Contacts of the helix formed by residues 214 - 235 (chain A) in PDB entry 3QFR
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ASP 3.5 3.2 + - - -
213A GLY* 1.3 74.2 + - - +
215A LEU* 1.3 66.6 + - - +
216A GLU* 3.1 13.7 - - - +
217A GLU* 2.8 38.8 + - + +
218A ASP* 3.1 24.8 + - - +
416A LYS* 5.8 0.4 - - - +
419A TYR* 4.6 2.3 - - - -
420A LEU* 3.7 28.8 - - + +
424A VAL* 3.8 24.2 - - - +
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.7 24.9 - - + -
97A PHE* 3.8 15.0 - - + -
174A PHE* 4.7 1.3 - - + -
176A LEU* 3.9 16.2 - - + -
177A GLY 4.6 0.9 - - - +
209A GLY* 3.4 38.1 - - - +
210A ASP 3.4 7.4 + - - +
211A ASP* 4.0 28.8 + - + +
213A GLY 4.0 0.2 - - - -
214A ASN* 1.3 69.2 - - - +
216A GLU* 1.3 68.1 + - - +
218A ASP* 2.8 16.7 + - - +
219A PHE* 2.9 11.7 + - - +
385A ARG* 6.0 1.1 - - - +
751A FMN 3.4 24.5 - - - +
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 3.6 10.0 - - - -
100A ARG* 3.2 24.8 + - - -
214A ASN* 3.1 12.2 + - - +
215A LEU* 1.3 77.3 - - - +
217A GLU* 1.3 60.5 + - - +
219A PHE* 2.8 23.7 + - - +
220A ILE* 2.9 14.9 + - + +
385A ARG* 2.8 30.1 - - + +
386A THR* 2.5 55.4 + - + -
419A TYR* 4.0 13.5 - - + +
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ASN* 2.8 32.9 + - + +
215A LEU 3.3 0.2 - - - -
216A GLU* 1.3 73.2 - - - +
218A ASP* 1.3 63.6 + - - +
220A ILE* 3.1 33.2 - - - +
221A THR* 2.9 32.3 + - - -
386A THR* 4.2 1.4 - - - +
408A MET 5.3 0.3 - - - +
410A SER 4.9 0.5 - - - +
411A SER 3.2 15.6 - - - +
416A LYS* 3.1 43.9 + - - +
419A TYR* 3.4 25.3 - - + +
420A LEU* 4.0 11.9 - - + -
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Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PHE* 3.8 5.5 - - + -
208A LEU 3.4 8.9 - - - +
209A GLY* 3.8 16.2 - - - +
210A ASP* 2.7 36.6 + - - +
214A ASN 3.1 15.3 + - - +
215A LEU 2.8 12.0 + - - +
217A GLU* 1.3 77.3 - - - +
219A PHE* 1.3 55.0 + - - +
221A THR* 3.9 4.8 - - - +
222A TRP* 3.1 27.9 + - - +
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 3.9 64.2 - + + -
100A ARG* 3.4 45.3 - - + -
101A LEU* 4.1 28.9 - - + -
139A CYS* 5.3 0.7 - - - -
174A PHE* 3.7 20.8 - + + -
215A LEU 2.9 9.4 + - - +
216A GLU* 2.8 10.8 + - - +
218A ASP* 1.3 74.0 - - - +
220A ILE* 1.3 62.5 + - - +
221A THR 3.1 1.3 - - - -
222A TRP* 2.9 11.1 + + - +
223A ARG* 2.7 45.5 + - + +
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.7 17.0 - - - +
216A GLU* 2.9 13.8 + - - +
217A GLU* 3.1 44.4 - - - +
219A PHE* 1.3 76.4 - - + +
221A THR* 1.3 66.1 + - - +
223A ARG* 3.8 24.3 + - - +
224A GLU* 3.0 26.2 + - - +
386A THR* 3.6 33.9 - - + +
409A ALA 4.2 8.1 - - - +
410A SER 4.0 16.6 - - - +
411A SER* 4.3 7.9 - - - +
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Residues in contact with THR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLU* 2.9 29.3 + - - -
218A ASP* 3.9 6.5 - - - +
220A ILE* 1.3 79.8 - - - +
222A TRP* 1.3 67.7 + - - +
224A GLU* 3.4 12.6 + - - +
225A GLN* 3.6 15.0 + - + +
411A SER* 4.0 19.8 + - - +
416A LYS* 5.0 5.5 + - - +
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Residues in contact with TRP 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.1 22.4 - - + -
137A VAL* 4.4 14.1 - - + -
172A ALA* 4.3 6.7 - - + -
173A VAL 4.1 16.2 - - - -
174A PHE* 3.6 35.2 - + + -
204A PHE* 3.3 31.1 - + - -
205A GLU* 3.1 25.1 + - - -
206A LEU 4.6 1.1 - - - -
207A GLY* 3.5 21.4 - - - -
218A ASP 3.1 16.4 + - - +
219A PHE* 2.9 8.6 + + - +
221A THR* 1.3 81.4 - - - +
223A ARG* 1.3 78.6 + - + +
225A GLN* 3.1 9.1 + - - +
226A PHE* 3.0 48.7 + + + +
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Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 4.8 13.7 + - - +
101A LEU* 4.0 14.1 - - + -
104A ASP* 3.0 35.9 + - - -
107A ARG* 4.5 10.0 - - - +
219A PHE* 2.7 34.9 + - + +
220A ILE* 3.8 28.7 + - - +
222A TRP* 1.3 84.2 - - + +
224A GLU* 1.3 61.2 + - - +
226A PHE* 2.8 20.6 + - + +
227A TRP* 3.1 32.4 + - + +
386A THR* 5.5 1.0 + - - -
387A ASN* 6.2 1.6 - - - +
409A ALA 5.4 3.8 + - - -
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ILE 3.0 16.2 + - - +
