Contacts of the helix formed by residues 226 - 235 (chain B) in PDB entry 1A1A
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 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B TRP* 3.9 26.7 - - + -
152B TYR* 5.0 3.8 - - + -
177B VAL* 4.1 13.0 - - + -
187B TYR* 4.1 31.4 - - + +
207B ILE* 3.9 41.1 - - + -
215B PHE* 3.6 22.3 - - + -
225B SER* 1.3 72.5 - - - +
227B GLN* 1.3 64.9 + - - +
229B LEU* 3.3 9.7 - - + +
230B VAL* 3.2 21.6 + - + +
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 3.5 33.2 - - - +
151B TRP* 3.9 16.9 - - + +
225B SER* 3.3 7.7 + - - +
226B LEU* 1.3 76.8 - - - +
228B GLN* 1.3 69.5 + - - +
230B VAL* 3.2 2.6 + - - +
231B ALA* 2.8 39.9 + - - +
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Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 3.8 13.7 - - + +
224B ASN* 3.7 21.7 + - - +
225B SER* 2.7 40.1 + - - +
226B LEU 3.3 0.2 - - - -
227B GLN* 1.3 85.0 - - - +
229B LEU* 1.4 56.1 + - - +
231B ALA* 3.6 6.3 - - - +
232B TYR* 2.8 36.0 + - - +
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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
----------------------------------------------------------
189B LEU* 4.6 7.4 - - + -
207B ILE* 3.7 45.8 - - + -
215B PHE* 4.1 8.5 - - + -
216B TYR* 4.3 5.8 - - - +
217B ILE* 4.2 16.4 - - + -
223B PHE* 3.6 34.4 - - + -
225B SER 3.4 6.5 + - - +
226B LEU* 3.3 14.3 + - + +
228B GLN* 1.4 78.2 - - - +
230B VAL* 1.3 68.5 + - + +
232B TYR* 3.3 0.9 + - - +
233B TYR* 2.9 53.3 + - + -
244B LEU* 5.2 0.4 - - + -
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TRP* 3.6 43.5 - - + +
175B PHE* 3.6 32.5 - - + -
177B VAL* 4.0 16.4 - - + -
226B LEU* 3.4 13.9 - - + +
227B GLN 3.2 7.5 + - - +
229B LEU* 1.3 84.4 - - + +
231B ALA* 1.3 59.1 + - - +
233B TYR 3.4 0.7 + - - -
234B SER* 2.7 35.9 + - - +
244B LEU* 4.1 9.0 - - + +
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Residues in contact with ALA 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 GLN* 2.8 36.7 + - - +
228B GLN* 3.6 7.9 - - - +
230B VAL* 1.3 75.4 - - - +
232B TYR* 1.4 61.7 + - - +
234B SER* 3.3 17.9 + - - -
235B LYS* 3.6 11.8 + - - +
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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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220B ARG* 3.6 13.0 + - - -
221B THR* 3.7 23.5 - - + +
223B PHE* 3.2 38.4 - + + -
228B GLN 2.8 13.0 + - - +
229B LEU 3.5 2.0 - - - +
231B ALA* 1.4 72.5 - - - +
233B TYR* 1.3 71.0 + + - +
235B LYS* 3.0 9.6 + - - +
236B HIS* 2.9 56.8 + + + +
238B ASP* 2.8 31.9 + - - -
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Residues in contact with TYR 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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217B ILE* 3.9 30.4 + - + +
218B THR* 4.0 19.8 + - - +
221B THR* 4.1 8.2 + - - -
223B PHE* 3.7 24.7 - + - -
229B LEU* 2.9 44.9 + - + +
230B VAL 3.8 0.4 - - - -
232B TYR* 1.3 78.2 - + - +
234B SER* 1.3 62.6 + - - +
235B LYS 3.2 1.3 + - - -
236B HIS 3.2 26.1 - - - +
237B ALA* 3.4 19.2 - - - -
238B ASP* 4.1 14.9 + - + +
240B LEU* 3.6 18.3 - - + +
243B ARG* 3.4 9.5 - - - +
244B LEU* 2.9 40.4 + - + -
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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
----------------------------------------------------------
175B PHE* 4.7 1.4 - - - -
230B VAL* 2.7 24.5 + - - +
231B ALA* 3.4 13.2 - - - -
232B TYR 3.2 0.4 - - - -
233B TYR* 1.3 77.8 - - - +
235B LYS* 1.3 74.6 + - - +
243B ARG* 3.4 17.8 + - - +
244B LEU* 3.0 29.0 + - - +
245B THR* 4.1 8.9 - - - +
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Residues in contact with LYS 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 ALA 3.9 10.5 - - - +
232B TYR* 3.0 7.4 + - - +
234B SER* 1.3 93.5 + - - +
236B HIS* 1.3 82.8 + - + +
243B ARG* 3.0 31.2 + - - +
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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