Contacts of the helix formed by residues 200 - 210 (chain B) in PDB entry 1PBW
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 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B ASN* 5.7 3.0 + - - +
196B PRO* 4.6 10.5 - - + +
198B ILE 3.7 0.4 + - - -
199B PRO* 1.3 72.3 - - - +
201B ALA* 1.3 55.7 + - - +
203B TYR* 3.2 10.1 + - - +
204B SER* 2.9 34.9 + - - +
273B PHE 6.1 0.7 - - - -
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Residues in contact with ALA 201 (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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199B PRO* 3.2 2.9 + - + +
200B ALA* 1.3 77.8 - - - +
202B VAL* 1.3 62.5 + - + +
204B SER* 3.7 6.0 - - - -
205B GLU* 3.5 26.0 + - - +
232B ILE* 4.6 19.1 - - + -
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Residues in contact with VAL 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 ILE* 3.7 20.9 - - + -
199B PRO* 3.0 23.4 + - + +
201B ALA* 1.3 75.5 - - + +
203B TYR* 1.3 66.7 + - - +
205B GLU* 3.4 3.2 + - - +
206B MET* 3.0 28.3 + - + +
223B LEU* 3.8 19.7 - - + -
226B LEU* 3.9 44.8 - - + +
227B ILE* 4.2 9.9 - - + +
232B ILE* 4.5 14.8 - - + -
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Residues in contact with TYR 203 (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 ILE* 4.6 1.5 - - - +
199B PRO 3.1 12.1 + - - +
200B ALA* 3.2 13.0 + - - +
202B VAL* 1.3 75.0 - - - +
204B SER* 1.3 68.8 + - - +
206B MET* 3.2 9.8 + - - +
207B ILE* 3.0 34.7 + - + +
273B PHE* 3.9 32.5 - + + +
274B ARG 5.9 1.3 - - - -
275B PHE* 4.0 21.7 - + + +
279B SER* 4.0 1.6 + - - -
281B ASP* 2.9 38.8 + - - +
283B THR* 3.6 11.3 - - - +
286B LEU* 3.2 33.4 - - + -
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Residues in contact with SER 204 (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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200B ALA 2.9 17.4 + - - -
201B ALA* 3.7 8.3 - - - -
203B TYR* 1.3 82.5 - - - +
205B GLU* 1.3 61.0 + - - +
207B ILE* 3.4 7.6 + - - +
208B SER* 3.0 31.7 + - - -
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Residues in contact with GLU 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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201B ALA 3.5 13.6 + - - +
202B VAL 3.4 2.8 + - - +
204B SER* 1.3 76.6 - - - +
206B MET* 1.3 63.0 + - - +
208B SER* 4.4 5.7 - - - +
209B LEU* 2.8 57.6 + - + +
226B LEU* 3.5 34.1 - - + +
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Residues in contact with MET 206 (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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202B VAL* 3.0 28.1 + - + +
203B TYR* 3.3 9.9 - - - +
205B GLU* 1.3 82.2 - - - +
207B ILE* 1.3 59.4 + - - +
210B ALA 3.2 13.7 + - - -
219B TYR* 2.6 59.6 + - + +
222B LEU* 4.1 15.9 - - - -
223B LEU* 3.7 43.1 - - + -
226B LEU* 4.1 6.3 - - + -
273B PHE* 5.0 3.8 - - + -
286B LEU* 3.9 25.8 - - + -
289B VAL* 4.7 7.2 - - + -
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Residues in contact with ILE 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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203B TYR* 3.0 28.8 + - + +
204B SER* 3.8 7.0 - - - +
206B MET* 1.3 76.2 - - - +
208B SER* 1.3 68.3 + - - +
210B ALA* 3.1 21.0 - - + +
211B PRO* 3.8 2.6 - - - +
219B TYR* 4.1 9.4 - - - +
281B ASP* 4.0 34.8 - - + +
282B ASN* 3.9 24.0 - - + +
286B LEU* 3.9 24.0 - - + -
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Residues in contact with SER 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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204B SER 3.0 17.8 + - - -
205B GLU* 4.0 7.6 - - - -
207B ILE* 1.3 81.0 - - - +
209B LEU* 1.3 66.6 + - - +
211B PRO* 3.1 20.1 - - - +
212B GLU* 5.7 0.3 - - - +
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Residues in contact with LEU 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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205B GLU* 2.8 49.7 + - + +
206B MET 3.9 1.3 - - - -
208B SER* 1.3 80.5 - - - +
210B ALA* 1.3 63.9 + - - +
211B PRO* 3.3 1.1 - - - -
212B GLU* 3.2 25.6 + - + +
213B VAL* 3.0 27.0 + - + +
222B LEU* 3.5 41.5 - - + -
225B LYS* 5.7 2.0 - - - +
226B LEU* 5.0 1.6 - - + -
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Residues in contact with ALA 210 (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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206B MET 3.2 11.6 + - - +
207B ILE* 3.1 20.4 - - + +
208B SER 3.1 0.6 - - - -
209B LEU* 1.3 77.8 - - - +
211B PRO* 1.3 68.0 - - + +
213B VAL* 3.1 19.1 + - - +
219B TYR* 3.8 19.3 - - + +
282B ASN* 6.3 2.7 - - + -
285B ASN* 5.5 8.3 - - - +
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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