Contacts of the helix formed by residues 207 - 224 (chain B) in PDB entry 2QUH
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TYR* 3.9 2.7 - - - -
206B LEU* 1.3 75.9 - - - +
208B LEU* 1.3 63.6 + - - +
209B ASP* 2.9 29.6 - - + +
210B GLN* 2.7 35.1 + - + +
211B ALA* 2.9 22.9 + - - +
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Residues in contact with LEU 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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249A LYS* 4.0 23.8 - - + +
252A VAL* 4.8 3.4 - - + -
253A LYS* 3.6 34.8 - - + +
201B TYR* 3.6 38.8 - - + -
207B THR* 1.3 73.4 - - - +
209B ASP* 1.3 62.2 + - - +
211B ALA* 3.7 2.3 - - - +
212B TYR* 2.9 30.9 + - - +
238B LEU* 3.8 36.5 - - + +
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Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 2.9 11.7 - - + +
208B LEU* 1.3 78.4 - - - +
210B GLN* 1.3 56.7 + - + +
212B TYR* 3.8 9.7 - - - +
213B SER* 2.7 41.9 + - - +
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Residues in contact with GLN 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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205B ASP 4.1 2.4 - - - +
206B LEU* 3.4 24.6 - - + +
207B THR* 2.7 48.3 + - + +
209B ASP* 1.3 75.8 - - + +
211B ALA* 1.3 65.6 + - - +
213B SER* 2.8 8.6 + - - -
214B TYR* 2.8 48.3 + - + +
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PRO* 4.3 4.0 - - - +
197B ASP* 3.2 37.5 - - + +
200B LYS* 5.2 1.1 - - + -
201B TYR* 4.2 16.6 - - + +
206B LEU* 4.5 8.6 - - + +
207B THR 2.9 15.6 + - - +
208B LEU* 3.7 4.9 - - - +
210B GLN* 1.3 75.1 - - - +
212B TYR* 1.3 62.5 + - - +
214B TYR* 3.2 13.0 + - - +
215B ALA 3.1 17.5 + - - -
238B LEU* 4.7 1.8 - - + -
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Residues in contact with TYR 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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197B ASP* 3.7 23.3 - - - +
208B LEU 2.9 19.0 + - - +
209B ASP* 3.8 9.9 - - - +
211B ALA* 1.3 77.2 - - - +
213B SER* 1.3 67.0 + - - +
215B ALA* 3.2 4.2 + - - +
216B VAL* 3.1 48.6 + - + +
236B SER* 3.7 11.7 - - - -
238B LEU* 4.3 8.7 - - + +
239B ASP* 2.9 33.5 + - - -
461B MET* 5.5 2.3 - - - -
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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
----------------------------------------------------------
167B GLU* 6.2 0.9 - - - -
209B ASP* 2.7 26.0 + - - +
210B GLN* 2.8 7.8 + - - -
212B TYR* 1.3 79.6 - - - +
214B TYR* 1.3 65.1 + - - +
216B VAL* 3.4 5.4 + - - +
217B GLU* 3.0 35.5 + - - +
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Residues in contact with TYR 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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164B PRO* 3.3 31.0 - - + +
165B SER 3.8 8.3 - - - -
166B SER* 3.7 19.7 - - - +
167B GLU* 3.5 35.9 - - + -
206B LEU* 3.4 33.0 - - + +
210B GLN* 2.8 46.9 + - + +
211B ALA* 3.2 2.7 + - - +
213B SER* 1.3 75.0 - - - +
215B ALA* 1.3 60.4 + - - +
217B GLU* 4.3 4.3 - - - -
218B ASN* 2.8 37.1 + - - +
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Residues in contact with ALA 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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164B PRO* 3.5 17.4 - - + +
195B MET* 3.2 35.8 - - + +
197B ASP* 4.0 13.5 - - + +
211B ALA 3.1 11.7 + - - +
212B TYR 3.2 9.6 + - - +
214B TYR* 1.3 77.4 - - - +
216B VAL* 1.3 57.9 + - + +
219B ALA* 3.0 25.9 + - - +
236B SER* 4.5 7.9 - - - -
461B MET* 5.1 1.3 - - - -
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TYR* 3.1 50.3 + - + +
213B SER* 3.9 5.4 - - - +
215B ALA* 1.3 76.9 - - + +
217B GLU* 1.3 69.4 + - - +
219B ALA* 3.4 12.6 - - - +
220B LYS* 3.6 16.2 + - - +
457B VAL* 3.9 9.3 - - + +
461B MET* 3.5 30.3 - - + -
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Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 3.5 33.8 - - + +
