Contacts of the helix formed by residues 18 - 28 (chain A) in PDB entry 1AYJ
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 ASN 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ASN* 1.3 70.9 + - - +
19A ASN* 1.3 61.4 + - - +
21A CYS* 3.2 1.9 + - - +
22A LYS* 2.9 38.6 + - - +
34A GLY 4.1 2.2 + - - -
35A SER* 2.8 27.7 + - - +
36A CYS* 2.8 36.1 + - + +
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Residues in contact with ASN 19 (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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17A ASN* 3.3 9.9 + - - +
18A ASN* 1.3 79.6 - - - +
20A ALA* 1.3 59.2 + - - +
22A LYS* 2.7 55.0 + - - +
23A ASN* 2.9 20.2 + - - +
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Residues in contact with ALA 20 (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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11A TRP* 3.8 20.6 - - + -
17A ASN* 2.8 27.8 + - + +
19A ASN* 1.3 72.0 - - - +
21A CYS* 1.3 61.0 + - - +
23A ASN* 3.0 8.3 + - - +
24A GLN* 2.7 35.9 + - + +
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Residues in contact with CYS 21 (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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8A SER* 4.4 0.2 - - - -
11A TRP* 3.6 8.7 - - + -
15A CYS* 4.4 5.4 - - + -
17A ASN 3.0 19.8 + - - +
18A ASN 3.5 5.2 - - - +
20A ALA* 1.3 74.0 - - - +
22A LYS* 1.3 64.8 + - - +
24A GLN* 4.0 0.3 - - - +
25A CYS* 2.8 26.9 + - - +
34A GLY* 4.3 0.7 - - - -
35A SER 3.5 27.4 - - - -
36A CYS 4.2 1.1 - - - +
45A CYS* 2.1 64.4 - - + -
46A ILE 3.7 2.0 - - - -
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Residues in contact with LYS 22 (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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18A ASN* 2.9 19.6 + - - +
19A ASN* 2.7 48.3 + - - +
21A CYS* 1.3 74.7 - - - +
23A ASN* 1.3 74.0 + - - +
25A CYS* 3.2 0.7 + - - +
26A ILE* 3.0 39.3 + - + +
33A HIS* 5.2 3.8 - - + -
34A GLY* 3.3 38.3 - - - +
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Residues in contact with ASN 23 (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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19A ASN* 2.9 26.7 + - - +
20A ALA* 3.5 7.0 - - - +
22A LYS* 1.3 84.0 - - - +
24A GLN* 1.3 56.5 + - - +
26A ILE* 3.6 5.8 - - - +
27A ASN* 2.7 65.6 + - - +
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Residues in contact with GLN 24 (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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8A SER* 4.4 1.0 - - - -
10A THR* 2.7 34.7 + - - -
11A TRP* 3.4 43.0 - - + +
20A ALA* 2.7 19.6 + - + +
21A CYS 4.1 1.8 + - - -
23A ASN* 1.3 75.1 - - - +
25A CYS* 1.3 77.9 + - - +
27A ASN* 4.1 5.4 - - - -
28A LEU* 2.9 45.6 + - + +
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Residues in contact with CYS 25 (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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8A SER* 3.7 10.3 - - - +
21A CYS 2.8 23.8 + - - +
22A LYS* 3.5 4.3 - - - +
23A ASN 3.1 0.2 + - - -
24A GLN* 1.3 80.0 - - - +
26A ILE* 1.3 55.6 + - - +
29A GLU* 2.8 57.1 + - - +
31A ALA* 3.5 10.5 - - - -
47A CYS* 2.1 50.5 - - + -
49A PHE* 4.4 1.1 - - - -
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Residues in contact with ILE 26 (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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22A LYS* 3.0 32.1 + - + +
23A ASN* 3.7 5.2 - - - +
25A CYS* 1.3 77.2 - - + +
27A ASN* 1.3 58.3 + - - +
29A GLU 2.7 22.4 - - - +
30A LYS* 2.9 14.6 + - - +
31A ALA* 3.3 32.5 - - + +
32A ARG* 3.4 23.3 - - - +
33A HIS* 4.3 7.9 - - - -
34A GLY 4.6 0.2 - - - +
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Residues in contact with ASN 27 (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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23A ASN* 2.7 42.6 + - - +
24A GLN* 3.8 3.8 - - - +
26A ILE* 1.3 76.8 - - + +
28A LEU* 1.3 66.3 + - + +
30A LYS* 2.7 19.4 + - - -
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Residues in contact with LEU 28 (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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10A THR* 4.1 15.3 - - + -
24A GLN* 2.9 47.6 + - + +
27A ASN* 1.3 83.8 - - + +
29A GLU* 1.3 67.0 + - - +
30A LYS* 2.8 17.5 + - - +
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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