Contacts of the strand formed by residues 229 - 236 (chain B) in PDB entry 2PWP
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 CYS 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B SER* 3.3 27.2 + - - -
194B LEU* 4.5 7.0 - - - -
195B TRP* 3.8 23.8 - - - -
219B ASN* 3.5 24.5 - - - +
220B ILE 3.2 16.4 - - - +
221B SER* 4.5 1.8 - - - -
222B ILE* 3.6 7.2 + - - +
225B TYR* 3.9 5.0 + - - +
226B PRO 3.5 12.9 + - - +
227B CYS 3.3 4.0 - - - -
228B GLY* 1.3 80.9 - - - +
230B ILE* 1.3 65.8 + - - +
221C SER* 4.3 7.4 - - - +
228C GLY 6.1 0.4 - - - +
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Residues in contact with ILE 230 (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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63B TYR* 4.1 20.2 - - + -
190B GLN* 3.4 35.9 - - + +
191B CYS 3.1 20.6 - - - +
192B GLU* 3.9 8.7 - - - +
193B SER* 4.5 1.3 - - - +
219B ASN* 3.9 4.7 - - - -
220B ILE* 3.0 39.2 + - + +
222B ILE* 4.1 7.9 - - + -
225B TYR* 3.8 35.7 - - + -
229B CYS* 1.3 78.2 - - - +
231B GLY* 1.3 60.9 + - - +
401B SPD 4.2 13.9 - - + +
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Residues in contact with GLY 231 (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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63B TYR* 5.7 0.2 - - - -
67B MET* 5.0 1.0 - - - +
190B GLN* 3.8 4.9 - - - +
191B CYS* 2.9 25.3 + - - +
192B GLU 2.9 14.0 + - - -
217B TYR* 3.3 21.1 + - - -
218B ALA 3.1 11.4 - - - -
219B ASN* 4.5 0.7 - - - -
230B ILE* 1.3 82.5 - - - +
232B ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 232 (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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66B MET* 4.1 25.6 - - + +
67B MET* 3.9 15.3 - - - -
70B VAL* 4.9 8.5 - - + -
188B VAL* 3.6 24.7 - - + -
189B ALA 3.5 5.4 - - - +
217B TYR* 3.4 10.0 - - - -
218B ALA* 2.8 45.7 + - + +
220B ILE* 3.6 36.6 - - + -
231B GLY* 1.3 77.9 - - - +
233B LEU* 1.3 61.6 + - - +
234B CYS* 3.5 22.4 + - - -
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Residues in contact with LEU 233 (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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174B TYR* 3.7 32.1 - - + +
187B CYS 3.7 1.7 - - - +
188B VAL* 3.1 5.5 - - - -
189B ALA* 2.9 40.5 + - + +
191B CYS* 3.9 17.9 - - + +
204B MET* 4.0 30.1 - - + +
205B ILE* 3.8 23.1 - - + +
208B ALA* 4.5 2.0 - - + -
215B VAL* 3.7 26.2 - - + -
216B GLU 3.8 5.6 - - - +
217B TYR* 4.6 3.4 - - + -
232B ILE* 1.3 69.6 - - - +
234B CYS* 1.3 61.8 + - - +
235B CYS* 4.1 12.0 - - - -
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Residues in contact with CYS 234 (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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70B VAL* 4.6 4.3 - - - -
187B CYS 3.7 3.4 - - - -
188B VAL* 4.1 8.3 - - - -
214B LYS 3.7 1.6 - - - +
215B VAL* 3.4 5.5 - - - +
216B GLU* 2.9 46.7 + - + +
218B ALA* 4.7 0.7 - - - -
232B ILE* 3.5 33.4 - - - -
233B LEU* 1.3 71.6 - - - +
235B CYS* 1.3 61.2 + - - +
242B LEU* 3.4 23.1 - - + -
269B PHE* 3.7 30.3 - - + -
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Residues in contact with CYS 235 (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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174B TYR* 4.3 14.6 - - - -
185B GLY 4.3 0.5 - - - +
186B TYR* 3.4 8.1 - - - +
187B CYS* 2.7 41.8 + - + +
189B ALA* 6.2 0.4 - - - -
208B ALA* 3.9 26.5 - - - -
212B PHE* 3.6 31.9 - - + -
214B LYS 3.7 4.0 - - - -
215B VAL* 4.9 2.0 - - - -
233B LEU* 4.1 17.7 - - - -
234B CYS* 1.3 75.2 - - - +
236B SER* 1.3 63.6 + - - +
242B LEU* 3.8 1.5 - - - +
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Residues in contact with SER 236 (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 GLY 4.4 0.4 - - - -
186B TYR* 3.2 33.0 - - - -
212B PHE* 3.5 7.3 - - - +
213B LYS 3.1 6.8 + - - -
214B LYS* 2.9 35.4 + - - +
216B GLU* 4.6 1.0 + - - -
234B CYS 5.0 0.2 + - - -
235B CYS* 1.3 76.1 - - - +
237B LYS* 1.3 60.7 + - - +
238B THR* 3.3 11.4 - - - -
241B GLY* 3.4 27.0 - - - -
242B LEU* 3.5 8.1 - - - +
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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