Contacts of the helix formed by residues 214 - 235 (chain B) in PDB entry 3QFC
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 ASN 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASP 3.1 7.5 + - - -
211B ASP* 4.1 3.1 + - - -
213B GLY* 1.3 79.6 + - - +
215B LEU* 1.3 62.6 + - - +
216B GLU* 3.4 12.3 - - - +
217B GLU* 3.0 39.7 + - + +
218B ASP* 3.2 23.8 + - - +
419B TYR* 5.2 0.4 - - - -
420B LEU* 2.9 32.0 - - + +
424B VAL* 4.5 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 3.3 26.7 - - + -
97B PHE* 3.5 14.4 - - + -
174B PHE* 4.2 9.6 - - + -
176B LEU* 3.8 11.4 - - + -
177B GLY 4.8 0.4 - - - +
209B GLY* 3.5 37.5 - - - +
210B ASP 3.6 5.7 + - - +
211B ASP* 3.8 25.7 + - - +
214B ASN* 1.3 69.5 + - - +
216B GLU* 1.3 68.1 + - - +
218B ASP* 2.9 6.3 + - - +
219B PHE* 2.8 22.2 + - - +
385B ARG* 4.9 5.6 - - - +
751B FMN 3.2 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.9 5.3 - - - -
100B ARG* 3.0 21.8 + - - -
214B ASN* 3.4 8.5 + - - +
215B LEU* 1.3 78.4 - - - +
217B GLU* 1.3 58.4 - - - +
219B PHE* 3.3 3.6 + - - +
220B ILE* 3.0 36.3 + - + +
385B ARG* 2.6 59.0 + - - +
386B THR* 2.6 32.1 + - + +
419B TYR* 3.8 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ASN* 3.0 33.5 + - + +
216B GLU* 1.3 72.4 - - - +
218B ASP* 1.3 68.9 + - - +
220B ILE* 3.1 19.6 + - - +
221B THR* 3.0 27.5 + - - -
386B THR* 4.5 0.7 - - - +
408B MET 5.0 0.3 - - - +
410B SER 4.2 5.1 - - - +
411B SER 4.1 4.9 - - - +
416B LYS* 3.1 49.6 + - - +
419B TYR* 3.4 27.5 - - - +
420B LEU* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 4.1 3.5 - - + -
208B LEU 3.9 4.8 - - - +
209B GLY* 3.6 16.4 - - - -
210B ASP* 2.7 37.8 + - - +
214B ASN 3.2 11.5 + - - +
215B LEU 2.9 8.6 + - - +
217B GLU* 1.3 78.7 - - - +
219B PHE* 1.3 63.6 + - - +
221B THR* 3.2 6.4 + - - -
222B TRP* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.7 59.9 - + + -
100B ARG* 3.6 33.7 - - + -
101B LEU* 3.8 25.8 - - + -
174B PHE* 3.6 33.9 - + + -
215B LEU 2.8 10.5 + - - +
216B GLU 3.4 8.7 - - - +
218B ASP* 1.3 76.2 - - - +
220B ILE* 1.3 55.7 - - - +
222B TRP* 3.2 3.7 + + - +
223B ARG* 2.7 69.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 4.3 6.7 - - - +
216B GLU* 3.0 28.3 + - + +
217B GLU* 3.1 24.0 + - - +
219B PHE* 1.3 76.1 - - + +
221B THR* 1.3 63.2 + - - +
223B ARG* 3.8 17.4 + - - +
224B GLU* 3.1 24.6 + - + +
386B THR* 3.4 39.5 - - + +
409B ALA* 3.9 20.9 - - - +
410B SER 4.6 2.7 - - - +
411B SER* 4.0 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 3.0 13.8 + - - -
218B ASP* 3.6 9.4 - - - -
219B PHE 3.2 0.2 - - - -
220B ILE* 1.3 76.4 - - - +
222B TRP* 1.3 65.2 + - - +
224B GLU* 3.5 3.0 + - - +
225B GLN* 3.1 48.0 + - + +
411B SER* 3.9 22.6 + - - +
416B LYS* 5.2 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.8 26.0 - - + -
137B VAL* 4.1 17.3 - - + -
172B ALA* 4.2 4.0 - - + -
173B VAL 3.6 25.1 - - - -
174B PHE* 3.6 34.1 - + + -
204B PHE* 3.2 29.4 - + - -
205B GLU* 2.9 25.7 + - + -
206B LEU 4.5 0.4 - - - -
207B GLY* 3.4 20.6 - - - +
218B ASP 3.0 16.4 + - - +
219B PHE* 3.6 5.6 - + - +
221B THR* 1.3 77.2 - - - +
223B ARG* 1.3 67.9 + - + +
225B GLN* 3.1 11.6 + - - +
226B PHE* 2.6 59.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 5.0 13.5 + - - +
101B LEU* 3.9 9.2 - - + -
104B ASP* 2.6 40.7 + - - +
107B ARG* 3.4 23.4 - - - +
219B PHE* 2.7 56.5 + - + +
220B ILE* 3.8 19.3 + - - +
222B TRP* 1.3 82.2 - - - +
224B GLU* 1.3 65.2 + - - +
