Contacts of the helix formed by residues 219 - 235 (chain A) in PDB entry 3FZ7
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 PHE 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A PHE* 4.7 1.1 - + - -
217A TYR* 3.9 34.5 - + + -
218A GLU* 1.3 72.4 - - - +
220A PRO* 1.3 70.3 - - - +
221A GLN* 3.2 2.0 + - + +
222A PRO* 3.4 23.9 - - + +
223A LEU* 3.8 14.7 - - - +
258A ILE* 4.0 31.9 - - + -
372A ASP 3.2 28.3 - - - -
373A GLU* 4.2 9.4 - - + -
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Residues in contact with PRO 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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207A PRO* 4.5 4.7 - - + -
209A PHE* 4.0 8.7 - - + -
218A GLU 3.1 11.4 - - - +
219A PHE* 1.3 83.1 - - + +
221A GLN* 1.3 57.7 + - - +
223A LEU* 3.2 6.4 + - + +
224A HIS* 2.8 29.8 + - - +
240A MET* 3.5 11.5 - - + +
242A ILE* 3.6 28.7 - - + -
259A VAL 4.9 0.7 - - - +
260A TRP* 3.5 36.6 - - + +
264A LEU* 3.6 20.9 - - + -
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Residues in contact with GLN 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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219A PHE* 3.2 3.0 + - + +
220A PRO* 1.3 78.3 - - - +
222A PRO* 1.4 71.8 - - + +
224A HIS* 3.1 7.5 + - + +
225A ASP* 2.9 34.3 + - - +
259A VAL* 3.7 41.9 + - - +
264A LEU* 4.0 18.9 - - + +
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Residues in contact with PRO 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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191A PRO* 4.2 20.1 - - + +
219A PHE* 3.4 24.9 - - + +
221A GLN* 1.4 92.5 - - + +
223A LEU* 1.3 60.2 + - + +
225A ASP* 3.3 12.7 + - + +
226A ALA* 3.0 22.0 + - - +
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Residues in contact with LEU 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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189A MET* 3.8 34.5 - - + +
190A ASP 3.8 5.2 - - - +
191A PRO* 3.4 39.7 - - + -
194A MET* 3.5 23.7 - - + +
207A PRO* 4.2 18.6 - - + -
218A GLU* 4.9 5.6 - - + -
219A PHE 3.8 17.3 - - - +
220A PRO 3.2 2.0 + - - +
221A GLN 3.2 0.4 - - - -
222A PRO* 1.3 78.2 - - + +
224A HIS* 1.3 57.6 + - - +
226A ALA* 3.3 1.6 + - - -
227A LEU* 2.9 32.4 + - - +
240A MET* 3.5 16.6 - - + -
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Residues in contact with HIS 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 PRO 2.8 17.5 + - - +
221A GLN* 3.1 8.9 + - - +
223A LEU* 1.3 74.0 - - - +
225A ASP* 1.3 68.8 + - - +
227A LEU* 3.2 6.1 + - - +
228A ASP* 3.0 46.9 + - - +
240A MET* 3.9 12.9 - - - +
264A LEU* 3.6 30.4 - - + +
265A PRO* 3.5 24.7 - - + +
266A ARG* 3.0 44.2 + - + +
267A VAL 4.6 0.2 - - - -
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Residues in contact with ASP 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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221A GLN* 2.9 34.2 + - - +
222A PRO* 3.6 12.4 - - + +
224A HIS* 1.3 73.8 + - - +
226A ALA* 1.3 57.3 - - - +
228A ASP* 3.2 14.6 + - - +
229A LYS* 3.1 27.6 + - - +
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Residues in contact with ALA 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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191A PRO* 3.9 16.4 - - + -
194A MET* 3.8 15.5 - - + -
195A ILE* 3.6 16.0 - - + +
222A PRO 3.0 12.7 + - - +
223A LEU 3.6 8.1 - - - +
224A HIS 3.2 0.4 - - - -
225A ASP* 1.3 72.5 - - - +
227A LEU* 1.3 59.9 + - - +
229A LYS* 3.5 8.7 + - - +
230A PHE* 3.0 26.9 + - - +