213B SER* 3.0 22.5 + - - +
214B TYR* 3.8 5.8 - - - +
215B ALA 3.3 0.2 - - - -
216B VAL* 1.3 78.4 - - + +
218B ASN* 1.3 69.0 + - - +
219B ALA 3.1 1.3 - - - -
220B LYS* 2.9 40.0 + - - +
221B ASP* 3.3 3.7 - - - +
449B ARG* 2.9 47.4 + - - +
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Residues in contact with ASN 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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162B ARG* 2.8 32.8 + - + +
164B PRO* 3.3 14.0 - - - +
166B SER 2.9 19.8 + - - +
167B GLU* 3.9 12.5 + - - +
169B MET* 3.2 27.8 - - + +
195B MET* 3.7 17.9 - - + -
214B TYR 2.8 23.6 + - - +
217B GLU* 1.3 73.9 - - - +
219B ALA* 1.3 57.3 - - - +
221B ASP* 3.0 7.3 + - - +
222B ILE* 3.0 28.4 + - - +
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Residues in contact with ALA 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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195B MET* 3.8 6.9 - - + +
215B ALA 3.0 18.5 + - - +
216B VAL 3.4 8.7 - - - +
217B GLU 3.1 0.4 - - - -
218B ASN* 1.3 75.7 - - - +
220B LYS* 1.3 58.9 + - - +
222B ILE* 3.3 6.7 + - - +
223B ILE* 2.8 36.5 + - + +
234B ILE* 4.1 21.5 - - + -
457B VAL* 4.2 2.7 - - + -
461B MET* 3.6 21.3 - - + -
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Residues in contact with LYS 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 VAL* 3.7 16.5 - - - +
217B GLU* 2.9 35.2 + - - +
219B ALA* 1.3 78.3 - - - +
221B ASP* 1.3 56.8 + - - +
223B ILE* 3.3 3.9 + - - +
224B ALA* 3.0 26.9 + - - +
449B ARG* 4.0 33.0 - - + +
452B VAL* 3.7 39.4 - - + +
453B THR 5.6 0.4 - - - -
454B ASP* 4.3 14.1 + - - -
457B VAL* 3.8 24.0 - - + -
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Residues in contact with ASP 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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167B GLU 4.9 4.4 - - - +
169B MET* 3.0 39.9 - - + +
174B LEU* 5.7 2.0 - - + -
217B GLU 3.3 7.6 - - - +
218B ASN* 3.0 1.9 + - - -
220B LYS* 1.3 74.2 - - - +
222B ILE* 1.3 64.9 + - - +
224B ALA* 3.3 16.3 + - - +
225B CYS* 3.6 9.4 + - - -
361B LEU* 3.8 11.3 - - + +
445B HIS* 2.8 39.9 + - - +
449B ARG* 2.8 30.2 + - - +
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Residues in contact with ILE 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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162B ARG* 3.9 6.7 - - + -
169B MET* 5.2 4.7 - - - -
177B PHE* 3.5 38.8 - - + -
193B ILE* 3.6 20.4 - - + -
195B MET* 3.8 37.0 - - + -
218B ASN 3.0 9.5 + - - +
219B ALA* 3.3 8.0 + - - +
221B ASP* 1.3 79.3 - - + +
223B ILE* 1.3 62.0 + - - +
225B CYS* 3.0 19.3 + - - +
227B PHE* 3.2 39.1 - - + -
234B ILE* 4.2 8.3 - - + -
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Residues in contact with ILE 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 ALA* 2.8 23.2 + - + +
220B LYS* 3.7 4.9 - - - +
221B ASP 3.3 0.2 - - - -
222B ILE* 1.3 76.1 - - - +
224B ALA* 1.3 57.1 + - - +
225B CYS 3.1 0.2 - - - -
226B GLY* 3.1 19.9 + - - -
227B PHE* 4.1 7.6 + - - +
234B ILE* 3.6 17.7 - - + -
452B VAL* 4.2 23.8 - - + -
456B ILE* 4.5 2.5 - - + -
457B VAL* 4.0 25.4 - - + -
460B PHE* 3.3 55.4 - - + -
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Residues in contact with ALA 224 (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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220B LYS 3.0 13.8 + - - +
221B ASP* 3.4 13.5 - - - +
222B ILE 3.1 0.6 - - - -
223B ILE* 1.3 72.4 - - - +
225B CYS* 1.3 59.4 + - - +
226B GLY* 3.1 6.5 + - - -
445B HIS* 4.1 17.7 - - + +
448B ARG* 3.7 28.8 - - + +
449B ARG* 3.7 28.3 - - - +
452B VAL* 5.2 0.7 - - - -
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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
------------------------------------------------------------
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