Contacts of the helix formed by residues 233 - 245 (chain A) in PDB entry 1ASA
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.7 30.3 - - + -
227A GLN* 3.1 49.5 - - + +
228A GLY* 3.8 9.6 - - - +
232A GLY* 1.3 70.5 - - - +
234A GLU* 1.3 74.9 + - + +
235A GLU* 3.8 2.0 + - - +
236A ASP* 3.8 3.5 - - - +
237A ALA* 3.9 2.9 + - - +
259A ASN* 5.4 0.9 - - - +
316A ARG* 3.9 14.8 - - - +
319A TRP* 3.8 21.1 - - + -
320A GLU* 3.9 26.0 - - + +
323A LEU* 4.5 9.6 - - + -
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Residues in contact with GLU 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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93A LEU* 4.4 11.3 - - - +
97A LYS* 2.9 43.3 + - - +
233A LEU* 1.3 87.5 - - + +
235A GLU* 1.3 76.3 + - - +
236A ASP 3.2 1.8 - - - -
237A ALA* 3.2 13.2 + - - +
238A GLU* 3.6 11.3 + - - +
241A ARG* 3.2 37.7 + - - +
316A ARG* 5.4 3.5 + - - -
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Residues in contact with GLU 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 ARG* 2.7 44.5 + - + +
232A GLY* 3.5 22.1 - - - +
233A LEU* 3.8 1.2 + - - +
234A GLU* 1.3 96.2 + - + +
236A ASP* 1.3 56.3 + - - +
238A GLU* 3.1 34.6 + - - +
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Residues in contact with ASP 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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191A GLY 4.0 4.7 - - - +
192A CYS* 3.6 24.6 - - - +
206A TRP* 5.3 2.4 - - - -
224A PHE* 3.3 13.4 - - - -
227A GLN* 4.4 3.8 - - + -
228A GLY* 2.7 26.8 + - - +
229A PHE 3.4 0.5 + - - -
230A ALA* 3.1 26.8 + - - +
231A ARG* 2.9 36.3 + - - +
232A GLY 2.8 22.2 + - - +
233A LEU 3.8 6.7 - - - +
235A GLU* 1.3 78.6 - - - +
237A ALA* 1.3 58.0 + - - +
238A GLU 3.4 1.0 + - - -
239A GLY 4.7 2.8 + - - -
240A LEU 5.5 0.2 + - - -
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Residues in contact with ALA 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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94A LEU* 3.6 11.4 - - - +
224A PHE* 3.5 17.5 - - + -
227A GLN* 4.2 7.0 - - - +
233A LEU 3.9 7.8 + - - +
234A GLU 3.2 8.6 + - - +
236A ASP* 1.3 78.1 - - - +
238A GLU* 1.3 57.1 + - - +
239A GLY 3.4 2.6 + - - -
240A LEU* 3.4 6.5 + - + +
241A ARG* 2.9 54.5 + - - +
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Residues in contact with GLU 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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203A LEU* 4.2 34.5 - - + +
206A TRP* 5.9 1.8 - - + -
231A ARG* 4.4 6.0 + - - +
234A GLU 3.6 6.8 + - - +
235A GLU* 3.1 29.1 - - - +
236A ASP 3.4 2.0 - - - -
237A ALA* 1.3 76.4 - - - +
239A GLY* 1.3 51.6 + - - +
241A ARG* 3.3 10.0 + - - +
242A ALA* 2.8 33.5 + - - +
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Residues in contact with GLY 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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191A GLY 5.7 0.2 - - - -
203A LEU* 5.3 0.9 - - - -
206A TRP* 3.5 45.6 - - - -
222A PHE* 4.3 6.1 - - - -
236A ASP 4.7 2.2 + - - -
237A ALA 3.4 0.6 - - - -
238A GLU* 1.3 74.0 - - - +
240A LEU* 1.3 64.6 - - - +
242A ALA* 3.1 4.9 + - - +
243A PHE* 2.9 28.3 + - - -
