Contacts of the helix formed by residues 206 - 220 (chain B) in PDB entry 1QYR
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 ASP 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B VAL* 3.6 9.5 - - - +
205B LYS* 1.3 81.4 - - + +
207B VAL* 1.3 58.8 + - - +
208B ARG* 2.8 55.2 + - - +
209B VAL* 3.0 46.3 + - + +
261B ALA 5.2 0.3 - - - +
265B ALA* 4.2 12.7 - - + +
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Residues in contact with VAL 207 (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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163B MET* 3.6 23.1 - - + -
166B TYR* 3.3 41.1 - - + +
167B TYR* 3.4 28.7 - - + +
204B VAL* 3.9 12.8 - - + +
206B ASP* 1.3 70.0 + - - +
208B ARG* 1.3 65.7 + - - +
210B LEU* 3.0 7.1 + - + +
211B SER* 2.9 22.5 + - - -
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Residues in contact with ARG 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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206B ASP* 2.8 36.1 + - - +
207B VAL* 1.3 75.9 - - - +
209B VAL* 1.3 57.7 + - + +
211B SER* 3.4 7.1 + - - -
212B ARG* 2.9 29.5 + - - +
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Residues in contact with VAL 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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206B ASP* 3.0 33.1 + - + +
208B ARG* 1.3 74.8 - - + +
210B LEU* 1.3 60.1 + - - +
212B ARG* 3.1 10.1 + - + +
213B ILE* 2.9 30.0 + - + +
261B ALA* 3.5 30.3 - - - +
264B LEU* 3.7 30.7 - - + -
265B ALA* 4.6 9.4 - - + -
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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
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162B VAL* 4.1 6.1 - - + -
163B MET* 3.6 24.0 - - + -
166B TYR* 3.8 38.6 - - + -
204B VAL* 4.5 3.4 - - + -
206B ASP 3.7 1.2 + - - -
207B VAL* 3.0 16.6 + - + +
209B VAL* 1.3 77.9 - - - +
211B SER* 1.3 59.9 + - - +
213B ILE* 3.5 3.4 - - + +
214B THR* 2.9 39.9 + - + +
257B TYR* 3.7 44.2 - - + +
258B CYS* 4.1 7.2 - - - +
261B ALA* 3.7 15.5 - - + +
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 2.9 25.0 + - - +
163B MET* 3.8 19.7 - - - -
207B VAL* 2.9 15.4 + - - -
208B ARG* 3.7 8.5 - - - -
210B LEU* 1.3 77.0 - - - +
212B ARG* 1.3 53.4 + - - +
214B THR* 3.1 6.8 + - - -
215B THR* 2.8 38.2 + - - -
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Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG 2.9 17.9 + - - +
209B VAL* 3.1 10.7 + - - +
211B SER* 1.3 76.9 - - - +
213B ILE* 1.3 61.7 + - - +
215B THR* 3.7 5.4 - - - -
216B GLU* 3.2 54.0 + - + +
231B ASN* 6.3 0.4 - - - +
232B LEU* 3.0 51.2 - - - +
264B LEU* 4.7 5.7 - - - +
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Residues in contact with ILE 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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209B VAL* 2.9 25.0 + - + +
210B LEU* 3.4 9.2 + - + +
212B ARG* 1.3 73.6 - - + +
214B THR* 1.3 58.6 + - - +
216B GLU 3.5 0.3 + - - -
217B ALA* 2.8 37.5 + - - +
229B LEU* 3.9 15.6 - - + +
232B LEU* 3.8 29.6 - - + -
233B PHE* 4.1 6.3 - - + -
257B TYR* 3.6 22.7 - - + +
260B MET* 3.8 15.7 - - + -
261B ALA* 3.6 33.7 - - + +
264B LEU* 3.9 13.9 - - + -
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Residues in contact with THR 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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159B ARG* 3.2 29.5 - - - +
162B VAL* 3.8 33.7 - - + -
163B MET* 4.2 2.9 - - - -
210B LEU* 2.9 30.6 + - + +
211B SER* 3.1 11.3 + - - -
213B ILE* 1.3 73.3 - - - +
215B THR* 1.3 64.7 + - - +
217B ALA* 4.4 2.7 - - - -
218B PHE* 3.0 36.2 + - + +
257B TYR* 4.1 14.6 - - + -
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Residues in contact with THR 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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159B ARG* 3.2 25.8 + - - +
211B SER* 2.8 25.6 + - - -
212B ARG* 3.7 8.4 - - - -
213B ILE 3.4 0.2 - - - -
214B THR* 1.3 77.6 + - - +
216B GLU* 1.3 65.4 + - + +
218B PHE* 4.0 1.2 - - - +
219B ASN* 3.2 40.7 + - - +
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Residues in contact with GLU 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 ARG* 3.2 53.5 + - + +
213B ILE 3.9 0.2 - - - +
214B THR 3.2 0.2 - - - -
215B THR* 1.3 83.5 - - + +
217B ALA* 1.3 65.0 + - - +
219B ASN* 3.3 22.1 + - - +
220B GLN* 3.9 4.2 + - - +
228B SER* 3.9 13.3 + - - +
229B LEU* 3.8 23.7 - - + +
232B LEU* 4.4 4.5 - - - +
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Residues in contact with ALA 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 ILE 2.8 23.6 + - - +
214B THR* 3.4 2.7 + - - +
216B GLU* 1.3 74.6 - - - +
218B PHE* 1.3 59.5 + - + +
220B GLN 3.4 17.3 + - - +
225B ILE* 3.8 20.6 - - + -
228B SER* 3.5 12.6 + - - -
229B LEU* 4.2 2.6 - - + +
249B ALA* 3.3 17.6 - - + +
257B TYR* 3.7 28.9 - - + +
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Residues in contact with PHE 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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157B TYR* 3.6 41.5 - + - -
158B GLY* 3.6 25.1 - - - -
159B ARG* 3.5 19.5 - - + +
162B VAL* 4.1 6.5 - - + -
214B THR* 3.0 30.5 + - - +
215B THR 4.0 1.8 - - - +
217B ALA* 1.3 73.3 - - - +
219B ASN* 1.3 64.2 + - - +
220B GLN 3.2 2.2 + - - -
221B ARG* 3.8 30.2 + - + +
249B ALA* 3.8 17.7 - - + -
250B GLU* 4.1 8.3 - - + -
257B TYR* 3.6 30.5 - + - -
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Residues in contact with ASN 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 THR* 3.2 33.0 + - - +
216B GLU* 3.3 15.5 + - - +
218B PHE* 1.3 78.4 - - - +
220B GLN* 1.3 58.0 + - + +
221B ARG 3.7 1.1 + - - -
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Residues in contact with GLN 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 GLU 3.9 5.0 + - - +
217B ALA 3.4 12.5 + - - +
219B ASN* 1.3 78.3 - - + +
221B ARG* 1.3 65.2 + - - +
222B ARG 3.2 3.4 - - - -
223B LYS* 3.0 38.4 + - + +
228B SER* 4.9 8.7 - - - +
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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