Contacts of the helix formed by residues 207 - 221 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E LYS* 5.7 4.0 - - + -
205E ASP 5.1 0.2 - - - +
206E CYS 1.3 74.9 - - - +
208E VAL* 1.3 63.3 + - - +
209E GLU* 3.4 10.0 + - - +
210E GLN* 2.3 55.3 + - - +
211E ILE* 2.8 19.2 + - - +
245E GLY* 3.9 1.1 - - - -
246E THR* 3.6 16.6 - - + +
247E ASP* 3.4 30.5 - - + +
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Residues in contact with VAL 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E THR* 1.3 73.2 - - - +
209E GLU* 1.3 65.3 - - - +
211E ILE* 2.9 20.7 + - + +
212E TYR* 3.0 39.8 + - + -
243E ILE* 6.1 0.2 - - + -
245E GLY* 3.5 12.5 - - - +
247E ASP* 3.4 5.9 + - - -
254E GLN* 3.2 48.5 - - + +
255E GLU 3.5 18.2 - - - +
256E ALA* 4.0 7.6 - - + +
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Residues in contact with GLU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E THR* 3.3 8.4 + - - +
208E VAL* 1.3 82.2 - - - +
210E GLN* 1.3 58.5 + - - +
212E TYR* 3.3 8.5 + - + +
213E GLU* 2.8 46.5 + - - +
247E ASP* 5.1 1.0 + - - +
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Residues in contact with GLN 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E ASP 3.7 5.3 + - - +
206E CYS* 3.0 22.0 - - + +
207E THR* 2.3 60.1 + - - +
209E GLU* 1.3 80.4 - - + +
211E ILE* 1.3 58.3 + - - +
213E GLU* 3.2 17.6 + - - +
214E ILE* 2.8 38.0 + - + +
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Residues in contact with ILE 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ILE* 3.4 46.9 - - + -
170E ASN* 4.1 9.2 - - - +
206E CYS* 3.8 15.7 - - + +
207E THR 2.8 26.2 - - - +
208E VAL* 2.9 10.5 + - + +
210E GLN* 1.3 75.7 - - - +
212E TYR* 1.3 62.9 + - + +
214E ILE* 3.2 6.5 + - - +
215E LEU* 3.0 27.6 + - + +
234E ILE* 4.8 2.2 - - + -
243E ILE* 4.7 14.4 - - + -
245E GLY* 4.7 5.6 - - - -
256E ALA* 5.9 0.4 - - + -
261E LEU* 4.5 26.5 - - + -
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Residues in contact with TYR 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E VAL* 3.0 44.1 + - + -
209E GLU* 3.7 9.6 - - + +
211E ILE* 1.3 73.9 - - + +
213E GLU* 1.3 57.4 + - - +
215E LEU* 3.1 4.4 + - + +
216E LYS* 2.7 36.9 + - - +
255E GLU 5.2 0.7 - - - -
256E ALA* 3.4 21.6 - - + +
257E PRO* 3.9 1.7 - - - +
260E GLU* 3.1 38.0 + - + +
261E LEU* 3.4 22.0 - - + -
264E GLN* 4.1 21.1 + - - +
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Residues in contact with GLU 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E GLU* 2.8 35.1 + - - +
210E GLN* 3.3 22.1 - - - +
212E TYR* 1.3 76.7 - - - +
214E ILE* 1.3 62.6 + - + +
216E LYS* 3.4 9.6 + - - +
217E ILE* 3.3 24.8 + - - +
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Residues in contact with ILE 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E LEU* 3.8 23.8 - - + -
168E ILE* 4.4 12.6 - - + -
203E HIS* 3.3 54.1 - - + +
206E CYS* 4.0 16.6 - - - -
210E GLN* 2.8 27.5 + - + +
211E ILE* 3.4 7.6 - - - +
213E GLU* 1.3 74.6 - - + +
215E LEU* 1.3 66.9 + - - +
217E ILE* 3.1 18.2 + - + +
218E TYR* 3.2 20.0 - - + -
