Contacts of the helix formed by residues 226 - 235 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ILE* 4.0 28.5 - - + -
151A TRP* 3.8 18.8 - - + -
177A VAL* 4.6 10.3 - - + -
187A TYR* 4.1 27.4 - - + -
207A ILE* 3.8 43.5 - - + -
215A PHE* 3.9 21.8 - - + -
225A SER* 1.3 72.3 - - - +
227A GLN* 1.3 62.6 + - - +
229A LEU* 3.0 9.0 + - + +
230A VAL* 2.8 34.5 + - + +
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Residues in contact with GLN 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER* 4.5 14.5 + - - -
146A ILE* 4.6 9.7 - - - +
149A GLU* 2.9 34.9 + - - +
151A TRP* 3.7 22.2 - - + +
225A SER* 3.4 21.3 - - - +
226A LEU* 1.3 77.1 + - - +
228A GLN* 1.3 59.0 + - + +
230A VAL* 3.4 2.5 + - - +
231A ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.8 16.7 - - + -
224A ASN* 3.6 20.2 - - - +
225A SER* 2.6 40.0 + - - +
227A GLN* 1.3 75.2 - - + +
229A LEU* 1.3 59.8 + - - +
231A ALA* 3.8 6.4 - - + +
232A TYR* 2.9 28.9 + - - +
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.3 10.8 - - + -
207A ILE* 3.7 43.1 - - + -
215A PHE* 4.2 9.0 - - + -
216A TYR* 4.6 2.9 - - - +
217A ILE* 4.1 18.4 - - + -
223A PHE* 3.6 34.2 - - + -
225A SER 3.1 10.7 + - - +
226A LEU* 3.0 12.4 + - + +
228A GLN* 1.3 73.7 - - - +
230A VAL* 1.3 74.2 + - + +
232A TYR* 3.3 1.0 + - - +
233A TYR* 3.0 48.9 + - + -
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TRP* 4.1 28.0 - - + +
175A PHE* 3.5 34.3 - - + -
177A VAL* 3.9 28.0 - - + -
226A LEU* 2.8 21.3 + - - +
227A GLN 3.7 4.3 - - - +
229A LEU* 1.3 82.3 - - + +
231A ALA* 1.3 58.4 + - - +
233A TYR 3.8 0.7 - - - -
234A SER* 2.7 36.1 + - - +
244A LEU* 3.9 10.5 - - + +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN 2.9 18.4 + - - +
228A GLN* 3.8 8.5 - - + +
230A VAL* 1.3 77.5 - - - +
232A TYR* 1.3 64.7 + - - +
234A SER* 3.3 17.3 + - - -
235A LYS* 3.4 25.4 + - - +
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Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 3.8 7.8 + - - -
221A THR* 4.5 15.9 - - + -
223A PHE* 3.4 33.9 - + + -
228A GLN 2.9 19.3 + - - +
229A LEU 3.6 2.0 - - - +
231A ALA* 1.3 76.3 - - - +
233A TYR* 1.3 73.0 + + - +
235A LYS* 2.8 27.3 + - + +
236A HIS* 3.0 44.9 + + + -
238A ASP* 2.7 31.7 + - + -
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Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 4.0 26.6 + - + +
218A THR* 4.0 21.0 + - - +
221A THR* 4.9 4.9 + - - -
223A PHE* 3.6 31.2 - + - -
229A LEU* 3.0 41.6 + - + +
230A VAL 3.8 0.2 - - - -
232A TYR* 1.3 83.6 - + - +
234A SER* 1.3 61.7 + - - +
235A LYS 3.2 0.4 - - - -
236A HIS 3.2 26.1 - - - +
237A ALA* 3.2 18.8 - - - -
238A ASP* 4.1 13.5 + - + -
240A LEU* 3.5 29.2 - - + -
242A HIS 4.8 0.2 - - - +
243A ARG* 3.5 7.6 - - - -
244A LEU* 2.8 34.3 + - + -
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PHE* 4.8 3.5 - - - -
230A VAL* 2.7 30.5 + - - +
231A ALA* 3.3 11.0 - - - -
232A TYR 3.0 0.2 - - - -
233A TYR* 1.3 80.2 - - - +
235A LYS* 1.3 58.8 + - - +
243A ARG* 2.8 38.3 + - - +
244A LEU* 3.4 24.0 + - - +
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA* 3.6 23.7 - - - +
232A TYR* 2.8 12.1 + - + +
234A SER* 1.3 80.8 - - - +
236A HIS* 1.3 86.1 + - + +
243A ARG* 3.8 14.5 - - - +
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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