221A THR 3.5 5.5 - - - +
223A ARG* 1.3 79.6 - - - +
225A GLN* 1.3 75.1 + - - +
227A TRP* 5.5 1.3 - - - -
228A PRO* 3.1 23.8 - - - +
411A SER* 2.7 43.1 + - - -
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Residues in contact with GLN 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A PHE* 3.2 35.0 - - + -
221A THR* 3.6 18.8 - - + +
222A TRP* 3.1 5.0 + - - +
223A ARG 3.0 0.8 - - - -
224A GLU* 1.3 104.7 + - - +
226A PHE* 1.3 63.8 + - - +
227A TRP 3.6 0.4 - - - -
228A PRO* 3.8 6.4 - - - +
229A ALA* 3.3 13.5 + - - +
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.5 9.2 - - + -
135A LEU* 4.0 7.2 - - + -
137A VAL* 3.4 27.4 - - + -
172A ALA* 3.3 26.2 - - + -
203A ILE* 5.2 1.3 - - + -
204A PHE* 4.0 22.2 - - + -
222A TRP* 3.0 38.7 + + + +
223A ARG* 2.8 12.6 + - - +
225A GLN* 1.3 77.0 - - - +
227A TRP* 1.3 108.0 + + - +
229A ALA* 3.1 5.0 + - - +
230A VAL* 2.9 40.6 + - + +
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Residues in contact with TRP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 4.1 28.0 - - + -
101A LEU* 3.3 21.8 - - + -
104A ASP* 2.9 46.2 + - + +
105A ALA* 3.8 14.1 - - + -
107A ARG* 4.6 3.1 - - - -
108A TYR* 3.4 49.8 - + + +
110A MET* 5.6 0.4 - - - -
223A ARG* 3.1 31.4 + - + +
224A GLU* 5.5 1.3 - - - -
226A PHE* 1.3 104.9 - + - +
228A PRO* 1.3 64.1 - - + +
230A VAL* 2.6 41.0 + - + +
231A CYS* 2.7 16.7 + - - +
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Residues in contact with PRO 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 5.1 4.0 - - + +
224A GLU* 3.1 28.0 - - - +
225A GLN* 3.8 6.3 - - - +
226A PHE 3.7 2.2 - - - -
227A TRP* 1.3 93.6 - - + +
229A ALA* 1.3 56.6 + - - +
231A CYS* 3.2 12.0 + - + +
232A GLU* 2.9 31.2 + - - +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 4.2 14.5 - - + +
204A PHE* 3.7 21.8 - - + -
225A GLN 3.3 19.4 + - - +
226A PHE 3.1 5.6 + - - +
227A TRP 3.1 0.6 - - - -
228A PRO* 1.3 79.6 - - - +
230A VAL* 1.3 60.8 + - - +
232A GLU* 3.8 9.0 + - - +
233A HIS* 3.4 21.3 + - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 5.8 1.1 - - + -
110A MET* 4.4 16.6 - - - -
135A LEU* 3.6 26.5 - - + -
203A ILE* 4.2 14.1 - - + -
226A PHE* 2.9 33.0 + - + +
227A TRP* 2.6 30.7 + - + +
229A ALA* 1.3 70.4 - - - +
231A CYS* 1.3 68.1 + - - +
233A HIS* 3.0 11.3 + - - -
234A PHE* 3.0 31.9 + - + +
236A VAL* 4.6 4.7 - - + -
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Residues in contact with CYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 3.1 43.3 - - - -
227A TRP 2.7 11.1 + - - -
228A PRO* 3.4 13.0 - - + +
230A VAL* 1.3 79.3 - - - +
232A GLU* 1.3 56.9 + - - +
235A GLY* 3.0 24.9 + - - -
236A VAL* 3.0 42.1 + - - +
237A GLU* 4.2 4.7 - - - -
238A ALA 4.6 0.9 - - - -
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PRO 2.9 15.5 + - - +
229A ALA* 4.1 8.7 - - - +
230A VAL 3.2 0.2 - - - -
231A CYS* 1.3 77.1 - - - +
233A HIS* 1.3 63.8 + - + +
235A GLY* 4.2 3.4 + - - -
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Residues in contact with HIS 233 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A LYS* 3.2 32.2 + - + -
201A GLN* 3.9 12.6 + - - -
203A ILE* 3.1 35.6 - - + +
229A ALA 3.4 14.1 + - - +
230A VAL 3.0 5.3 + - - +
232A GLU* 1.3 83.3 - - + +
234A PHE* 1.3 78.7 + + + +
235A GLY 3.3 0.4 + - - -
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Residues in contact with PHE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A MET* 4.3 21.1 - - + -
133A ASN* 3.5 46.6 + - + +
134A ALA 3.7 19.5 - - - -
135A LEU* 4.1 28.9 - - + -
170A LYS* 4.0 19.1 - - + -
203A ILE* 5.1 2.5 - - + -
230A VAL* 3.0 31.4 + - + +
233A HIS* 1.3 100.9 - + + +
235A GLY* 1.3 63.6 + - - +
236A VAL* 4.4 9.8 - - + +
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Residues in contact with GLY 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A CYS 3.0 10.3 + - - -
232A GLU* 4.2 3.3 + - - -
233A HIS 3.3 3.2 - - - +
234A PHE* 1.3 82.1 - - - +
236A VAL* 1.3 62.5 + - - +
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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