Contacts of the helix formed by residues 227 - 243 (chain D) in PDB entry 1PZY
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 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220D GLN* 2.9 9.1 + - - -
225D MET 3.5 0.4 + - - -
226D PHE* 1.3 73.2 - - - +
228D ARG* 1.3 61.8 + - - +
229D ALA* 3.8 5.0 + - - +
230D LYS* 3.0 27.5 + - - +
231D LEU* 3.2 24.2 + - - +
309D ASN 2.7 28.0 + - - +
311D TYR 3.1 18.7 + - - +
312D TRP* 3.2 35.6 - - + -
398D ILE* 3.6 18.8 - - + -
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Residues in contact with ARG 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PRO* 4.1 15.5 - - + +
226D PHE* 3.7 26.8 + - + -
227D ASN* 1.3 72.1 + - - +
229D ALA* 1.3 64.4 + - - +
231D LEU* 3.2 6.3 + - - +
232D LEU* 3.0 45.1 + - + +
250D PHE* 4.9 6.5 + - - +
251D SER 5.5 0.2 - - - -
252D ASP* 2.7 31.3 + - - +
290D PHE 5.3 1.0 + - - -
291D GLY* 4.4 2.9 - - - -
292D GLY 3.6 28.0 + - - +
311D TYR 4.8 1.6 + - - -
313D GLY 5.9 0.4 + - - -
317D GLU* 2.7 45.9 + - - +
318D ASP* 4.3 11.1 - - - +
321D ILE* 5.2 3.6 - - - +
409D UDP 4.2 16.8 - - - -
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Residues in contact with ALA 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D ASN* 3.4 4.6 + - - +
228D ARG* 1.3 78.9 - - - +
230D LYS* 1.3 57.7 + - - +
232D LEU* 3.2 16.0 + - - +
233D ASN* 3.0 28.4 + - - -
307D PHE* 4.2 13.8 - - + +
308D PRO* 3.3 22.7 - - + +
311D TYR* 5.2 2.4 + - + -
317D GLU* 3.8 29.6 - - + +
321D ILE* 5.0 1.6 - - + -
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Residues in contact with LYS 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D ASN* 3.0 40.3 + - + +
229D ALA* 1.3 74.0 - - - +
231D LEU* 1.3 66.4 + - - +
233D ASN* 3.2 4.0 + - - +
234D VAL* 3.1 26.3 + - - +
308D PRO 3.9 1.5 + - - -
309D ASN* 3.5 38.3 + - + +
312D TRP* 4.4 7.0 - - + -
378D LEU* 4.1 13.5 - - + -
379D THR* 3.5 36.4 + - - +
398D ILE* 2.7 44.5 + - + +
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PRO* 4.2 6.7 - - + -
188D PHE 3.9 11.9 - - - +
218D ILE* 3.5 35.1 - - + +
220D GLN* 3.7 33.7 - - + +
226D PHE* 3.2 42.2 - - + -
227D ASN 3.2 13.2 + - - +
228D ARG 3.2 5.4 + - - +
230D LYS* 1.3 75.2 - - - +
232D LEU* 1.3 63.8 + - - +
234D VAL* 3.2 6.1 + - - +
235D GLY 3.0 17.7 + - - -
396D VAL* 4.2 8.5 - - + -
398D ILE* 4.0 15.3 - - + -
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ILE* 3.8 15.0 - - + +
187D PRO* 3.7 31.0 - - + -
228D ARG* 3.0 48.1 + - - +
229D ALA* 3.2 11.0 + - + +
231D LEU* 1.3 77.8 - - - +
233D ASN* 1.3 63.3 + - - +
235D GLY* 3.0 10.6 + - - -
236D PHE* 3.0 10.4 + - - +
250D PHE* 3.7 42.9 - - + -
307D PHE* 3.9 27.4 - - + -
321D ILE* 5.2 1.8 - - + -
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Residues in contact with ASN 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 ALA 3.0 15.1 + - - -
230D LYS 3.2 7.4 + - - +
232D LEU* 1.3 75.4 - - - +
234D VAL* 1.3 64.7 + - - +
236D PHE* 3.1 11.0 + - - +
237D LYS* 3.0 24.3 + - - +
301D PHE* 3.2 14.1 - - - -
306D GLY* 4.0 0.2 - - - -
307D PHE* 2.9 47.1 + - - +
308D PRO 4.1 1.0 + - - -
309D ASN* 2.9 25.1 + - - +
374D GLY 4.5 4.0 - - - -
375D LEU* 4.6 8.9 - - + +
378D LEU* 3.8 18.8 - - + +
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Residues in contact with VAL 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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218D ILE* 3.7 18.6 - - + -
230D LYS 3.1 15.0 + - - +
231D LEU* 3.3 9.0 - - - +
232D LEU 3.2 0.2 - - - -
233D ASN* 1.3 76.9 - - - +
235D GLY* 1.3 54.2 + - - +
237D LYS* 3.1 4.1 + - - +
238D GLU* 2.7 44.6 + - + +
378D LEU* 4.4 10.3 - - + -
380D TYR* 3.8 45.3 - - + -
394D ILE* 5.2 0.2 - - + -
396D VAL* 4.0 11.0 - - + -
398D ILE* 4.3 16.2 - - + -
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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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185D ILE* 3.8 15.7 - - - +
216D TYR* 5.3 0.9 - - - -
218D ILE* 3.5 28.2 - - - +
