDB entry 2R5Y
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 SER 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B ASN 3.7 1.2 + - - -
208B PHE* 1.3 79.9 - - - +
210B LYS* 1.3 65.4 + - - +
211B GLN* 3.8 7.7 + - - +
212B ALA* 3.3 23.4 + - - +
213B SER* 3.3 19.9 + - - -
238B CYS 4.8 3.3 + - - -
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Residues in contact with LYS 210 (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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209B SER* 1.3 76.3 - - - +
211B GLN* 1.3 62.2 + - - +
213B SER* 3.6 4.9 + - - -
214B GLU* 3.2 44.0 + - + +
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Residues in contact with GLN 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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209B SER* 3.2 7.7 + - - +
210B LYS* 1.3 78.6 - - - +
212B ALA* 1.3 62.3 + - - +
214B GLU* 3.4 15.6 + - - +
215B ILE* 3.0 52.9 + - + +
237B LYS 4.7 8.5 + - - -
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Residues in contact with ALA 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 PHE* 4.2 17.3 - - + -
209B SER* 3.3 22.0 + - - +
210B LYS 3.4 0.2 - - - -
211B GLN* 1.3 80.1 - - - +
213B SER* 1.3 56.3 + - - +
215B ILE* 3.3 4.6 + - - +
216B LEU* 3.0 37.7 + - + +
238B CYS* 3.6 37.6 - - + +
240B ILE* 5.5 1.3 - - + -
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Residues in contact with SER 213 (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 PHE* 4.3 13.7 + - - +
209B SER 3.3 13.6 + - - -
210B LYS* 4.0 6.1 - - - -
211B GLN 3.3 0.2 - - - -
212B ALA* 1.3 76.0 - - - +
214B GLU* 1.3 62.7 + - - +
216B LEU* 3.9 7.8 - - - +
217B ASN* 2.8 44.1 + - - +
248B TRP* 5.0 6.9 + - - +
8C G 4.4 7.4 + - - -
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Residues in contact with GLU 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 LYS* 3.2 42.6 + - + +
211B GLN* 3.7 17.1 - - - +
212B ALA 3.3 0.2 - - - -
213B SER* 1.3 76.6 - - - +
215B ILE* 1.3 60.6 - - + +
217B ASN* 4.0 4.3 - - - +
218B GLU* 2.9 33.3 + - - +
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Residues in contact with ILE 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 GLN* 3.0 45.4 + - + +
212B ALA* 3.6 4.9 - - - +
213B SER 3.2 0.2 - - - -
214B GLU* 1.3 79.9 - - + +
216B LEU* 1.3 55.7 + - - +
218B GLU* 3.4 10.5 + - - +
219B TYR* 2.9 27.4 + - - +
234B LEU* 3.9 16.8 - - + -
237B LYS* 3.9 46.9 - - + +
238B CYS* 3.8 18.6 - - - -
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Residues in contact with LEU 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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208B PHE* 4.4 13.2 - - + -
212B ALA* 3.0 24.7 + - + +
213B SER* 3.9 3.1 - - - +
215B ILE* 1.3 72.2 - - - +
217B ASN* 1.3 56.3 + - - +
219B TYR* 3.2 5.3 + - - +
220B PHE* 2.7 36.9 + - - +
234B LEU* 4.4 14.8 - - + -
238B CYS* 3.9 19.3 - - - -
240B ILE* 4.5 6.7 - - + -
245B VAL* 4.6 11.2 - - + -
248B TRP* 3.5 53.0 - - + +
249B PHE* 4.2 21.8 - - + -
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Residues in contact with ASN 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 SER* 2.8 28.8 + - - +
214B GLU* 4.0 4.2 - - - +
216B LEU* 1.3 77.2 - - - +
218B GLU* 1.3 57.9 + - - +
220B PHE* 4.1 0.7 - - - -
221B TYR* 2.9 50.4 + - + -
248B TRP* 3.2 22.8 - - - -
252B LYS* 2.9 33.2 + - - +
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Residues in contact with GLU 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 GLU 2.9 21.5 + - - +
215B ILE* 3.7 11.1 - - - +
217B ASN* 1.3 74.1 - - - +
219B TYR* 1.3 68.8 + - - +
221B TYR* 4.4 2.6 - - - +
222B SER* 2.7 38.4 + - - +
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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 ILE 2.9 18.3 + - - +
216B LEU 3.7 3.4 - - - +
218B GLU* 1.3 82.0 - - - +
220B PHE* 1.3 65.8 + - - +
222B SER* 3.0 2.2 + - - -
223B HIS* 3.0 71.6 + + + -
224B PRO* 5.6 1.6 - - + -
225B TYR 5.3 0.8 - - - -
226B PRO* 3.7 38.1 - - + +
230B ALA* 4.0 13.0 - - + +
234B LEU* 3.9 28.5 - - + -
249B PHE* 3.6 18.6 - + + -
1225B ASN 5.8 0.2 - - - -
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Residues in contact with PHE 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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84A TRP* 4.1 21.3 - + - -
216B LEU 2.7 22.1 + - - +
217B ASN* 3.6 4.0 - - - +
219B TYR* 1.3 78.5 - - - +
221B TYR* 1.3 80.7 + + - +
223B HIS* 3.0 19.9 + - - +
224B PRO* 3.6 26.3 - - + +
248B TRP* 3.9 10.3 - - + -
249B PHE* 4.0 16.2 - + - -
252B LYS* 3.5 45.8 - - + -
253B ARG* 4.1 13.0 - - + -
256B TYR* 4.2 8.1 - + + -
1223B LEU* 3.2 29.6 + - + -
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Residues in contact with TYR 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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76A LYS* 3.7 18.6 + - + -
217B ASN* 2.9 52.4 + - + +
218B GLU* 4.4 1.6 - - - +
220B PHE* 1.3 88.2 - + - +
222B SER* 1.3 64.7 + - - +
223B HIS 3.1 0.6 + - - -
252B LYS* 3.0 24.7 + - - -
256B TYR* 4.0 21.1 - + - -
1223B LEU* 3.5 28.5 + - + +
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Residues in contact with SER 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 GLU* 2.7 35.0 + - - +
219B TYR* 3.5 4.9 - - - -
221B TYR* 1.3 78.0 - - - +
223B HIS* 1.3 71.0 + - - +
1223B LEU 3.5 0.6 + - - -
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Residues in contact with HIS 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* 3.0 74.6 + + + +
220B PHE 3.0 5.8 + - - +
222B SER* 1.3 90.4 - - - +
224B PRO* 3.1 12.0 - - + +
1223B LEU* 1.3 55.7 + - - -
1224B SER* 3.1 7.2 - - - -
1225B ASN 2.8 33.5 + - - +
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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