Contacts of the helix formed by residues 219 - 235 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189D MET 6.0 0.2 + - - -
209D PHE* 4.7 1.1 - + - -
217D TYR* 3.9 32.8 - - + -
218D GLU* 1.3 71.2 - - - +
220D PRO* 1.4 69.2 - - - +
221D GLN* 3.4 0.7 - - + +
222D PRO* 3.4 25.6 - - + +
223D LEU* 3.3 19.7 - - - +
258D ILE* 3.7 35.4 - - + -
372D ASP 3.2 27.6 - - - -
373D GLU* 4.2 9.2 - - + -
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Residues in contact with PRO 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D PRO* 4.5 5.6 - - + -
209D PHE* 4.1 7.9 - - + -
218D GLU 3.0 12.3 - - - +
219D PHE* 1.4 84.0 - - + +
221D GLN* 1.3 53.8 + - - +
223D LEU* 3.1 12.9 + - + +
224D HIS* 2.5 37.4 + - - +
240D MET* 3.6 8.6 - - + +
242D ILE* 3.8 26.5 - - + -
258D ILE* 5.6 0.2 - - + -
259D VAL 5.0 0.7 - - - +
260D TRP* 3.6 36.6 - - + +
264D LEU* 3.8 17.0 - - + -
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Residues in contact with GLN 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D PHE* 3.4 0.6 - - + +
220D PRO* 1.3 76.5 - - - +
222D PRO* 1.4 66.4 - - + +
224D HIS* 2.8 6.2 + - - +
225D ASP* 2.8 40.1 + - - +
259D VAL* 3.6 50.2 + - - +
264D LEU* 3.8 18.9 - - + +
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Residues in contact with PRO 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D PRO* 4.1 19.8 - - + +
219D PHE* 3.4 29.2 - - + +
221D GLN* 1.4 93.5 - - + +
223D LEU* 1.3 62.2 + - + +
225D ASP* 3.3 14.4 + - - +
226D ALA* 3.2 20.6 + - - +
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Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D MET* 3.9 31.9 - - + +
190D ASP 4.0 1.1 - - - -
191D PRO* 3.6 37.0 - - + -
194D MET* 3.5 24.4 - - - +
207D PRO* 4.0 29.8 - - + -
218D GLU* 5.0 4.7 - - + -
219D PHE 3.3 20.2 - - - +
220D PRO* 3.1 4.7 + - + +
222D PRO* 1.3 77.4 - - + +
224D HIS* 1.3 63.0 + - - +
226D ALA* 3.3 2.1 + - - -
227D LEU* 3.1 21.0 + - - +
240D MET* 3.5 12.6 - - + -
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Residues in contact with HIS 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D PRO 2.5 17.3 + - - +
221D GLN* 2.8 17.2 + - - +
223D LEU* 1.3 70.9 - - - +
225D ASP* 1.3 65.5 + - - +
227D LEU* 3.1 8.0 + - - +
228D ASP* 3.0 38.0 + - - +
240D MET* 4.2 13.2 - - - -
264D LEU* 3.5 29.2 - - + +
265D PRO* 3.6 25.1 - - + +
266D ARG* 2.9 54.9 + - + +
267D VAL 4.7 0.2 - - - -
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Residues in contact with ASP 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D GLN* 2.8 30.2 + - - +
222D PRO* 3.3 14.6 + - + +
224D HIS* 1.3 75.6 + - - +
226D ALA* 1.3 60.8 + - - +
228D ASP* 3.1 22.0 + - - +
229D LYS* 3.2 14.4 + - - +
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Residues in contact with ALA 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D PRO* 3.9 14.4 - - + -
194D MET* 3.8 7.9 - - + -
195D ILE* 3.7 25.1 - - + +
222D PRO 3.2 9.9 + - - +
223D LEU 3.7 7.4 - - - +
224D HIS 3.2 0.4 - - - -
225D ASP* 1.3 78.7 - - - +
227D LEU* 1.3 56.8 + - - +
229D LYS* 3.3 10.7 + - + +
230D PHE* 2.8 29.8 + - - +
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Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D MET* 3.9 17.7 - - + -
195D ILE* 4.1 10.1 - - + -
198D CYS* 4.2 6.7 - - - -
205D VAL* 4.0 23.3 - - + -
223D LEU 3.1 13.1 + - - +
224D HIS* 3.1 7.8 + - - +
226D ALA* 1.3 76.2 - - - +
228D ASP* 1.3 57.0 + - - +
230D PHE* 3.7 6.9 - - + +
231D GLN* 3.1 20.1 + - - +
236D ILE 4.8 1.2 - - - +
238D ILE* 3.7 36.3 + - + +
240D MET* 3.8 37.7 - - + -
266D ARG* 3.4 23.6 + - - -
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Residues in contact with ASP 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D HIS* 3.0 31.7 + - - +
225D ASP* 3.1 16.5 + - - +
227D LEU* 1.3 73.8 - - - +
229D LYS* 1.3 61.6 + - - +
230D PHE 3.1 0.2 - - - -
231D GLN* 3.3 3.5 + - - +
232D ALA* 2.8 29.0 + - - +
265D PRO* 5.8 0.3 - - - +
266D ARG* 2.8 33.9 + - - +
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Residues in contact with LYS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D ASP 3.2 8.9 + - - +
226D ALA* 3.6 12.1 - - + +
228D ASP* 1.3 80.6 - - - +
230D PHE* 1.4 53.3 + - - +
232D ALA* 3.2 7.2 + - + +
233D ASP* 2.7 63.6 + - - +
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Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ILE* 3.7 38.1 - - + -
198D CYS* 3.8 28.0 - - + -
226D ALA 2.8 17.9 + - - +
227D LEU* 3.7 8.7 - - + +
228D ASP 3.1 0.2 - - - -
229D LYS* 1.4 73.2 - - - +
231D GLN* 1.3 60.6 + - - +
233D ASP* 3.4 5.2 + - + +
234D THR* 2.7 52.3 + - + +
236D ILE* 3.7 36.1 - - + -
238D ILE* 3.6 33.4 - - + -
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Residues in contact with GLN 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LEU 3.1 5.2 + - - +
228D ASP 3.3 3.1 + - - +
230D PHE* 1.3 78.8 - - - +
232D ALA* 1.3 59.2 + - - +
235D GLY* 2.7 37.3 + - - -
236D ILE 3.2 27.4 + - - +
237D ASP* 3.4 30.5 + - - +
266D ARG* 2.6 39.7 + - - +
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ASP 2.8 17.8 + - - +
229D LYS* 3.2 13.0 + - + +
231D GLN* 1.3 75.3 - - - +
233D ASP* 1.3 64.5 + - - +
235D GLY 4.6 0.9 + - - -
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Residues in contact with ASP 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D LYS* 2.7 50.1 + - - +
230D PHE* 4.0 5.3 - - + +
231D GLN 3.3 0.2 - - - -
232D ALA* 1.3 79.2 - - - +
234D THR* 1.3 65.8 + - + +
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Residues in contact with THR 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PHE* 2.7 46.2 + - + +
233D ASP* 1.3 86.0 - - + +
235D GLY* 1.3 60.8 + - - +
236D ILE* 3.2 36.8 + - + +
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Residues in contact with GLY 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D GLN* 2.7 32.7 + - - +
232D ALA 4.6 0.8 + - - -
233D ASP 3.9 0.2 - - - -
234D THR* 1.3 71.2 - - - +
236D ILE* 1.3 60.3 + - - +
237D ASP* 3.4 5.9 + - - +
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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