231D LEU 3.0 10.9 + - - -
232D LEU 3.0 4.4 + - - -
234D VAL* 1.3 76.9 - - - +
236D PHE* 1.3 56.6 + - - +
238D GLU* 4.5 1.1 - - - -
239D ALA* 2.8 36.0 + - - +
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Residues in contact with PHE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ILE* 4.1 2.4 - - - +
232D LEU 3.0 10.5 + - - +
233D ASN 3.2 7.9 - - - +
235D GLY* 1.3 76.9 - - - +
237D LYS* 1.3 72.8 + - + +
240D LEU* 3.3 43.2 + - + +
248D PHE* 3.3 55.6 - + + -
250D PHE* 4.8 3.6 - - + -
298D LYS* 4.2 10.8 - - + -
301D PHE* 3.4 39.5 - + + -
302D LEU* 3.4 24.5 - - + -
375D LEU* 3.6 30.1 - - + -
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Residues in contact with LYS 237 (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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233D ASN 3.0 8.9 + - - +
234D VAL* 3.6 5.2 - - - +
236D PHE* 1.3 90.7 - - + +
238D GLU* 1.3 63.6 + - - +
240D LEU* 3.5 15.2 + - + +
241D LYS* 3.6 19.5 + - - +
375D LEU* 4.2 27.7 - - + +
378D LEU* 3.9 21.5 - - + -
380D TYR* 3.6 19.5 - - + +
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Residues in contact with GLU 238 (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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216D TYR* 4.9 2.0 - - + -
234D VAL* 2.7 39.1 + - + +
235D GLY* 4.1 2.5 - - - +
237D LYS* 1.3 71.8 - - - +
239D ALA* 1.3 66.5 + - - +
241D LYS* 3.1 49.2 + - - +
242D ASP* 3.8 7.3 + - - +
380D TYR* 2.5 26.6 + - + +
382D VAL* 4.0 20.5 - - - +
385D VAL* 5.1 4.9 - - - +
394D ILE* 3.4 35.5 - - + +
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Residues in contact with ALA 239 (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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183D ALA* 3.9 28.5 - - + -
185D ILE* 4.8 0.9 - - + -
216D TYR* 3.8 26.8 - - + -
235D GLY 2.8 24.6 + - - +
236D PHE 4.0 2.9 - - - +
238D GLU* 1.3 72.6 - - - +
240D LEU* 1.3 58.8 + - - +
242D ASP* 2.9 19.8 + - - +
243D TYR 3.4 0.3 + - - -
245D TYR* 3.2 19.9 - - + -
248D PHE* 4.2 4.0 - - + -
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Residues in contact with LEU 240 (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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236D PHE* 3.3 49.0 + - + +
237D LYS* 3.8 11.7 - - + +
238D GLU 3.3 0.6 - - - -
239D ALA* 1.3 78.2 - - - +
241D LYS* 1.3 62.2 + - + +
242D ASP 3.2 0.9 + - - -
243D TYR 3.2 24.1 + - - +
244D ASP* 4.9 1.3 - - - -
245D TYR* 3.8 19.3 - - + +
248D PHE* 3.8 19.1 - - + -
298D LYS* 3.9 26.2 - - - +
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Residues in contact with LYS 241 (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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237D LYS* 3.6 15.5 - - - +
238D GLU* 3.1 46.2 + - - +
239D ALA 3.0 0.6 - - - -
240D LEU* 1.3 78.7 - - + +
242D ASP* 1.3 64.3 + - - +
380D TYR* 4.6 4.3 + - - -
382D VAL* 5.4 4.0 - - - +
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Residues in contact with ASP 242 (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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170D ARG* 6.1 1.8 - - - +
216D TYR* 3.1 32.7 + - - +
238D GLU 4.4 5.1 - - - +
239D ALA 2.9 5.6 + - - +
240D LEU 4.2 0.2 - - - -
241D LYS* 1.3 87.0 - - - +
243D TYR* 1.3 64.8 + - + +
387D ARG* 2.8 45.4 + - - -
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Residues in contact with TYR 243 (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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170D ARG* 3.2 31.0 + - - +
172D THR* 4.9 2.8 + - - +
181D LYS* 3.7 22.5 + - + -
212D ASP* 2.6 32.9 + - - -
239D ALA 3.4 2.0 + - - -
240D LEU* 3.2 20.3 + - - +
242D ASP* 1.3 83.3 - - + +
244D ASP* 1.3 80.0 + - - +
245D TYR* 3.0 51.5 + + + +
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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
------------------------------------------------------------
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