Contacts of the helix formed by residues 221 - 233 (chain B) in PDB entry 3THY
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 THR 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B ILE 4.4 0.4 - - - +
220B TYR* 1.3 76.8 - - - +
222B PRO* 1.3 78.0 - - - +
223B LEU* 3.8 6.4 + - - +
224B GLU* 3.0 37.4 + - - +
225B LEU* 3.2 16.3 + - - +
269B HIS* 3.2 42.0 - - + +
270B ASN* 5.0 0.7 - - - +
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Residues in contact with PRO 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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220B TYR 3.8 2.0 - - - +
221B THR* 1.3 87.3 - - - +
223B LEU* 1.3 64.2 + - - +
225B LEU* 3.0 16.5 + - + +
226B GLN* 2.9 19.9 + - - +
316B LEU* 3.7 26.8 - - + +
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Residues in contact with LEU 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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221B THR* 3.3 6.8 + - - +
222B PRO* 1.3 80.1 - - - +
224B GLU* 1.3 58.7 + - + +
226B GLN* 2.9 14.9 + - + +
227B TYR* 2.8 28.6 + - + +
241B VAL* 4.8 7.9 - - + -
243B CYS* 3.9 22.7 - - + -
248B ARG* 3.9 24.9 - - - +
250B PHE* 4.0 18.2 - - + -
316B LEU* 3.5 14.7 - - + +
319B ARG* 3.4 37.7 - - - +
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Residues in contact with GLU 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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220B TYR* 3.6 9.1 - - + -
221B THR* 3.0 44.8 + - - +
223B LEU* 1.3 77.8 - - + +
225B LEU* 1.3 56.7 + - - +
227B TYR* 3.1 9.4 + - - +
228B ILE* 2.8 35.0 + - - +
250B PHE* 5.2 13.1 - - + -
268B ASP* 3.6 5.4 - - - +
269B HIS* 3.1 23.9 - - - +
270B ASN* 3.1 26.3 + - - +
271B PHE* 3.9 28.8 + - + +
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Residues in contact with LEU 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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217B LYS* 3.9 33.2 - - + +
218B SER* 5.9 0.4 - - - -
220B TYR* 3.8 28.3 - - + +
221B THR 3.2 15.0 + - - +
222B PRO* 3.0 11.9 + - + +
224B GLU* 1.3 72.9 - - - +
226B GLN* 1.3 66.9 + - - +
228B ILE* 3.8 12.8 - - + +
229B GLU* 3.1 24.8 + - - +
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Residues in contact with GLN 226 (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 PRO 2.9 9.9 + - - +
223B LEU* 2.9 17.1 + - + +
225B LEU* 1.3 78.1 - - - +
227B TYR* 1.3 61.2 + - - +
229B GLU* 3.7 12.2 - - - +
230B MET* 3.3 31.7 + - + +
316B LEU* 3.2 21.2 + - + +
317B PHE 3.0 23.3 + - - -
318B SER* 3.7 13.1 - - - +
319B ARG* 2.8 40.5 + - + +
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Residues in contact with TYR 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 LEU* 2.8 11.9 + - + +
224B GLU* 3.2 13.9 - - - +
226B GLN* 1.3 74.5 - - - +
228B ILE* 1.3 82.7 + - + +
230B MET* 2.8 11.7 + - - +
231B LYS* 2.8 53.7 + - + +
239B LEU* 4.3 16.4 - - + -
241B VAL* 4.3 14.4 - - + -
250B PHE* 3.4 55.8 + + + -
251B GLY* 5.0 1.4 - - - -
252B GLU 5.3 0.5 + - - -
253B ASP* 2.9 26.7 + - - -
271B PHE* 4.4 22.7 - + - -
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Residues in contact with ILE 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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220B TYR* 4.0 33.4 - - + -
224B GLU 2.8 24.4 + - - +
225B LEU* 3.8 16.6 - - + +
227B TYR* 1.3 78.2 - - + +
229B GLU* 1.3 65.5 + - - +
230B MET 3.1 1.0 + - - -
231B LYS* 3.2 12.0 + - - +
232B GLN* 3.2 37.5 + - + +
271B PHE* 4.2 24.0 - - + -
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Residues in contact with GLU 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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225B LEU 3.1 15.4 + - - +
226B GLN* 3.7 11.2 - - - +
227B TYR 3.1 0.2 + - - -
228B ILE* 1.3 81.7 - - - +
230B MET* 1.3 76.7 + - - +
232B GLN* 4.0 17.2 + - - +
233B GLN* 3.9 14.0 + - - +
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Residues in contact with MET 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 GLN* 3.3 27.5 + - + +
227B TYR* 2.8 9.0 + - + +
229B GLU* 1.3 91.9 - - - +
231B LYS* 1.3 59.3 + - - +
232B GLN 3.0 5.6 - - - -
233B GLN* 2.9 41.7 + - - +
234B HIS* 3.5 10.2 + - + +
239B LEU* 4.2 9.8 - - + +
241B VAL* 5.4 3.8 - - + -
298B VAL* 3.8 27.8 - - + -
319B ARG* 4.0 17.0 - - + +
320B LYS* 4.0 11.7 - - - -
321B LEU* 3.9 25.1 - - + -
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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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227B TYR* 2.8 50.1 + - + +
228B ILE* 3.2 4.7 + - - +
230B MET* 1.3 71.4 - - - +
232B GLN* 1.3 58.4 + - + +
234B HIS 3.4 13.7 - - - +
235B LYS* 3.0 45.7 + - + +
237B ALA 3.3 19.5 - - - -
239B LEU* 3.7 19.0 - - + +
252B GLU* 5.4 5.9 - - - +
253B ASP* 2.9 29.5 + - - +
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Residues in contact with GLN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ILE* 3.2 30.8 + - + +
229B GLU* 4.1 11.3 - - - +
230B MET 3.0 0.4 - - - -
231B LYS* 1.3 77.3 - - + +
233B GLN* 1.3 58.5 + - - +
234B HIS 2.9 7.4 + - - -
235B LYS* 2.9 50.2 + - + +
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Residues in contact with GLN 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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229B GLU* 3.9 17.2 + - - +
230B MET* 2.9 42.8 - - - +
232B GLN* 1.3 77.0 - - - +
234B HIS* 1.3 96.4 + - + +
236B ASP* 4.9 0.5 - - - +
321B LEU* 4.7 9.5 - - - +
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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