Contacts of the helix formed by residues 228 - 240 (chain A) in PDB entry 1ASZ
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A VAL 3.7 0.8 + - - -
227A ASN* 1.3 68.1 - - - +
229A ASP* 1.3 62.9 + - - +
231A ARG* 2.8 19.9 + - + +
232A LEU* 2.7 43.3 + - + +
235A ARG* 5.4 2.2 - - - +
541A ASN* 3.3 34.3 - - - +
543A ARG* 4.5 12.3 - - + +
544A ARG* 3.8 50.3 - - + +
669R C 4.2 17.9 - - - +
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Residues in contact with ASP 229 (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 ASN* 4.1 7.4 + - - +
228A LEU* 1.3 78.0 - - - +
230A THR* 1.3 73.4 + - - +
232A LEU* 2.5 35.2 + - + +
233A ASP* 2.7 24.7 + - - +
554A ARG* 4.1 11.0 + - - +
667R C 5.3 1.0 + - - -
668R G 4.0 47.7 + - - +
669R C 4.6 3.4 + - - +
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Residues in contact with THR 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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206A ILE* 3.0 24.2 - - - +
226A VAL* 3.0 16.6 - - - +
227A ASN* 3.4 7.7 + - + +
228A LEU 3.3 0.8 - - - -
229A ASP* 1.3 92.7 - - - +
231A ARG* 1.3 60.1 + - - +
233A ASP* 3.5 10.0 + - - +
234A TYR* 3.1 18.2 - - - -
611R U 3.8 10.0 + - - +
612R U 2.9 38.3 + - - +
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Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 4.0 9.2 - - - -
211A ALA* 2.5 45.7 + - - +
225A VAL* 4.6 7.7 - - - +
226A VAL* 2.8 39.9 + - + +
227A ASN 2.6 23.8 + - - +
228A LEU* 2.8 27.0 + - + +
230A THR* 1.3 74.2 - - - +
232A LEU* 1.3 69.4 + - + +
234A TYR 2.9 5.5 + - - -
235A ARG* 2.8 22.8 + - - +
238A ASP* 3.0 40.9 + - + +
241A THR* 5.0 2.0 + - - +
244A ASN* 5.2 1.4 - - - +
383A GLN* 4.5 5.9 + - - +
384A TYR* 4.5 16.6 + - - -
544A ARG* 5.2 6.7 - - - +
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Residues in contact with LEU 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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228A LEU* 2.7 29.6 + - + +
229A ASP* 2.5 19.1 + - + +
231A ARG* 1.3 72.0 - - + +
233A ASP* 1.3 54.3 + - - -
235A ARG* 3.0 56.8 + - + +
543A ARG* 3.9 24.2 - - + +
549A PRO* 3.5 33.4 - - + -
554A ARG* 2.9 36.4 + - - +
557A PRO* 3.8 8.1 - - - +
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Residues in contact with ASP 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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229A ASP* 2.7 24.2 + - - +
230A THR* 3.7 7.8 - - - +
231A ARG 3.1 0.6 - - - -
232A LEU* 1.3 70.6 - - - +
234A TYR* 1.3 86.3 + - + +
235A ARG 3.5 0.4 - - - -
554A ARG* 2.6 35.0 + - - +
556A ARG* 3.3 38.7 + - - +
557A PRO* 4.8 6.1 - - - +
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Residues in contact with TYR 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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205A PRO* 3.3 36.9 - - + +
206A ILE* 3.5 30.3 - - + -
230A THR* 3.1 20.2 - - - -
231A ARG 2.9 6.8 + - - -
233A ASP* 1.3 96.1 - - + +
235A ARG* 1.3 52.3 + - - +
236A VAL* 2.8 7.8 + - - -
237A ILE* 2.6 37.8 + - + +
238A ASP* 3.3 6.9 + - - +
556A ARG* 5.5 4.1 + - - -
517B TYR* 4.1 19.1 - - - -
610R G 5.3 1.6 + - - -
611R U 4.9 11.7 + - - -
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Residues in contact with ARG 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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228A LEU* 5.4 2.8 - - - +
