Contacts of the strand formed by residues 212 - 220 (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 ASP 212 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170D ARG* 3.2 14.4 + - - -
171D TYR 3.4 3.8 - - - -
172D THR* 2.7 37.9 + - + +
173D PRO* 4.2 3.1 - - + -
178D SER* 3.9 14.8 + - - +
180D HIS 3.0 16.6 + - - +
181D LYS* 3.3 17.8 - - + +
182D VAL 2.9 22.9 + - - -
211D LEU* 1.3 69.6 - - - +
213D TYR* 1.3 56.9 + - - +
243D TYR* 2.6 32.8 + - - -
245D TYR* 4.7 2.8 - - - -
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Residues in contact with TYR 213 (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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165D VAL* 3.8 0.2 - - - +
169D GLY 4.3 2.9 - - - -
170D ARG* 2.8 25.4 + - - -
171D TYR* 3.0 61.0 + + + +
182D VAL* 3.0 17.5 - - + +
184D ILE* 4.7 7.2 - - + -
203D HIS* 3.0 48.5 + + - -
206D LEU* 3.5 42.0 - - + -
207D GLN* 3.6 5.9 + - - +
211D LEU* 3.4 24.0 - - + -
212D ASP* 1.3 75.0 - - - +
214D GLY* 1.3 60.4 + - - +
215D ILE* 3.8 18.8 - - + -
245D TYR* 4.6 1.1 - - - -
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Residues in contact with GLY 214 (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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168D GLY 5.3 0.2 - - - -
169D GLY 3.3 8.5 - - - -
170D ARG* 3.7 6.1 - - - -
182D VAL 3.1 6.5 + - - -
183D ALA* 3.7 0.3 - - - -
184D ILE* 2.9 28.4 + - - +
213D TYR* 1.3 77.1 - - - +
215D ILE* 1.3 64.3 + - - -
216D TYR* 3.5 9.7 - - - -
245D TYR* 3.7 18.7 + - - -
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Residues in contact with ILE 215 (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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168D GLY 3.8 2.2 + - - +
169D GLY 3.1 15.4 + - - +
184D ILE* 3.6 24.9 - - + +
186D ILE* 4.2 12.1 - - + -
198D TRP* 3.4 42.6 - - + -
199D LEU* 4.4 2.9 - - + -
203D HIS* 3.9 21.5 - - + +
206D LEU* 3.8 10.5 - - + -
213D TYR* 3.8 5.8 - - + -
214D GLY* 1.3 72.6 - - - -
216D TYR* 1.3 64.3 + - - +
217D VAL* 4.8 2.5 - - + -
390D LEU 4.1 0.7 - - - +
391D TYR* 3.9 22.7 - - + -
392D THR* 3.0 30.4 + - - -
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Residues in contact with TYR 216 (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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168D GLY 5.8 0.4 - - - -
170D ARG* 4.6 4.0 - - - -
183D ALA* 4.2 4.9 - - + -
184D ILE 2.8 16.5 + - - +
185D ILE* 3.4 8.8 - - + +
186D ILE* 2.7 34.6 + - - +
214D GLY* 3.5 20.2 - - - -
215D ILE* 1.3 77.5 - - - +
217D VAL* 1.3 58.3 + - - +
218D ILE* 3.8 14.2 + - + -
235D GLY* 5.4 0.2 - - - -
238D GLU 4.8 0.2 - - - -
239D ALA* 3.8 32.1 - - + -
242D ASP* 3.1 32.4 + - - +
245D TYR* 2.6 40.2 + + - -
387D ARG* 4.8 0.6 + - - -
392D THR* 3.5 28.5 - - + +
394D ILE* 4.2 15.0 - - + -
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Residues in contact with VAL 217 (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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186D ILE* 3.5 15.9 - - + +
188D PHE* 3.4 46.4 - - + -
195D LEU* 3.9 26.5 - - + -
215D ILE* 4.8 1.1 - - + -
216D TYR* 1.3 75.8 - - - +
218D ILE* 1.3 61.1 + - - +
219D ASN 3.6 0.5 + - - -
391D TYR* 3.8 26.2 - - + -
392D THR 2.8 11.9 + - - +
393D LYS* 3.4 13.5 - - + +
394D ILE* 2.9 27.0 + - - +
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Residues in contact with ILE 218 (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 15.0 - - + -
186D ILE 2.9 9.5 + - - +
187D PRO* 3.8 0.6 - - + -
188D PHE* 2.9 28.3 + - - +
216D TYR* 4.2 11.4 - - + +
217D VAL* 1.3 76.4 - - - +
219D ASN* 1.3 59.9 + - - +
220D GLN 3.7 0.7 + - - -
231D LEU* 3.5 41.7 - - + +
234D VAL* 3.7 21.5 - - + -
235D GLY* 3.5 24.5 - - - -
394D ILE* 3.6 27.4 - - + +
396D VAL* 4.0 15.3 - - + -
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Residues in contact with ASN 219 (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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188D PHE* 3.3 30.2 - - + +
189D ARG* 3.8 7.8 - - - +
190D ASN 4.7 0.9 + - - -
217D VAL 3.6 1.2 + - - -
218D ILE* 1.3 70.6 - - - +
220D GLN* 1.3 69.6 + - - +
221D ALA* 3.3 1.2 + - - +
231D LEU* 4.5 0.4 - - - -
393D LYS* 3.9 26.0 - - + +
394D ILE 2.8 11.9 + - - +
395D THR* 2.9 38.6 + - - +
396D VAL* 2.9 31.5 + - - +
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Residues in contact with GLN 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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188D PHE 3.0 14.9 + - - +
189D ARG* 3.5 40.0 - - - +
218D ILE 3.7 1.6 + - - -
219D ASN* 1.3 76.3 + - - +
221D ALA* 1.3 71.6 + - - +
222D GLY 3.9 0.3 + - - -
224D SER* 3.7 10.9 + - - -
225D MET 3.0 24.9 + - - -
226D PHE* 3.1 17.0 - - + +
227D ASN 2.9 22.1 + - - +
231D LEU* 3.7 17.5 - - + +
312D TRP* 4.5 0.8 - - - -
396D VAL 4.0 2.2 - - - -
398D ILE* 3.6 31.0 - - + +
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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