Contacts of the helix formed by residues 221 - 232 (chain B) in PDB entry 1PT6
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 MET 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B TYR* 3.3 10.4 - - + -
187B GLY 2.9 23.3 + - - +
188B GLU* 3.6 19.1 - - - +
189B ASN 5.4 0.4 - - - +
219B GLN* 4.1 31.0 - - + +
220B THR* 1.3 70.0 - - - +
222B THR* 1.3 59.1 + - - +
223B ALA 3.3 2.7 - - - -
224B LEU* 3.1 19.5 + - + +
225B GLY 3.0 22.5 + - - -
257B HIS* 4.3 16.4 - - + +
258B ASP* 3.4 30.3 - - - +
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Residues in contact with THR 222 (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 TYR* 2.8 31.8 + - + +
220B THR* 3.2 18.8 + - - +
221B MET* 1.3 71.1 - - - +
223B ALA* 1.3 64.6 + - - +
225B GLY* 3.3 0.7 + - - -
226B THR* 2.9 39.0 + - - +
250B ILE* 4.3 7.6 - - + -
252B THR* 3.9 8.0 + - + +
254B GLY 4.4 1.9 + - - -
256B SER* 3.6 15.9 - - - -
258B ASP* 3.4 1.8 + - - -
262B LEU* 4.6 3.6 - - + -
298B GLU* 5.2 1.5 + - - -
299B ILE* 5.5 1.8 - - + +
302B ILE* 3.9 28.9 - - + -
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Residues in contact with ALA 223 (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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222B THR* 1.3 76.9 - - - +
224B LEU* 1.3 57.7 - - - +
226B THR* 3.8 2.9 - - - -
227B ASP* 2.8 34.0 + - - +
258B ASP* 3.0 35.5 + - - +
261B ARG* 3.6 22.7 - - + +
262B LEU* 3.9 22.4 - - + +
265B VAL* 3.9 5.9 - - + +
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Residues in contact with LEU 224 (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 GLU 4.0 20.2 - - - +
189B ASN* 4.1 10.1 - - - +
190B VAL* 3.4 22.7 - - + +
221B MET* 3.1 16.6 + - + +
223B ALA* 1.3 76.2 - - - +
225B GLY* 1.3 54.2 + - - +
227B ASP* 4.5 1.1 - - + +
228B THR* 2.7 46.7 + - - +
231B LYS* 6.5 0.7 - - - -
258B ASP* 2.9 13.6 + - - +
261B ARG* 3.8 19.9 - - - +
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Residues in contact with GLY 225 (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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148B VAL* 3.7 11.4 - - - +
184B VAL* 4.2 3.5 - - - +
186B TYR* 3.9 30.3 - - - -
190B VAL* 4.0 8.0 - - - +
221B MET 3.0 10.7 + - - -
222B THR 3.8 2.2 - - - -
224B LEU* 1.3 76.5 - - - +
226B THR* 1.3 56.9 + - - +
228B THR* 3.5 2.1 + - - -
229B ALA* 3.0 27.5 + - - +
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 4.1 2.9 - - - +
222B THR* 2.9 30.7 + - - +
223B ALA* 3.8 3.4 - - - -
225B GLY* 1.3 73.0 - - - +
227B ASP* 1.3 65.6 + - - +
229B ALA* 3.2 4.5 + - - +
230B ARG* 3.0 19.6 + - - +
248B MET* 3.6 28.6 - - - +
250B ILE* 4.1 19.5 - - + +
262B LEU* 5.2 1.8 - - - +
265B VAL* 3.7 18.4 - - + -
266B ILE* 4.6 11.9 - - + -
269B CYS* 4.0 12.1 - - - -
276B ARG* 5.4 0.7 - - - -
302B ILE* 5.1 1.8 - - + +
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Residues in contact with ASP 227 (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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223B ALA 2.8 20.2 + - - +
224B LEU* 4.0 2.6 - - + +
226B THR* 1.3 77.4 - - - +
228B THR* 1.3 62.2 + - - +
230B ARG* 2.8 35.9 + - - +
231B LYS* 3.0 51.7 + - - +
261B ARG* 3.8 18.8 + - - +
265B VAL* 3.7 29.0 - - + +
268B ASP* 4.7 1.4 - - - +
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Residues in contact with THR 228 (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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184B VAL* 4.9 1.6 - - + -
190B VAL* 3.8 25.8 - - + +
192B HIS* 3.7 13.2 - - + +
224B LEU* 2.7 35.7 + - - +
225B GLY 3.7 4.0 - - - -
227B ASP* 1.3 74.0 - - - +
229B ALA* 1.3 66.2 + - - +
231B LYS* 4.5 11.2 - - - +
232B GLU* 2.9 53.9 + - - +
233B ALA 3.3 1.2 + - - -
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Residues in contact with ALA 229 (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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146B VAL* 3.9 14.1 - - + -
148B VAL* 3.6 31.2 - - + -
184B VAL* 4.5 5.5 - - + +
225B GLY 3.0 9.4 + - - +
226B THR 3.2 9.2 + - - +
228B THR* 1.3 75.3 - - - +
230B ARG* 1.3 58.9 + - - +
233B ALA* 3.1 12.5 + - - +
234B PHE* 2.9 33.4 + - + -
248B MET* 3.8 10.3 - - + -
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Residues in contact with ARG 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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226B THR 3.0 12.7 + - - +
227B ASP* 2.8 36.8 + - - +
228B THR 3.2 0.2 - - - -
229B ALA* 1.3 79.6 - - - +
231B LYS* 1.3 87.7 + - - +
232B GLU 3.7 0.2 + - - -
234B PHE* 3.5 21.4 - - - +
235B THR* 4.6 0.2 - - - +
248B MET* 4.2 0.8 - - - +
265B VAL 4.8 0.2 + - - -
268B ASP* 3.5 48.9 + - - +
269B CYS* 3.8 10.1 - - - +
272B GLU* 3.0 45.7 + - - +
274B ILE* 3.8 26.9 - - + -
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Residues in contact with LYS 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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224B LEU* 6.5 0.4 - - - -
227B ASP* 3.0 36.3 + - - +
228B THR* 4.5 7.0 - - - +
230B ARG* 1.3 107.9 - - - +
232B GLU* 1.3 77.0 + - + +
235B THR* 3.1 17.4 - - - +
261B ARG* 5.8 0.4 - - - +
272B GLU* 5.2 0.9 - - - -
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Residues in contact with GLU 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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192B HIS* 2.7 36.2 + - + +
228B THR* 2.9 25.2 + - + +
230B ARG 3.4 0.2 - - - -
231B LYS* 1.3 99.0 - - + +
233B ALA* 1.3 61.3 + - - +
234B PHE 3.4 0.9 - - - -
235B THR* 2.6 26.5 + - - -
238B ARG* 3.3 24.5 + - - +
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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