226B PHE* 3.3 2.8 + - - +
227B TRP* 3.0 35.6 + - + -
409B ALA 6.0 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ILE* 3.1 14.3 + - + +
221B THR 3.7 4.1 - - - +
222B TRP 3.2 0.2 - - - -
223B ARG* 1.3 85.7 - - - +
225B GLN* 1.3 66.6 + - + +
227B TRP* 3.4 6.5 + - - +
228B LEU* 3.2 36.6 + - + +
411B SER* 3.2 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.4 29.7 - - + -
205B GLU* 4.9 5.4 - - - +
221B THR* 3.1 32.6 - - + +
222B TRP* 3.1 6.1 + - - +
224B GLU* 1.3 76.4 - - + +
226B PHE* 1.3 68.0 + - - +
228B LEU* 3.2 14.3 + - + +
229B ALA* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 5.9 0.4 - - + -
101B LEU* 4.5 8.1 - - + -
135B LEU* 3.7 20.6 - - + -
137B VAL* 3.7 16.8 - - + -
172B ALA* 3.6 26.7 - - + -
203B ILE* 5.3 1.8 - - + -
204B PHE* 3.8 23.0 - - + -
222B TRP* 2.6 51.3 + + + +
223B ARG 3.4 3.4 - - - +
225B GLN* 1.3 73.7 - - - +
227B TRP* 1.3 100.2 + + - +
229B ALA* 3.1 5.4 + - - +
230B VAL* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 3.9 14.6 - - + -
101B LEU* 3.3 34.8 - - - +
104B ASP* 3.1 30.3 + - + +
105B ALA* 3.7 17.9 - - - -
108B TYR* 3.4 44.0 - + + +
110B MET* 3.5 26.2 - - + -
223B ARG* 3.0 32.3 + - + +
224B GLU* 3.8 6.3 - - - +
225B GLN 3.3 0.2 - - - -
226B PHE* 1.3 102.9 - + - +
228B LEU* 1.3 62.5 + - + +
230B VAL* 3.2 13.8 + - + +
231B CYS* 2.8 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 6.5 0.7 - - + -
224B GLU* 3.2 27.4 + - + +
225B GLN* 3.2 16.7 + - + +
227B TRP* 1.3 76.5 - - + +
229B ALA* 1.3 63.1 + - - +
231B CYS* 3.4 10.4 + - + +
232B GLU* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.9 23.3 - - + +
204B PHE* 3.9 18.4 - - + -
225B GLN 3.0 12.3 + - - +
226B PHE 3.3 9.4 - - - +
228B LEU* 1.3 77.8 - - - +
230B VAL* 1.3 56.9 + - - +
232B GLU* 3.3 7.3 + - - +
233B HIS* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B MET* 3.5 33.0 - - + -
135B LEU* 4.1 9.4 - - + -
203B ILE* 4.6 9.4 - - + -
226B PHE* 2.9 54.9 + - + +
227B TRP* 3.5 13.5 - - + +
229B ALA* 1.3 74.7 - - - +
231B CYS* 1.3 60.4 + - - +
234B PHE* 2.9 51.3 + - + +
236B VAL* 4.2 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 3.4 37.7 - - - -
227B TRP 2.8 19.6 + - - +
228B LEU* 3.4 11.9 + - + +
230B VAL* 1.3 76.3 - - - +
232B GLU* 1.3 58.1 + - - +
235B GLY* 2.9 24.3 + - - -
236B VAL* 3.1 38.2 + - - +
237B GLU* 4.0 5.2 - - - -
238B ALA 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU 3.0 15.9 + - - +
229B ALA* 3.6 7.4 - - - +
230B VAL 3.2 0.2 - - - -
231B CYS* 1.3 81.4 - - - +
233B HIS* 1.3 64.2 + - - +
235B GLY* 3.5 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LYS* 2.8 34.7 + - - +
201B GLN* 3.7 19.5 + - - -
203B ILE* 3.5 27.0 - - + +
229B ALA 2.9 17.0 + - - +
230B VAL 4.1 1.3 - - - +
232B GLU* 1.3 80.7 - - - +
234B PHE* 1.3 83.3 + + + +
235B GLY 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B MET* 5.3 6.1 - - - -
133B ASN* 3.5 54.1 + - + +
134B ALA 4.0 14.6 - - - -
135B LEU* 4.2 26.0 - - + -
170B LYS* 4.2 15.9 - - + -
203B ILE* 4.6 7.0 - - + -
230B VAL* 2.9 40.7 + - + +
233B HIS* 1.3 97.9 - + + +
235B GLY* 1.3 65.9 + - - +
236B VAL* 3.5 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B CYS 2.9 14.1 + - - -
232B GLU 3.5 5.0 + - - -
233B HIS 3.3 3.8 + - - -
234B PHE* 1.3 80.4 - - - +
236B VAL* 1.3 59.1 + - - +
237B GLU* 5.4 1.5 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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