Contacts of the helix formed by residues 207 - 221 (chain G) in PDB entry 1QDU
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 THR 207 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175G LYS* 5.8 4.7 - - + -
205G ASP 5.1 0.2 - - - +
206G CYS* 1.3 79.6 - - - +
208G VAL* 1.3 66.2 + - - +
209G GLU* 3.3 9.4 + - - +
210G GLN* 2.6 43.7 + - - +
211G ILE* 3.0 15.0 + - - +
245G GLY* 4.0 0.4 - - - -
246G THR* 3.7 18.8 - - + +
247G ASP* 3.0 32.8 - - + +
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Residues in contact with VAL 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G THR* 1.3 71.6 - - - +
209G GLU* 1.3 69.0 + - - +
211G ILE* 2.8 23.8 + - + +
212G TYR* 3.0 36.5 + - + -
245G GLY* 3.5 8.3 - - - +
247G ASP* 3.1 9.0 + - - +
254G GLN* 3.3 51.1 - - + +
255G GLU 3.6 17.3 - - - +
256G ALA* 3.9 9.2 - - + -
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Residues in contact with GLU 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G THR* 3.4 9.2 - - - +
208G VAL* 1.3 83.9 - - - +
210G GLN* 1.3 66.8 + - + +
212G TYR* 3.0 10.6 + - - +
213G GLU* 3.0 40.0 + - - +
247G ASP* 4.4 2.6 + - - +
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Residues in contact with GLN 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G HIS 5.1 0.9 - - - +
205G ASP 3.8 6.2 - - - +
206G CYS* 3.5 24.6 - - + -
207G THR* 2.6 52.8 + - - +
209G GLU* 1.3 81.2 + - + +
211G ILE* 1.3 58.6 + - - +
213G GLU* 3.1 19.1 + - - +
214G ILE* 2.8 37.8 + - + +
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Residues in contact with ILE 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G ILE* 3.5 35.7 - - + -
170G ASN* 4.5 6.5 - - - +
206G CYS* 4.0 17.9 - - + +
207G THR 3.0 18.2 + - - +
208G VAL* 2.8 18.6 + - + +
210G GLN* 1.3 73.2 - - - +
212G TYR* 1.3 66.8 + - + +
214G ILE* 3.2 3.1 + - - +
215G LEU* 2.9 38.5 + - + +
234G ILE* 5.4 3.6 - - + -
243G ILE* 3.8 25.8 - - + -
245G GLY* 4.2 6.7 - - - -
256G ALA* 5.1 0.7 - - + -
261G LEU* 4.6 16.8 - - + -
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Residues in contact with TYR 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208G VAL* 3.0 43.6 + - + -
209G GLU* 3.0 10.1 + - - +
211G ILE* 1.3 76.0 - - + +
213G GLU* 1.3 67.1 + - - +
215G LEU* 3.0 5.9 + - + +
216G LYS* 2.7 26.4 + - - +
255G GLU 4.7 1.4 + - - -
256G ALA* 4.0 9.4 - - + -
257G PRO* 3.7 14.7 - - - +
260G GLU* 3.4 36.4 + - + +
261G LEU* 3.9 21.2 - - + +
264G GLN* 5.0 15.7 - - + -
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Residues in contact with GLU 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G GLU* 3.0 33.0 + - - +
210G GLN* 3.1 23.3 - - - +
212G TYR* 1.3 76.6 - - - +
214G ILE* 1.3 64.3 - - + +
216G LYS* 3.1 10.6 + - + +
217G ILE* 3.0 25.1 + - + +
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Residues in contact with ILE 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G LEU* 3.3 28.3 - - + -
168G ILE* 4.4 11.4 - - + -
203G HIS* 3.0 51.4 - - + +
206G CYS* 4.0 14.1 - - + -
210G GLN* 2.8 25.7 + - + +
211G ILE* 3.5 7.6 - - - +
213G GLU* 1.3 74.6 - - + +
215G LEU* 1.3 62.3 + - - +
217G ILE* 3.1 18.6 + - + +
218G TYR* 3.2 23.2 - - + -
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Residues in contact with LEU 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G LEU* 4.0 21.3 - - + -
168G ILE* 4.9 6.5 - - + -
211G ILE* 2.9 26.5 + - + +
212G TYR* 3.7 8.1 - - + +
214G ILE* 1.3 75.0 - - - +
216G LYS* 1.3 53.8 + - - +
217G ILE 3.0 0.7 + - - -
218G TYR* 3.0 3.9 + - - -
219G GLN* 2.7 37.7 + - - +
232G CYS* 4.2 19.1 - - + -
234G ILE* 5.8 1.1 - - + -
261G LEU* 3.9 48.7 - - + +
264G GLN* 4.4 10.8 - - + -
265G PHE* 3.7 27.1 - - + -
280G PHE* 5.3 1.3 - - + -
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Residues in contact with LYS 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G TYR 2.7 17.6 + - - +
213G GLU* 3.1 17.0 - - - +
215G LEU* 1.3 72.5 - - - +
217G ILE* 1.3 60.9 + - + +
219G GLN* 3.2 23.5 + - - +
220G LEU* 3.1 49.1 + - + +
264G GLN* 5.5 8.2 - - - +
269G LYS* 5.8 2.4 - - - +
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Residues in contact with ILE 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203G HIS* 6.4 0.2 - - - +
213G GLU* 3.0 17.3 + - + +
214G ILE* 3.3 14.8 - - + +
215G LEU 3.1 0.4 - - - -
216G LYS* 1.3 74.0 - - + +
218G TYR* 1.3 77.2 + - + +
219G GLN 2.9 5.1 + - - -
220G LEU* 2.9 16.9 + - - +
221G MET* 3.0 36.1 + - + +
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Residues in contact with TYR 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G TYR* 3.7 39.3 - + + -
166G LEU* 3.5 41.3 - - + -
201G LYS* 3.0 33.1 - - + +
203G HIS* 4.5 7.7 - + - -
214G ILE* 3.2 22.7 - - + +
215G LEU 3.0 5.4 + - - +
217G ILE* 1.3 90.5 - - + +
219G GLN* 1.3 62.4 + - - +
221G MET* 3.6 24.5 - - + +
224G HIS* 2.8 27.5 + + - +
230G PHE* 4.1 10.1 - + + -
265G PHE* 3.8 17.4 - - + -
270G CYS* 4.6 0.3 - - - -
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Residues in contact with GLN 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G LEU 2.7 16.6 + - - +
216G LYS* 3.2 24.3 + - - +
217G ILE 2.9 0.2 + - - -
218G TYR* 1.3 82.1 - - - +
220G LEU* 1.3 85.6 + - - +
221G MET 3.5 1.2 + - - +
264G GLN* 3.0 47.1 + - + +
265G PHE* 3.8 11.2 - - + -
269G LYS* 3.2 32.1 + - - +
270G CYS* 3.5 19.7 - - + -
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Residues in contact with LEU 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216G LYS* 3.3 40.8 - - + +
217G ILE* 2.9 6.5 + - - +
219G GLN* 1.3 91.8 - - - +
221G MET* 1.3 68.7 + - - +
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Residues in contact with MET 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G TYR* 3.5 38.4 - - + +
217G ILE* 3.0 37.1 + - + +
218G TYR* 3.6 31.0 - - + +
219G GLN 3.3 5.7 - - - +
220G LEU* 1.3 85.4 - - - +
222G ASP* 1.3 62.2 + - - +
224G HIS* 3.7 11.4 - - + +
272G SER* 3.1 15.2 + - - -
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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