231A ARG* 2.8 8.1 + - - +
232A LEU* 3.0 45.4 + - + +
233A ASP 3.5 0.4 - - - -
234A TYR* 1.3 75.2 - - - +
236A VAL* 1.3 57.3 + - - +
237A ILE 3.3 0.2 - - - -
238A ASP* 3.9 19.2 + - - -
239A LEU* 2.9 58.0 + - + +
244A ASN* 4.7 5.0 + - - -
248A PHE* 3.5 18.6 - - - -
543A ARG 4.0 3.8 + - - -
544A ARG* 3.8 17.4 + - - +
546A SER 3.4 21.9 + - - -
547A LEU 3.3 19.9 + - - +
548A PHE* 4.2 11.9 - - + -
549A PRO* 4.9 0.9 - - + +
557A PRO* 4.3 13.8 - - + +
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Residues in contact with VAL 236 (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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234A TYR* 2.8 4.2 + - - +
235A ARG* 1.3 74.1 - - + +
237A ILE* 1.3 67.1 + - - +
239A LEU* 3.9 3.9 + - + -
240A ARG* 3.6 7.6 + - - +
548A PHE* 4.8 11.9 - - + -
557A PRO* 5.7 5.8 - - + -
308B GLN* 3.3 54.7 - - + +
309B LEU* 5.1 0.2 - - - -
311B VAL* 3.6 15.5 - - + -
312B ALA* 3.3 40.4 - - + +
514B GLY* 5.4 2.2 - - - -
517B TYR* 5.1 12.6 - - + -
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Residues in contact with ILE 237 (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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163A GLU* 5.4 1.8 - - + -
204A LEU* 4.3 15.7 - - + -
205A PRO* 3.9 24.9 - - + +
206A ILE* 3.4 20.0 - - + -
207A LEU* 4.4 4.7 - - - +
208A LEU* 3.5 20.6 - - + +
234A TYR* 2.6 33.2 + - + +
236A VAL* 1.3 69.8 - - - +
238A ASP* 1.3 57.9 + - - +
240A ARG* 2.8 49.7 - - - +
517B TYR* 3.9 37.2 - - + -
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Residues in contact with ASP 238 (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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206A ILE* 4.2 9.8 - - + +
208A LEU* 5.2 0.2 - - - -
211A ALA* 4.3 3.3 - - - +
231A ARG* 3.0 57.6 + - + +
234A TYR 3.3 2.6 + - - +
235A ARG* 3.6 30.2 + - - +
237A ILE* 1.3 73.8 - - - +
239A LEU* 1.3 51.8 + - - +
240A ARG 2.6 17.8 + - - -
241A THR* 2.9 23.7 + - - +
244A ASN* 2.8 30.3 + - - -
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Residues in contact with LEU 239 (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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235A ARG* 2.9 64.6 + - + +
236A VAL* 4.6 0.4 - - - -
237A ILE 3.4 0.6 - - - -
238A ASP* 1.3 70.5 - - - +
240A ARG* 1.3 57.1 + - - +
241A THR 3.5 0.7 - - - -
244A ASN* 3.9 14.4 - - - +
245A GLN* 2.9 24.8 + - - -
248A PHE* 3.9 15.3 - - + -
547A LEU* 3.9 20.4 - - + +
548A PHE* 4.4 4.7 - - + -
309B LEU* 4.3 15.0 - - + -
312B ALA* 3.5 28.2 - - + +
314B PHE* 3.7 21.0 - - + -
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Residues in contact with ARG 240 (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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114A ARG* 2.6 35.9 - - - +
131A ARG* 3.1 26.2 + - - +
133A GLN 4.1 8.3 - - - +
163A GLU* 3.0 24.8 + - - +
204A LEU* 5.2 0.2 - - - +
208A LEU* 4.2 7.2 - - + -
236A VAL 3.6 9.5 + - - +
237A ILE* 2.8 53.3 + - - +
238A ASP 2.6 6.7 + - - -
239A LEU* 1.3 75.7 - - - +
241A THR* 1.3 62.0 + - - +
242A VAL 3.7 1.2 + - - -
245A GLN* 4.0 9.7 - - - +
311B VAL* 3.2 25.1 + - - +
312B ALA 4.0 10.5 - - - -
313B ASP* 3.0 19.4 + - + +
517B TYR* 3.4 16.5 + - - +
518B GLY 3.4 4.8 + - - -
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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