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Residues in contact with LEU 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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94A LEU* 3.8 32.5 - - + +
95A PHE* 3.5 26.5 - - + -
191A GLY 5.6 0.6 + - - -
206A TRP* 5.5 0.2 - - - -
222A PHE* 3.7 46.1 - - + -
224A PHE* 3.8 25.8 - - + -
236A ASP 5.5 0.2 + - - -
237A ALA* 3.4 7.7 + - + +
239A GLY* 1.3 74.3 - - - +
241A ARG* 1.3 50.3 + - - +
243A PHE* 3.1 5.5 + - - +
244A ALA* 2.7 30.7 + - - +
250A LEU* 4.0 25.1 - - + -
252A VAL* 4.7 5.6 - - + -
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Residues in contact with ARG 241 (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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92A GLU 3.8 0.6 + - - -
93A LEU 2.7 28.7 + - - -
94A LEU 2.8 20.6 + - - +
95A PHE* 3.8 15.6 - - + +
96A GLY* 3.6 22.3 - - - +
97A LYS* 4.5 1.8 - - - +
234A GLU* 3.2 42.8 + - - +
237A ALA* 2.9 33.0 + - - +
238A GLU* 3.5 8.7 - - - +
239A GLY 3.2 0.2 - - - -
240A LEU* 1.3 72.7 - - + +
242A ALA* 1.3 61.5 + - - +
243A PHE 3.3 0.2 - - - -
244A ALA* 3.7 9.4 - - - +
245A ALA* 3.5 21.7 + - - +
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Residues in contact with ALA 242 (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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203A LEU* 4.6 12.6 - - + -
206A TRP 4.8 1.8 - - - -
207A GLN* 4.5 26.5 - - + +
210A ALA* 4.0 6.1 - - + +
238A GLU 2.8 13.5 + - - +
239A GLY* 3.1 12.3 + - - +
241A ARG* 1.3 75.3 - - - +
243A PHE* 1.3 66.3 + - - +
245A ALA* 3.9 8.1 + - - +
246A MET* 3.9 17.8 - - - +
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Residues in contact with PHE 243 (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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189A PHE* 3.7 26.5 - + - -
206A TRP* 3.4 37.9 - + - -
209A LEU* 3.7 20.4 - - + -
210A ALA* 3.8 15.0 - - + -
213A SER* 3.1 22.4 - - - -
220A PRO* 3.8 27.6 - - + -
222A PHE* 3.8 20.0 - + + -
239A GLY 2.9 18.1 + - - +
240A LEU 3.3 8.3 - - - +
242A ALA* 1.3 78.8 - - - +
244A ALA* 1.3 56.1 + - - +
246A MET 3.1 2.8 + - - -
247A HIS* 3.0 41.3 + - - +
250A LEU* 4.2 6.7 - - + -
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Residues in contact with ALA 244 (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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95A PHE* 3.9 31.6 - - + -
101A LEU* 4.2 25.7 - - + +
106A ARG* 4.5 5.4 + - - -
240A LEU 2.7 18.7 + - - +
241A ARG* 4.1 7.2 - - - +
242A ALA 3.5 0.6 - - - -
243A PHE* 1.3 71.4 - - - +
245A ALA* 1.3 59.8 + - - +
246A MET 3.1 1.7 + - - -
247A HIS 3.3 16.8 - - - +
250A LEU* 4.1 14.1 - - + +
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Residues in contact with ALA 245 (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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101A LEU* 5.8 1.3 - - - -
106A ARG* 6.2 0.2 - - - -
241A ARG 3.5 17.3 + - - +
242A ALA* 4.1 6.7 - - - +
243A PHE 3.2 0.4 + - - -
244A ALA* 1.3 76.4 - - - +
246A MET* 1.3 62.5 + - + +
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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