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Residues in contact with LEU 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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194A MET* 4.0 16.6 - - + -
195A ILE* 4.2 9.6 - - + -
198A CYS* 4.2 10.3 - - - -
205A VAL* 4.2 24.0 - - + -
223A LEU 2.9 21.2 + - - +
224A HIS 3.2 1.5 + - - +
226A ALA* 1.3 73.3 - - - +
228A ASP* 1.3 59.1 + - - +
230A PHE* 3.3 7.4 + - + +
231A GLN* 3.1 23.2 + - - +
236A ILE 4.7 1.0 - - - +
238A ILE* 3.9 29.0 + - + +
240A MET* 3.7 36.1 - - + -
266A ARG* 3.7 26.7 + - - -
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Residues in contact with ASP 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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224A HIS* 3.0 36.4 + - - +
225A ASP* 3.2 15.0 + - - +
227A LEU* 1.3 73.6 - - - +
229A LYS* 1.3 65.9 + - - +
231A GLN* 3.3 5.9 + - - +
232A ALA* 3.1 20.7 + - - +
266A ARG* 2.6 39.7 + - - +
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Residues in contact with LYS 229 (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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225A ASP 3.1 12.0 + - - +
226A ALA* 3.9 8.3 - - - +
227A LEU 3.4 0.2 - - - -
228A ASP* 1.3 79.4 - - - +
230A PHE* 1.3 51.9 + - - +
232A ALA* 3.3 8.7 + - + +
233A ASP* 2.7 72.1 + - - +
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Residues in contact with PHE 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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195A ILE* 3.8 39.7 - - + -
198A CYS* 3.7 38.4 - - + -
199A ASP* 4.4 1.1 - - - -
226A ALA 3.0 17.6 + - - +
227A LEU* 3.4 9.4 - - + +
228A ASP 3.2 0.4 - - - -
229A LYS* 1.3 75.6 - - - +
231A GLN* 1.3 56.3 + - - +
233A ASP* 3.1 5.6 + - + -
234A THR* 2.7 59.9 + - + +
236A ILE* 3.8 40.6 - - + -
238A ILE* 3.9 10.1 - - + -
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Residues in contact with GLN 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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227A LEU 3.1 12.6 + - - +
228A ASP 3.6 7.6 - - - +
230A PHE* 1.3 74.1 - - - +
232A ALA* 1.3 62.2 + - - +
235A GLY* 2.8 32.4 + - - -
236A ILE 3.2 23.2 + - - +
237A ASP* 3.3 40.2 + - - +
266A ARG* 2.8 29.3 + - - +
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Residues in contact with ALA 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 ASP 3.1 12.9 + - - +
229A LYS* 3.5 12.8 - - + +
230A PHE 3.2 0.2 - - - -
231A GLN* 1.3 79.5 - - - +
233A ASP* 1.3 66.5 + - - +
234A THR 3.5 0.3 + - - -
235A GLY 4.5 0.9 + - - -
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Residues in contact with ASP 233 (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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229A LYS* 2.7 55.1 + - - +
230A PHE* 3.1 7.6 + - + +
232A ALA* 1.3 82.3 - - - +
234A THR* 1.3 67.1 + - + +
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Residues in contact with THR 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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230A PHE* 2.7 42.2 + - + +
233A ASP* 1.3 88.1 - - + +
235A GLY* 1.3 60.0 + - - +
236A ILE* 3.0 39.1 + - + +
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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 GLN* 2.8 27.3 + - - +
232A ALA 4.5 1.0 + - - -
233A ASP 4.0 0.2 - - - -
234A THR* 1.3 75.6 - - - +
236A ILE* 1.3 61.4 - - - +
237A ASP* 3.5 5.7 + - - +
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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
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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