Contacts of the helix formed by residues 224 - 234 (chain B) in PDB entry 1TH1
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 HIS 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B GLU* 4.4 3.8 - - - -
185B ARG* 3.1 44.6 + - + -
186B HIS* 3.6 22.9 + + - -
189B MET* 3.5 35.4 - - + -
220B ASN 4.2 7.9 - - - -
221B LEU* 3.1 7.6 + - - +
223B HIS* 1.3 79.8 - - - +
225B ARG* 1.3 65.4 + - - +
227B GLY 3.3 0.7 + - - -
228B LEU* 3.1 25.5 + - - +
1516D ILE* 3.9 13.9 - - + +
1517D GLN 4.5 5.6 - - - -
1519D ASP* 3.0 28.9 + - - +
1522D LEU* 4.4 3.6 - - - -
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Residues in contact with ARG 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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224B HIS* 1.3 71.9 - - - +
226B GLU* 1.3 72.2 + - + +
228B LEU* 3.3 9.9 + - - +
229B LEU* 3.2 22.6 + - + +
266B GLN* 4.5 1.9 - - - +
1519D ASP* 3.3 16.4 + - - +
1521D GLU* 3.2 41.3 + - - +
1522D LEU* 3.9 28.2 - - + +
1525D MET* 5.4 3.2 - - - +
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Residues in contact with GLU 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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189B MET* 3.6 31.0 - - + +
190B ARG* 3.2 39.7 + - - -
224B HIS* 3.5 1.2 - - - +
225B ARG* 1.3 85.7 - - + +
227B GLY* 1.3 57.6 + - - +
229B LEU* 3.5 13.2 + - + +
230B ALA* 2.9 31.0 + - - +
1519D ASP* 5.7 1.4 - - - +
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Residues in contact with GLY 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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189B MET* 3.5 18.8 - - - +
221B LEU* 3.3 29.4 - - - +
224B HIS 3.3 3.8 + - - -
225B ARG 3.1 1.2 - - - -
226B GLU* 1.3 76.9 - - - +
228B LEU* 1.3 62.3 + - - +
230B ALA* 3.4 4.7 + - - +
231B ILE* 3.1 31.2 + - - +
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Residues in contact with LEU 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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221B LEU 3.9 0.2 + - - -
222B SER* 3.4 33.4 - - - +
224B HIS 3.1 19.3 + - - +
225B ARG* 3.3 8.7 + - - +
227B GLY* 1.3 74.1 - - - +
229B LEU* 1.3 63.5 + - - +
231B ILE* 3.5 3.1 + - - +
232B PHE* 3.1 24.3 + - - +
261B ASN 3.6 25.6 - - - +
262B LEU* 3.4 24.9 - - + +
265B HIS* 3.8 33.0 - - + +
266B GLN* 3.7 12.3 - - + +
1522D LEU* 4.0 15.0 - - + -
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Residues in contact with LEU 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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407A GLN* 6.3 1.6 - - - +
225B ARG* 3.2 15.6 + - + +
226B GLU* 3.8 12.3 - - + +
228B LEU* 1.3 79.2 - - - +
230B ALA* 1.3 53.3 + - - +
232B PHE* 3.3 6.5 + - + +
233B LYS* 2.7 70.4 + - + +
266B GLN* 3.4 27.1 + - - +
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Residues in contact with ALA 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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189B MET* 4.1 11.4 - - - +
192B PRO* 5.8 4.0 - - + -
195B VAL* 3.5 28.1 - - + +
221B LEU* 6.0 0.7 - - + -
226B GLU 2.9 19.6 + - - +
227B GLY* 3.7 6.1 - - - +
228B LEU 3.3 0.2 - - - -
229B LEU* 1.3 75.1 - - - +
231B ILE* 1.3 57.6 + - - +
233B LYS* 4.0 10.1 - - - +
234B SER* 2.6 37.0 + - - -
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Residues in contact with ILE 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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195B VAL* 4.2 5.8 - - + -
199B VAL* 5.1 0.7 - - - -
218B LEU* 3.3 50.7 - - + +
221B LEU* 4.2 5.6 - - + -
222B SER* 4.1 13.2 - - - +
227B GLY 3.1 20.2 + - - +
228B LEU* 3.8 7.9 - - + +
229B LEU 3.4 0.2 - - - -
230B ALA* 1.3 74.4 - - - +
232B PHE* 1.3 59.8 + - - +
234B SER* 3.4 9.5 + - - -
236B GLY* 2.8 47.8 + - - -
240B LEU* 4.1 10.8 - - + -
258B THR* 4.1 11.7 - - + -
262B LEU* 4.1 20.9 - - + -
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Residues in contact with PHE 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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399A GLU* 4.0 32.0 - - + +
400A GLY* 4.3 7.9 + - - -
403A GLY* 5.2 4.9 - - - -
437A MET* 3.4 28.7 - - + -
441A VAL* 4.3 10.1 - - + -
228B LEU 3.1 17.8 + - - +
229B LEU* 3.5 9.0 - - + +
231B ILE* 1.3 78.3 - - - +
233B LYS* 1.3 69.6 + - + +
234B SER 3.3 0.9 + - - -
235B GLY* 3.3 12.8 + - - -
236B GLY 4.3 0.6 + - - +
237B ILE* 3.8 23.2 + - + -
262B LEU* 4.5 5.1 - - + +
266B GLN* 4.1 27.4 - - + -
267B GLU 4.0 13.7 - - - -
268B GLY* 3.9 20.2 - - - -
269B ALA 4.1 1.6 - - - -
272B ALA* 4.3 6.3 - - + -
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Residues in contact with LYS 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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367A GLY 5.9 1.5 + - - +
368A LEU* 5.5 4.7 - - - +
371A THR* 3.5 28.7 + - - +
400A GLY* 3.4 30.3 + - - +
401A LEU 4.8 0.5 + - - -
403A GLY* 5.9 1.3 - - - -
404A THR* 3.2 28.6 + - - +
407A GLN* 6.0 1.4 - - - +
192B PRO* 5.1 15.8 - - + +
229B LEU* 2.7 54.2 + - + +
230B ALA* 4.1 7.9 - - - +
231B ILE 3.5 0.2 - - - -
232B PHE* 1.3 76.5 - - + +
234B SER* 1.3 57.0 + - - +
235B GLY 3.3 3.0 + - - -
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Residues in contact with SER 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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368A LEU* 5.2 4.3 - - - -
192B PRO* 4.7 3.4 - - - -
195B VAL* 3.3 16.5 - - - +
196B SER* 3.7 36.8 - - - +
199B VAL* 3.4 19.8 - - - +
230B ALA 2.6 22.4 + - - -
231B ILE 3.4 4.9 + - - -
232B PHE 3.2 0.6 - - - -
233B LYS* 1.3 77.2 - - - +
235B GLY* 1.3 61.2 + - - +
236B GLY 3.3 0.4 - - - -
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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