Contacts of the helix formed by residues 225 - 232 (chain B) in PDB entry 5H1C
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 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ALA* 1.3 86.6 - - + +
226B ALA* 1.3 66.5 + - - +
227B LEU 3.3 2.7 - - - -
228B TYR* 3.0 26.6 + - - +
229B ARG* 3.5 3.8 + - - +
245B LEU* 5.3 6.5 - - + -
265B ILE* 5.3 2.9 - - + -
266B THR 4.1 2.4 + - - +
267B ASN* 4.0 18.0 - - + +
268B GLN* 3.8 23.0 + - - +
287B ILE* 3.5 26.0 - - + +
292B ILE* 3.7 30.1 - - + -
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Residues in contact with ALA 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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163B GLU* 4.0 10.1 - - + +
223B SER* 3.5 29.5 + - - +
224B ALA 3.5 1.0 - - - -
225B THR* 1.3 80.3 + - - +
227B LEU* 1.3 66.9 + - + +
228B TYR 3.3 0.3 + - - -
229B ARG* 3.4 18.4 + - - +
230B THR* 3.7 14.6 + - - +
268B GLN* 3.5 17.0 - - - +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B THR* 4.3 26.5 - - + +
194B ALA* 4.7 0.7 - - + -
195B PHE* 3.2 34.3 - - - +
196B ASN 3.6 15.9 - - - +
197B THR* 3.6 15.9 - - + -
200B GLN* 3.3 32.5 - - + +
223B SER 4.6 0.9 + - - +
225B THR 3.3 0.8 - - - -
226B ALA* 1.3 79.7 - - + +
228B TYR* 1.3 62.6 + - + +
230B THR* 3.1 7.8 + - - -
231B ASP* 3.0 33.2 + - - +
250C ARG* 3.5 14.8 - - - +
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Residues in contact with TYR 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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197B THR* 4.2 13.6 + - + -
200B GLN* 3.6 17.9 + - - -
224B ALA 3.0 29.8 - - - -
225B THR* 3.0 12.7 + - - +
227B LEU* 1.3 77.5 - - + +
229B ARG* 1.3 64.5 + - - +
231B ASP 4.1 0.2 - - - -
232B TYR* 3.3 36.4 + + - +
241B ARG* 3.3 42.7 - - + +
244B HIS* 2.7 48.9 + + + -
245B LEU* 3.4 32.9 - - + +
248B PHE* 4.3 8.7 - + - +
287B ILE* 5.5 0.2 - - + -
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Residues in contact with ARG 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 THR 3.5 6.4 + - - +
226B ALA* 3.4 13.6 + - - +
227B LEU 3.2 0.8 - - - -
228B TYR* 1.3 82.9 - - - +
230B THR* 1.3 69.1 + - + +
231B ASP 3.2 0.3 + - - -
232B TYR 3.5 15.3 + - - +
233B SER* 4.1 4.2 + - - -
241B ARG* 5.3 1.8 - - - +
268B GLN* 3.9 12.0 - - - +
269B VAL 2.4 44.1 + - - +
270B VAL* 3.3 2.6 - - - +
287B ILE* 3.3 33.5 - - + +
246C ALA* 5.1 7.3 - - + +
290C ASN* 4.7 0.8 - - - +
291C ILE* 3.2 41.2 - - - +
294C HIS* 4.1 10.3 - - - +
6D T 3.7 29.1 + - - +
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Residues in contact with THR 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 ALA 3.7 9.1 + - - +
227B LEU 3.1 9.0 + - - -
229B ARG* 1.3 81.8 - - + +
231B ASP* 1.3 61.9 + - - +
233B SER* 5.0 1.9 + - - -
246C ALA* 3.4 39.3 - - + +
247C ARG* 4.1 21.3 + - - +
249C LEU* 6.3 0.4 - - + -
250C ARG* 3.0 49.6 + - + +
291C ILE* 6.1 0.9 - - + -
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Residues in contact with ASP 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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197B THR* 3.1 35.4 + - + +
227B LEU 3.0 15.4 + - - +
230B THR* 1.3 79.8 - - - +
232B TYR* 1.3 62.1 + - + +
233B SER* 3.5 4.9 + - - -
237B GLU* 5.2 0.5 - - - +
56C PRO* 4.3 13.8 - - - +
58C LYS* 2.6 42.6 + - - +
247C ARG* 5.3 3.5 + - - -
250C ARG* 3.0 42.1 + - - -
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Residues in contact with TYR 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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197B THR* 3.9 20.7 + - + -
198B ASP* 4.7 3.3 + - - -
228B TYR* 3.3 41.5 + + - +
229B ARG* 3.6 8.9 - - - +
231B ASP* 1.3 76.8 - - + +
233B SER* 1.3 58.2 + - - +
234B GLY* 2.8 9.4 + - - -
237B GLU* 4.1 22.4 - - + -
238B LEU 4.6 0.6 + - - +
240B ALA* 5.1 13.2 + - + -
241B ARG* 3.5 50.1 + - + -
244B HIS* 4.5 15.3 - - + +
58C LYS* 3.4 35.1 - - + +
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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