Contacts of the helix formed by residues 223 - 232 (chain B) in PDB entry 1AD5
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 LEU 223 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 6.2 6.3 - - + -
148B TRP* 3.8 27.6 - - + -
149B PHE* 5.8 2.2 - - + -
174B ILE* 5.0 10.3 - - + -
184B TYR* 4.1 30.3 - - + -
204B ILE* 6.3 0.9 - - + -
212B PHE* 3.7 25.8 - - + -
220B PHE* 5.6 0.7 - - - -
221B SER 3.1 16.5 + - - +
222B THR* 1.3 69.5 - - - +
224B GLN* 1.3 64.9 + - + +
226B LEU* 3.0 31.1 - - + +
227B VAL* 3.1 12.8 - - + +
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Residues in contact with GLN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLU* 2.8 40.8 + - - +
148B TRP* 3.0 30.4 + - + -
222B THR* 3.2 6.9 - - + -
223B LEU* 1.3 78.0 - - + +
225B GLU* 1.3 56.3 + - - +
227B VAL* 2.9 16.5 - - - +
228B ASP* 2.9 39.0 + - - +
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B PHE* 4.2 16.1 - - + -
222B THR* 2.8 35.3 + - + +
224B GLN* 1.3 70.6 - - - +
226B LEU* 1.3 56.7 + - - +
228B ASP* 3.7 7.5 - - - +
229B HIS* 2.8 37.7 + - - +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.5 10.3 - - + -
186B LEU* 6.4 0.7 - - + -
204B ILE* 4.4 25.8 - - + -
212B PHE* 5.0 16.6 - - + +
213B TYR* 5.5 0.7 - - - +
214B ILE* 4.5 16.6 - - + +
220B PHE* 3.7 35.5 - - + -
222B THR 3.1 6.8 + - - +
223B LEU* 3.0 24.9 + - + +
225B GLU* 1.3 78.0 - - - +
227B VAL* 1.3 64.8 + - + +
229B HIS* 3.0 14.6 + - - +
230B TYR* 3.2 44.2 + - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP* 3.9 34.1 - - + +
172B PHE* 4.4 17.9 - - + -
174B ILE* 3.7 28.0 - - + -
223B LEU 3.1 18.2 - - - +
224B GLN* 2.9 20.1 + - - +
226B LEU* 1.3 76.0 - - - +
228B ASP* 1.3 68.5 + - - +
230B TYR* 3.1 2.8 + - - -
231B LYS* 2.9 32.4 + - + +
241B LEU* 3.8 11.8 - - - +
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Residues in contact with ASP 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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224B GLN* 2.9 34.6 + - - +
225B GLU* 3.9 7.4 + - - +
227B VAL* 1.3 85.9 - - - +
229B HIS* 1.3 61.4 + - - +
231B LYS* 3.6 20.6 - - - +
232B LYS* 3.4 25.1 + - - +
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Residues in contact with HIS 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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218B SER* 3.8 23.3 - - - -
220B PHE* 3.0 33.8 - + + -
225B GLU 2.8 13.0 + - - +
226B LEU 3.0 10.5 - - - +
228B ASP* 1.3 77.2 - - - +
230B TYR* 1.3 82.3 + + - +
232B LYS* 3.1 23.8 + - + +
233B GLY 3.7 4.6 + - - +
235B ASP* 4.3 18.2 - - + +
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Residues in contact with TYR 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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186B LEU* 6.2 0.7 - - + -
214B ILE* 4.2 23.5 + - + +
215B SER* 4.4 12.0 + - - -
218B SER* 4.9 5.2 + - - -
220B PHE* 4.9 1.2 - + - -
226B LEU* 3.3 45.5 - - + -
227B VAL 3.1 2.2 + - - +
229B HIS* 1.3 93.2 - + - +
231B LYS* 1.3 59.7 + - - +
232B LYS 3.0 5.7 + - - -
233B GLY 3.6 24.0 + - - +
234B ASN* 5.5 0.2 - - - -
235B ASP* 3.3 43.2 + - + -
237B LEU* 3.9 27.9 - - + +
239B GLN 5.0 0.4 - - - +
240B LYS* 3.6 2.9 - - - -
241B LEU* 2.8 45.0 + - + -
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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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172B PHE* 4.7 12.8 - - + -
227B VAL* 2.9 18.6 + - + +
228B ASP* 3.6 24.7 - - - +
230B TYR* 1.3 78.0 - - - +
232B LYS* 1.3 64.3 + - - +
240B LYS* 2.6 33.1 + - - +
241B LEU* 3.0 25.9 - - + +
242B SER* 2.7 27.0 + - - +
243B VAL* 4.6 5.5 - - - +
244B PRO* 4.9 6.7 - - - +
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Residues in contact with LYS 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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228B ASP 3.4 10.8 + - - +
229B HIS* 3.1 15.0 + - - +
230B TYR 3.0 0.6 - - - -
231B LYS* 1.3 94.7 + - - +
233B GLY* 1.3 56.9 + - - +
240B LYS* 3.5 20.8 - - - +
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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