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Residues in contact with LEU 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E LEU* 4.0 20.2 - - + -
168E ILE* 4.8 5.6 - - + -
211E ILE* 3.0 26.5 + - + +
212E TYR* 3.8 2.9 - - - +
214E ILE* 1.3 75.2 - - - +
216E LYS* 1.3 55.4 + - - +
217E ILE 2.9 0.5 + - - -
218E TYR* 3.2 2.7 + - - +
219E GLN* 2.7 38.2 + - - +
232E CYS* 4.2 17.9 - - - -
234E ILE* 5.5 0.4 - - + -
261E LEU* 3.5 53.2 - - + +
264E GLN* 3.9 13.5 - - - +
265E PHE* 3.6 26.2 - - + -
280E PHE* 5.2 1.6 - - + -
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Residues in contact with LYS 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E TYR 2.7 19.6 + - - +
213E GLU* 3.4 9.9 - - - +
215E LEU* 1.3 77.7 - - - +
217E ILE* 1.3 61.0 + - + +
219E GLN* 3.8 15.5 - - - +
220E LEU* 3.0 46.3 + - + +
264E GLN* 4.0 9.3 - - - +
199K GLU* 5.3 6.7 + - - -
201K LYS* 5.9 3.2 - - - +
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Residues in contact with ILE 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E HIS* 6.5 0.9 - - + -
213E GLU 3.3 14.1 + - - +
214E ILE* 3.1 13.8 + - + +
215E LEU 3.0 0.8 - - - -
216E LYS* 1.3 75.2 - - + +
218E TYR* 1.3 78.3 + - + +
219E GLN 3.0 4.3 - - - -
220E LEU* 2.8 23.1 + - - +
221E MET* 3.1 27.6 + - + +
217K ILE* 5.4 20.6 - - + -
221K MET* 5.5 9.2 - - + +
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Residues in contact with TYR 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E TYR* 3.6 38.8 - + + -
166E LEU* 3.7 35.7 - - + -
201E LYS* 3.1 33.4 - - + +
203E HIS* 4.4 9.7 + + - -
214E ILE* 3.2 24.0 - - + +
215E LEU 3.2 3.0 + - - +
217E ILE* 1.3 92.6 - - + +
219E GLN* 1.3 61.6 + - - +
220E LEU 3.2 0.2 - - - -
221E MET* 3.7 21.5 + - + +
224E HIS* 2.7 28.9 + + - +
230E PHE* 4.2 9.9 - + + -
265E PHE* 3.7 20.8 - - + -
270E CYS* 4.5 0.5 - - - -
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Residues in contact with GLN 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU 2.7 19.0 + - - +
216E LYS* 3.4 19.4 - - - +
217E ILE 3.0 0.2 - - - -
218E TYR* 1.3 80.1 - - - +
220E LEU* 1.3 80.0 + - - +
221E MET 3.8 0.7 + - - +
264E GLN* 3.0 40.0 + - + +
265E PHE* 3.8 10.3 - - + -
269E LYS* 2.8 45.6 + - - +
270E CYS* 3.5 19.6 - - + +
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Residues in contact with LEU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E LYS* 3.0 43.7 - - + +
217E ILE* 2.8 7.6 + - - +
219E GLN* 1.3 98.3 - - - +
221E MET* 1.3 65.4 + - - +
164K TYR* 4.0 20.9 - - + +
221K MET* 4.1 26.1 - - + +
222K ASP* 3.2 22.7 + - - +
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Residues in contact with MET 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E TYR* 3.3 42.4 - - + +
201E LYS* 5.9 2.2 - - - -
217E ILE* 3.1 27.7 + - + +
218E TYR* 3.9 22.2 - - + +
219E GLN 3.5 4.9 - - - +
220E LEU* 1.3 82.3 - - - +
222E ASP* 1.3 63.2 + - - +
224E HIS* 3.7 20.3 - - + +
270E CYS* 4.7 0.3 - - - -
272E SER* 3.0 14.9 + - - -
217K ILE* 5.9 5.8 - - + +
220K LEU* 4.5 28.7 - - + +
221K MET* 4.2 9.9 - - + +
222K ASP* 3.5 6.4 - - - +
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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