Contacts of the helix formed by residues 226 - 236 (chain B) in PDB entry 5H8N
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 SER 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B GLN* 3.1 6.7 + - - +
146B GLY 2.7 36.8 + - - -
148B THR* 3.8 17.9 - - - -
224B TRP 3.7 1.0 + - - -
225B ASP* 1.4 69.1 - - - +
227B ALA* 1.4 61.2 + - - +
229B LEU 4.5 0.2 - - - +
230B GLU* 2.9 57.5 + - - +
245B LEU* 3.3 18.0 - - - +
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Residues in contact with ALA 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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16B PRO* 4.3 4.7 - - - +
17B PHE* 3.5 27.7 - - + -
143B LYS* 4.5 14.6 - - - +
145B GLN* 2.8 33.2 + - + +
226B SER* 1.4 74.2 + - - +
228B VAL* 1.4 59.0 + - - +
230B GLU* 4.9 2.0 - - - +
231B PHE* 3.5 19.4 + - - +
251B PHE* 4.2 3.6 - - + -
286B VAL* 4.3 13.2 - - + +
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Residues in contact with VAL 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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14B GLN* 3.7 25.4 - - + +
15B GLU 3.7 20.9 - - - +
16B PRO* 4.6 0.4 - - - -
17B PHE* 3.7 23.1 - - + -
125B PRO* 5.6 0.7 - - + -
207B ALA* 5.3 0.4 - - + -
211B ILE* 4.2 20.6 - - + -
224B TRP* 3.9 20.4 - - + +
225B ASP* 3.3 17.9 + - + +
226B SER 3.2 0.4 - - - -
227B ALA* 1.4 75.1 - - - +
229B LEU* 1.4 55.0 + - + +
230B GLU 3.5 0.2 - - - -
231B PHE* 3.2 5.9 + - - +
232B GLU* 2.9 39.5 + - + +
251B PHE* 5.6 1.3 - - + -
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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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148B THR* 3.7 37.0 - - + +
150B LEU* 3.8 33.2 - - + +
211B ILE* 4.5 8.5 - - + -
222B PHE* 3.8 38.6 - - + +
224B TRP* 3.7 24.5 - - + +
225B ASP 3.1 13.4 + - - +
228B VAL* 1.4 72.1 - - - +
230B GLU* 1.3 60.4 + - - +
232B GLU* 3.4 4.1 + - + +
233B ALA* 2.9 31.0 + - - +
241B THR* 3.7 9.8 - - + +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR* 4.7 3.6 + - - +
226B SER* 2.9 41.6 + - - +
227B ALA* 4.9 2.5 - - - +
229B LEU* 1.3 75.6 - - - +
231B PHE* 1.4 55.7 + - - +
233B ALA* 3.5 4.1 + - - +
234B SER* 3.0 29.9 + - - -
241B THR* 4.4 18.8 + - + +
244B GLU* 5.9 1.4 - - - -
245B LEU* 4.3 7.3 - - - +
286B VAL* 6.5 1.1 - - + -
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Residues in contact with PHE 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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15B GLU* 4.4 13.9 - - + -
16B PRO* 3.6 33.4 - - + -
19B TYR* 3.4 22.4 - + - -
227B ALA 3.5 16.3 + - - +
228B VAL 3.2 10.9 + - - +
230B GLU* 1.4 75.3 - - - +
232B GLU* 1.3 76.9 + - - +
234B SER* 2.6 20.8 + - - -
235B GLN* 3.2 42.8 + - + +
285B TRP 3.6 15.3 - - - -
286B VAL* 3.7 24.1 - - + +
288B TYR* 3.9 16.2 - + - -
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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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15B GLU* 4.6 19.2 - - - +
150B LEU* 4.8 4.3 - - + -
211B ILE* 3.7 41.0 - - + +
228B VAL* 2.9 22.8 + - + +
229B LEU* 3.4 7.8 + - - +
231B PHE* 1.3 87.5 - - + +
233B ALA* 1.4 52.1 + - - +
235B GLN* 3.1 3.6 + - - +
236B LYS* 2.8 76.0 + - - +
239B LEU* 4.8 7.6 - - + -
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Residues in contact with ALA 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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150B LEU* 4.5 2.0 - - + +
229B LEU 2.9 17.6 + - - +
230B GLU* 3.9 4.9 - - - +
232B GLU* 1.4 74.4 - - - +
234B SER* 1.3 59.4 + - - +
236B LYS 3.0 18.7 - - - +
237B CYS* 4.8 2.6 - - - -
239B LEU* 3.8 25.1 - - - +
240B VAL* 4.2 13.5 - - + -
241B THR* 4.4 11.0 - - + +
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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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230B GLU 3.0 14.2 + - - -
231B PHE* 2.6 26.0 + - - -
233B ALA* 1.3 75.5 - - - +
235B GLN* 1.4 74.8 + - - +
237B CYS* 6.0 1.3 - - - -
286B VAL 4.6 4.6 + - - -
288B TYR 4.0 4.1 + - - -
289B GLN* 3.7 37.0 - - - +
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Residues in contact with GLN 235 (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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231B PHE* 3.2 42.2 + - + +
232B GLU* 3.1 7.4 + - - +
234B SER* 1.4 108.7 + - - +
236B LYS* 1.3 72.7 + - + +
237B CYS* 4.1 6.9 + - - -
288B TYR* 3.7 34.1 + - + +
289B GLN* 3.9 9.7 - - - +
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Residues in contact with LYS 236 (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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211B ILE* 4.2 11.5 - - - +
212B GLN* 6.1 0.8 - - - +
215B ARG* 3.5 32.8 - - - +
232B GLU* 2.8 48.9 + - - +
233B ALA* 3.0 17.3 - - - +
235B GLN* 1.3 82.2 - - - +
237B CYS* 1.3 63.6 + - - +
238B ASP* 3.3 17.3 - - - +
239B LEU* 3.3 29.8 + - + +
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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