Contacts of the strand formed by residues 212 - 220 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 2.8 28.6 + - - -
171B TYR 3.3 3.6 - - - -
172B THR* 2.9 31.5 + - + +
173B PRO* 4.1 2.0 - - - -
178B SER* 3.9 15.3 + - - +
180B HIS 3.1 14.3 + - - +
181B LYS* 3.3 11.9 - - + +
182B VAL 2.8 23.4 + - - +
211B LEU* 1.3 70.7 - - - +
213B TYR* 1.3 57.4 + - - +
243B TYR* 2.4 31.6 + - - -
245B TYR* 4.7 1.6 - - - -
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Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B VAL* 4.1 0.7 - - - +
169B GLY 4.1 4.7 - - - -
170B ARG* 2.8 23.9 + - - -
171B TYR* 2.9 59.1 + + + +
182B VAL* 3.0 22.4 - - + +
184B ILE* 4.7 6.5 - - + -
203B HIS* 3.1 47.1 + + - -
206B LEU* 3.3 43.7 - - + -
207B GLN* 3.5 10.1 + - - +
211B LEU* 3.6 21.5 - - + -
212B ASP* 1.3 74.7 - - - +
214B GLY* 1.3 61.0 + - - +
215B ILE* 3.9 17.7 - - + -
245B TYR* 4.4 0.7 - - - -
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Residues in contact with GLY 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLY 5.3 0.4 - - - -
169B GLY 3.2 9.2 - - - -
170B ARG* 3.6 14.6 - - - -
182B VAL 3.0 5.9 + - - -
183B ALA* 3.7 0.3 - - - -
184B ILE* 3.0 28.1 + - - +
213B TYR* 1.3 76.8 - - - +
215B ILE* 1.3 64.0 + - - -
216B TYR* 3.5 9.5 - - - -
245B TYR* 3.7 10.0 - - - -
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B GLY 3.5 4.3 + - - +
169B GLY 3.0 14.9 + - - +
184B ILE* 3.7 25.6 - - + +
186B ILE* 4.4 10.3 - - + -
198B TRP* 3.5 41.7 - - + -
199B LEU* 4.4 3.1 - - + -
203B HIS* 3.9 20.6 - - + +
206B LEU* 3.8 10.8 - - + -
213B TYR* 3.9 3.4 - - + -
214B GLY* 1.3 72.5 - - - -
216B TYR* 1.3 66.5 + - - +
217B VAL* 4.7 2.2 - - + -
390B LEU 4.0 2.5 - - - +
391B TYR* 3.5 24.2 - - + -
392B THR* 2.8 29.8 + - - -
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Residues in contact with TYR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B GLY 5.9 0.4 - - - -
170B ARG* 4.8 3.8 - - + +
183B ALA* 4.2 5.6 - - + -
184B ILE 2.9 17.3 + - - +
185B ILE* 3.5 8.1 - - + -
186B ILE* 2.9 27.4 + - - +
214B GLY* 3.5 20.0 - - - -
215B ILE* 1.3 74.9 - - - +
217B VAL* 1.3 63.2 + - - +
218B ILE* 3.7 14.9 + - + +
235B GLY 5.4 0.4 - - - +
238B GLU 5.0 0.2 - - - -
239B ALA* 3.8 26.7 - - + -
242B ASP* 3.0 34.0 + - - +
245B TYR* 2.5 46.3 + + - -
387B ARG* 4.3 6.6 + - - -
392B THR* 3.4 17.7 - - + -
394B ILE* 4.2 18.2 - - + -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ILE* 3.6 17.7 - - + +
188B PHE* 3.4 46.4 - - + -
195B LEU* 3.8 25.8 - - + -
215B ILE* 4.7 2.9 - - + -
216B TYR* 1.3 73.8 - - - +
218B ILE* 1.3 60.5 + - - +
219B ASN 3.4 2.4 + - - -
391B TYR* 3.8 24.9 - - + -
392B THR 2.8 11.7 + - - +
393B LYS* 3.3 12.1 - - + +
394B ILE 2.9 24.3 + - - -
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ILE* 3.7 20.6 - - + -
186B ILE 3.0 9.4 + - - +
187B PRO* 3.9 1.2 - - + +
188B PHE* 2.9 28.3 + - - +
216B TYR* 4.3 11.4 - - + +
217B VAL* 1.3 73.9 - - - +
219B ASN* 1.3 60.1 + - - +
220B GLN 3.8 0.5 + - - -
231B LEU* 3.5 50.9 - - + +
234B VAL* 3.9 18.2 - - + -
235B GLY* 3.6 18.6 - - - +
394B ILE* 3.6 28.3 - - + +
396B VAL* 4.0 7.9 - - + -
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PHE* 3.2 27.2 - - + +
189B ARG* 3.7 7.1 - - - +
190B ASN 4.5 0.9 + - - -
217B VAL 3.4 1.2 + - - -
218B ILE* 1.3 72.4 - - - +
220B GLN* 1.3 68.7 + - - +
221B ALA* 3.5 1.4 + - - +
231B LEU* 4.5 1.3 - - - -
393B LYS* 3.4 35.8 - - + +
394B ILE 2.9 9.9 + - - +
395B THR* 3.0 34.6 + - - +
396B VAL* 2.9 31.2 + - - +
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Residues in contact with GLN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PHE 2.9 12.7 + - - +
189B ARG* 3.2 46.0 - - - +
218B ILE 3.8 1.0 + - - -
219B ASN* 1.3 74.6 + - - +
221B ALA* 1.3 70.9 + - - +
222B GLY 3.9 0.5 + - - +
224B SER* 3.6 8.5 + - - -
225B MET 3.2 22.2 + - - -
226B PHE* 3.6 9.4 - - + +
227B ASN 2.9 23.5 + - - -
231B LEU* 3.5 23.9 - - + +
312B TRP* 4.7 0.2 - - - -
396B VAL 3.8 3.1 - - - -
398B ILE* 3.1 35.0 - - + +
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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