Contacts of the helix formed by residues 11 - 24 (chain B) in PDB entry 2AOT
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 ASP 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B LEU 3.3 9.1 + - - +
9B PHE 3.2 0.6 - - - -
10B SER* 1.3 76.3 - - - +
12B HIS* 1.3 66.1 + - - +
13B GLY 3.1 2.5 - - - +
14B LYS* 3.0 12.6 + - + +
15B TYR 2.9 18.5 + - - -
248B CSO 2.9 27.5 + - - +
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Residues in contact with HIS 12 (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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9B PHE 4.0 5.8 + - - +
10B SER 3.7 4.9 + - - -
11B ASP* 1.3 70.4 - - - +
13B GLY* 1.3 65.8 + - - +
15B TYR* 3.0 18.6 + + - +
16B VAL* 3.0 50.2 + - + +
93B GLU* 3.8 27.8 + - - -
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Residues in contact with GLY 13 (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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11B ASP* 3.1 2.0 + - - +
12B HIS* 1.3 81.3 - - - +
14B LYS* 1.3 55.8 + - - +
16B VAL* 3.1 11.9 - - - +
17B GLU* 3.0 29.0 + - - +
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Residues in contact with LYS 14 (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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8B LEU* 3.4 15.1 - - + +
11B ASP* 3.0 20.9 + - + +
13B GLY* 1.3 74.3 - - - +
15B TYR* 1.3 57.8 + - - +
17B GLU* 3.6 7.1 - - - +
18B SER* 3.0 34.8 + - - +
239B LEU* 5.6 0.6 - - - +
242B ASP* 6.4 1.1 - - + -
248B CSO 4.6 9.2 - - + -
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Residues in contact with TYR 15 (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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8B LEU* 3.5 31.7 - - + +
9B PHE* 3.7 32.0 - + - -
11B ASP 2.9 11.5 + - - +
12B HIS* 3.0 24.9 + + - +
14B LYS* 1.3 78.9 - - - +
16B VAL* 1.3 73.1 + - + +
18B SER* 3.8 1.6 - - - -
19B PHE* 2.8 49.5 + + + +
147B TYR* 4.2 7.1 + - - -
243B PHE* 5.2 0.2 - - - -
401B 2PM 3.4 37.8 - + - -
501B SAH 6.0 2.3 - - - -
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Residues in contact with VAL 16 (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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12B HIS* 3.0 38.1 + - + +
13B GLY* 3.1 17.9 - - - +
15B TYR* 1.3 86.9 - - + +
17B GLU* 1.3 59.6 + - + +
19B PHE* 3.8 8.9 - - + +
20B ARG* 2.8 36.0 + - - +
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Residues in contact with GLU 17 (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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13B GLY 3.0 19.6 + - - +
14B LYS* 3.6 9.4 - - - +
16B VAL* 1.3 82.6 - - + +
18B SER* 1.3 59.9 + - - +
20B ARG* 3.6 5.3 - - - +
21B ARG* 2.9 28.6 + - - +
239B LEU* 4.5 15.4 - - + +
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Residues in contact with SER 18 (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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8B LEU* 4.1 10.3 - - - +
14B LYS* 3.0 20.5 + - - +
15B TYR 3.9 1.6 - - - -
17B GLU* 1.3 72.1 - - - +
19B PHE* 1.3 67.5 + - - +
21B ARG* 3.1 9.2 + - - +
22B PHE* 2.9 21.8 + - - +
239B LEU* 3.0 35.5 + - - +
240B LEU* 5.0 0.3 - - - +
242B ASP* 3.5 14.6 + - - +
243B PHE* 3.9 17.5 - - - +
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Residues in contact with PHE 19 (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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15B TYR* 2.8 43.6 + + + +
16B VAL* 3.8 9.2 - - + +
18B SER* 1.3 76.1 - - - +
20B ARG* 1.3 65.0 + - - +
22B PHE* 3.0 19.0 + + - +
23B LEU* 3.0 57.8 + - + +
28B GLU* 6.1 1.1 - - + -
243B PHE* 3.6 28.4 - + + -
401B 2PM 4.4 11.0 - + - -
501B SAH 5.6 11.0 - - - -
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Residues in contact with ARG 20 (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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16B VAL 2.8 19.9 + - - +
17B GLU* 3.6 7.9 - - - +
19B PHE* 1.3 81.1 - - - +
21B ARG* 1.3 55.3 + - - +
23B LEU* 3.3 8.2 + - - +
24B ASN* 2.5 41.6 + - - +
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Residues in contact with ARG 21 (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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17B GLU 2.9 19.1 - - - +
18B SER 3.1 6.7 + - - +
20B ARG* 1.3 74.6 - - - +
22B PHE* 1.3 65.7 + - - +
24B ASN* 2.8 29.9 + - - +
25B HIS* 3.0 24.4 + - - +
235B GLU* 4.4 0.4 - - - +
236B ASN* 2.2 69.0 + - - +
239B LEU* 3.4 30.1 - - + +
240B LEU* 4.0 10.6 - - + +
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Residues in contact with PHE 22 (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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18B SER 2.9 11.9 + - - +
19B PHE* 3.0 19.3 + + - +
21B ARG* 1.3 75.4 - - - +
23B LEU* 1.3 86.0 + - + +
25B HIS* 3.1 3.2 + - - -
26B SER* 2.8 43.2 + - - -
28B GLU* 3.6 26.9 - - - -
179B TRP* 4.5 2.0 - + - -
224B MET* 3.1 41.4 - - + +
240B LEU* 4.2 2.4 - - - +
243B PHE* 3.3 28.7 - + + -
283B ASN* 4.0 20.9 - - - -
401B 2PM 3.6 25.8 - - - -
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Residues in contact with LEU 23 (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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19B PHE* 3.0 46.6 + - + +
20B ARG* 3.6 9.6 - - - +
22B PHE* 1.3 88.8 - - + +
24B ASN* 1.3 59.2 + - - +
25B HIS 2.9 6.2 + - - -
26B SER* 3.1 22.3 + - - +
28B GLU* 4.0 29.7 + - + -
29B HIS* 5.1 16.6 - - + +
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Residues in contact with ASN 24 (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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20B ARG* 2.5 43.3 + - - +
21B ARG* 2.8 19.7 - - - +
23B LEU* 1.3 70.6 - - - +
25B HIS* 1.3 101.1 + - - +
26B SER 3.7 1.1 - - - -
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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