Contacts of the strand formed by residues 201 - 209 (chain B) in PDB entry 3PEJ
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 ALA 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ALA 2.9 14.8 + - - +
198B PHE* 3.4 24.4 - - - +
200B VAL* 1.3 79.2 - - - +
202B ASP* 1.3 61.1 + - - +
203B LYS 3.7 8.7 - - - +
204B VAL* 4.1 7.0 - - + -
222B ALA* 5.0 0.7 - - - +
245B LEU* 3.7 28.3 - - + -
246B HIS 3.5 14.1 - - - +
247B LEU* 3.9 1.1 - - + +
248B LYS* 3.7 12.0 - - - -
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Residues in contact with ASP 202 (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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198B PHE* 4.1 2.9 - - - -
201B ALA* 1.3 71.5 - - - +
203B LYS* 1.3 59.5 + - + +
221B THR* 3.7 5.7 - - - +
222B ALA* 3.0 41.8 + - + +
246B HIS 3.0 9.4 + - - +
247B LEU 4.5 1.5 - - - +
248B LYS* 3.4 42.3 - - - +
249B GLU 4.7 1.7 + - - -
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PHE* 4.4 0.2 - - - -
201B ALA* 3.7 1.4 - - - +
202B ASP* 1.3 79.7 - - + +
204B VAL* 1.3 68.5 + - - +
205B ILE* 3.6 27.6 - - + +
219B GLU* 3.1 33.3 + - + +
220B SER 3.4 11.2 - - - +
221B THR* 5.1 9.4 - - + +
245B LEU 3.7 0.2 - - - -
246B HIS* 2.8 57.4 + - + +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 3.6 27.8 - - + -
197B ALA* 3.8 15.3 - - + -
198B PHE* 3.6 26.7 - - + -
201B ALA* 4.1 6.3 - - + -
203B LYS* 1.3 77.9 - - - +
205B ILE* 1.3 64.3 + - - +
206B VAL* 4.2 3.4 - - + -
218B TRP 3.5 3.1 - - - +
219B GLU* 3.5 1.9 - - - -
220B SER* 2.8 37.7 + - - -
243B ILE* 3.8 23.8 - - + -
244B SER 3.5 2.0 - - - -
245B LEU* 3.8 20.2 - - + -
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Residues in contact with ILE 205 (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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203B LYS* 3.6 13.7 - - + +
204B VAL* 1.3 71.0 - - - +
206B VAL* 1.3 64.6 + - - +
207B TYR* 3.5 34.6 - - + +
217B ILE* 3.7 24.5 - - + -
218B TRP 3.9 2.0 - - - +
219B GLU* 3.6 37.5 - - + +
229B TYR* 5.6 0.7 - - - +
244B SER* 2.8 41.9 + - - +
246B HIS* 3.4 30.7 - - + +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B MET* 4.3 10.8 - - + -
194B PHE* 3.8 35.4 - - + -
204B VAL* 4.2 1.8 - - + -
205B ILE* 1.3 74.3 - - - +
207B TYR* 1.3 64.8 + - - +
208B THR* 4.5 4.2 - - + +
216B TYR 3.9 0.5 - - - +
217B ILE* 3.3 5.7 - - - +
218B TRP* 2.7 65.3 + - + +
241B THR* 3.8 25.1 - - + -
242B ARG 3.3 3.1 - - - -
243B ILE* 3.8 17.3 - - + -
1001B BC2 5.1 1.3 - - + -
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Residues in contact with TYR 207 (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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205B ILE* 3.5 33.0 - - + +
206B VAL* 1.3 71.2 - - - +
208B THR* 1.3 59.6 + - - +
215B GLN* 4.4 7.0 - - - +
216B TYR 3.5 4.3 - - - -
217B ILE* 3.6 28.3 - - + -
231B ASP* 4.5 4.0 - - - -
233B ARG* 3.3 29.6 + - - -
237B LEU* 3.4 12.2 - - + +
241B THR* 3.3 3.6 - - - +
242B ARG* 2.7 71.4 + - + +
244B SER* 3.2 28.2 - - - -
246B HIS* 5.4 1.2 + - - -
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Residues in contact with THR 208 (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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152B GLY 3.6 0.2 - - - -
153B MET* 2.8 61.3 + - + +
158B LEU* 4.4 17.3 - - + -
206B VAL* 4.5 5.8 - - + +
207B TYR* 1.3 74.2 - - - +
209B LYS* 1.4 58.0 + - - +
214B GLU 4.1 1.2 - - - +
215B GLN* 3.3 6.4 - - - +
216B TYR* 2.8 46.8 + - + +
218B TRP* 5.9 0.2 - - + -
237B LEU* 3.9 1.5 - - - +
240B GLY 3.5 4.0 - - - -
241B THR* 3.2 17.6 + - - -
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Residues in contact with LYS 209 (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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151B ILE 3.9 0.5 - - - +
152B GLY* 3.6 5.6 - - - -
153B MET 4.6 0.2 - - - -
208B THR* 1.4 75.9 + - - +
210B ASN* 1.3 85.8 + - - +
211B ASN* 3.7 12.3 + - - +
213B ASP 3.1 14.8 + - - +
214B GLU* 4.4 4.7 - - - +
215B GLN* 3.4 40.4 - - - +
235B ALA* 3.8 22.0 - - + -
237B LEU* 4.1 9.4 - - + -
238B LYS 3.3 30.0 + - - +
239B ARG* 3.4 4.3 - - - -
240B GLY 2.9 33.4 + - - +
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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