Contacts of the helix formed by residues 23 - 32 (chain E) in PDB entry 1A4Y
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 23 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D TYR* 5.0 7.3 + - + +
22E ASP* 1.3 76.4 - - + +
24E ARG* 1.3 66.2 + - - +
26E CYS* 2.7 15.4 + - - +
27E GLU* 2.9 21.2 + - - +
94E TYR 3.3 22.9 - - - +
95E ARG* 3.3 26.3 + - - +
96E ALA* 2.9 25.4 + - - +
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Residues in contact with ARG 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D SER* 6.0 0.4 - - - -
93D ASN* 3.3 39.0 - - - +
121D ASP* 5.4 8.3 - - + +
22E ASP* 3.3 17.9 + - - +
23E ASP* 1.3 76.8 - - - +
25E TYR* 1.3 63.0 + - - +
27E GLU* 3.5 12.7 + - - +
28E SER* 3.1 44.7 + - - -
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Residues in contact with TYR 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ASP* 2.4 34.9 + - - +
18E PRO 2.9 28.0 - - - -
19E GLN* 3.6 15.7 - - + +
20E GLY* 3.6 8.1 - - - -
21E ARG* 3.8 17.5 - - - +
22E ASP* 2.9 21.2 + - - +
23E ASP 2.9 0.2 + - - -
24E ARG* 1.3 75.9 - - - +
26E CYS* 1.3 66.2 + - - +
28E SER* 3.2 5.1 + - - -
29E ILE* 2.8 52.4 + - + +
45E PHE* 4.1 10.4 - + - +
47E HIS* 3.1 19.2 - + - -
79E THR* 3.9 27.8 - - + -
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Residues in contact with CYS 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ASP 3.0 5.3 + - - +
23E ASP* 2.7 14.9 + - - +
25E TYR* 1.3 79.5 - - - +
27E GLU* 1.3 63.9 + - - +
28E SER 3.0 0.2 + - - -
29E ILE* 3.7 2.7 - - - -
30E MET* 2.9 31.4 + - - +
79E THR* 4.4 2.0 - - - -
80E THR 4.2 0.9 - - - -
81E CYS* 2.0 55.0 - - - -
94E TYR* 3.7 16.6 - - + -
96E ALA* 3.5 25.6 - - - -
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Residues in contact with GLU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ASP* 5.2 4.7 - - - +
150D TYR* 4.3 14.9 + - - -
23E ASP* 2.9 23.7 + - - +
24E ARG* 3.8 14.3 + - - +
26E CYS* 1.3 73.6 - - - +
28E SER* 1.3 60.1 + - - +
30E MET* 4.0 1.9 - - - +
31E ARG* 3.4 26.3 + - - +
36E THR* 5.2 0.2 + - - -
92E CYS 3.6 22.2 - - - +
93E GLN* 3.6 12.1 - - - +
94E TYR* 3.1 32.8 + - + +
95E ARG* 3.4 13.9 + - - -
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Residues in contact with SER 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ASP* 4.8 3.6 + - - +
93D ASN* 5.9 0.7 - - - -
24E ARG* 3.1 36.4 + - - -
25E TYR* 3.6 4.9 - - - -
26E CYS 3.0 0.6 - - - -
27E GLU* 1.3 75.5 - - - +
29E ILE* 1.3 65.3 + - - +
30E MET 3.2 1.6 - - - -
31E ARG* 3.4 6.7 + - - +
32E ARG* 3.1 46.8 + - - +
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Residues in contact with ILE 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ASP* 3.7 30.5 - - - +
19E GLN* 4.3 9.0 - - - +
25E TYR* 2.8 42.3 + - + +
26E CYS* 3.3 14.1 - - - +
28E SER* 1.3 75.1 + - - +
30E MET* 1.3 59.9 + - - +
32E ARG* 3.3 17.1 + - + +
33E ARG* 2.9 57.0 + - + +
45E PHE* 3.7 35.4 - - + -
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Residues in contact with MET 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E CYS 2.9 25.4 + - - +
27E GLU 4.0 2.7 - - - +
29E ILE* 1.3 75.0 - - + +
31E ARG* 1.3 64.1 + - - +
33E ARG* 3.3 3.1 + - - -
34E GLY 3.2 3.5 + - - -
35E LEU* 3.1 38.4 + - + +
36E THR* 4.0 6.1 - - - +
40E LYS* 4.0 17.0 - - + +
43E ASN* 3.4 36.1 - - + +
45E PHE* 3.9 17.9 - - - -
81E CYS* 4.4 11.4 - - + -
94E TYR* 3.7 51.4 - - + +
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Residues in contact with ARG 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER* 4.2 7.1 + - - -
10D GLN* 3.4 27.1 + - - +
11D CYS* 4.3 15.6 - - - -
33D ARG* 4.4 2.2 - - - +
35D ASP* 2.5 46.0 + - - -
36D ASP* 4.5 2.0 + - - +
63D ARG* 3.7 31.3 - - - +
64D SER* 4.5 4.2 + - - -
27E GLU 3.4 15.2 + - - +
28E SER* 3.4 9.1 + - - +
30E MET* 1.3 76.4 - - - +
32E ARG* 1.3 65.5 + - - +
34E GLY* 3.0 14.6 + - - -
36E THR* 3.8 30.6 - - + +
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Residues in contact with ARG 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER* 4.0 13.5 + - - -
11D CYS* 4.0 18.7 - - + +
36D ASP* 3.3 37.4 + - - +
19E GLN* 4.3 21.0 - - - +
28E SER* 3.1 29.5 + - - +
29E ILE* 3.4 22.8 - - + +
31E ARG* 1.3 81.0 - - - +
33E ARG* 1.3 66.2 + - + +
34E GLY 3.5 0.5 + - - -
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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