Contacts of the helix formed by residues 21 - 33 (chain A) in PDB entry 1ANG
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 ARG 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PRO* 3.8 33.1 - - + +
19A GLN 3.8 5.1 + - - +
20A GLY* 1.3 71.9 - - - -
22A ASP* 1.3 57.3 + - - +
25A TYR* 4.1 9.4 - - + -
47A HIS* 3.8 8.0 + - - +
77A GLN* 2.8 42.0 + - - +
78A VAL 2.9 23.7 + - - +
79A THR* 3.1 28.7 + - + +
96A ALA* 3.6 16.4 - - - +
98A ALA* 3.5 30.5 + - + +
99A GLY 3.2 6.5 + - - +
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Residues in contact with ASP 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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20A GLY* 3.0 16.3 + - - +
21A ARG* 1.3 73.6 - - - +
23A ASP* 1.3 67.3 + - - +
24A ARG* 3.8 21.0 + - - +
25A TYR* 3.0 24.5 + - - +
26A CYS 3.1 9.9 + - - -
96A ALA* 3.5 12.7 - - - +
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Residues in contact with ASP 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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22A ASP* 1.3 71.1 - - - +
24A ARG* 1.3 87.4 + - - +
26A CYS* 3.1 14.0 + - - +
27A GLU* 3.1 16.7 + - - +
93A GLN* 4.2 0.5 - - - +
94A TYR 3.5 22.7 - - - +
95A ARG* 3.4 34.2 + - - +
96A ALA* 3.5 19.2 + - - +
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Residues in contact with ARG 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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22A ASP* 3.2 17.4 + - - +
23A ASP* 1.3 102.0 + - - +
25A TYR* 1.3 62.6 + - - +
27A GLU* 3.6 24.6 + - - +
28A SER* 3.0 26.2 + - - -
93A GLN* 5.2 2.2 + - - -
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Residues in contact with TYR 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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15A ASP* 2.7 34.1 + - - +
18A PRO* 3.5 18.6 - - + -
19A GLN 4.9 3.6 - - - -
20A GLY 3.3 25.1 - - - +
21A ARG* 4.1 4.7 - - + -
22A ASP* 3.0 15.7 + - - +
24A ARG* 1.3 76.9 - - - +
26A CYS* 1.3 69.5 + - - +
28A SER* 3.5 7.7 + - - -
29A ILE* 3.0 51.3 + - + +
32A ARG* 5.5 3.1 - - - -
45A PHE* 4.0 5.3 - + - +
47A HIS* 3.2 16.8 - + - -
79A THR* 3.8 34.3 - - + -
81A CYS* 4.8 2.0 - - - -
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Residues in contact with CYS 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 ASP 3.1 4.0 + - - +
23A ASP 3.3 9.2 - - - +
25A TYR* 1.3 81.2 - - - +
27A GLU* 1.3 58.9 + - - +
29A ILE* 3.4 1.4 - - - +
30A MET* 2.8 37.6 + - - +
79A THR* 4.1 8.3 - - - -
81A CYS* 2.0 55.4 - - + -
94A TYR* 3.6 13.5 - - + +
96A ALA* 3.3 30.7 - - - -
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Residues in contact with GLU 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 ASP 3.1 14.0 + - - +
24A ARG* 3.8 25.9 + - + +
26A CYS* 1.3 71.8 - - - +
28A SER* 1.3 66.0 + - - +
30A MET* 4.3 0.5 - - - +
31A ARG* 3.3 38.9 + - - +
92A CYS 3.7 14.6 - - - +
93A GLN* 3.6 20.4 - - - +
94A TYR* 3.5 39.7 + - - +
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Residues in contact with SER 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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24A ARG 3.0 22.1 + - - -
25A TYR* 3.6 8.3 + - - -
27A GLU* 1.3 74.1 - - - +
29A ILE* 1.3 60.0 + - - +
31A ARG* 3.8 15.6 - - - +
32A ARG* 2.8 36.9 + - - +
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Residues in contact with ILE 29 (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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15A ASP* 3.3 35.0 - - - +
25A TYR* 3.0 45.9 + - + +
26A CYS* 3.4 6.5 - - - +
28A SER* 1.3 70.0 + - - +
30A MET* 1.3 62.8 + - - +
32A ARG* 3.9 22.9 - - - +
33A ARG* 2.9 51.1 + - - +
45A PHE* 3.7 36.7 - - + -
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Residues in contact with MET 30 (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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26A CYS 2.8 26.1 + - - +
27A GLU 4.3 1.3 - - - +
29A ILE* 1.3 75.6 - - - +
31A ARG* 1.3 60.5 + - - +
33A ARG 3.4 2.8 + - - -
35A LEU* 3.1 44.6 + - + +
36A THR* 3.9 3.9 + - - -
40A LYS* 3.9 15.9 - - + +
43A ASN* 3.9 26.0 - - + +
45A PHE* 3.7 28.5 - - + -
81A CYS* 4.2 10.8 - - + -
94A TYR* 3.4 56.5 - - + +
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Residues in contact with ARG 31 (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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27A GLU* 3.3 31.7 + - - +
28A SER* 3.8 14.7 - - - +
30A MET* 1.3 75.9 - - - +
32A ARG* 1.3 62.7 + - - +
33A ARG 3.4 0.5 + - - -
34A GLY* 3.6 9.0 + - - -
36A THR* 3.9 29.6 - - + +
92A CYS 6.0 0.2 + - - -
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Residues in contact with ARG 32 (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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15A ASP* 4.5 10.3 + - - -
25A TYR* 5.5 2.6 - - - -
28A SER* 2.8 25.2 + - - +
29A ILE* 3.9 33.0 - - - +
31A ARG* 1.3 71.5 - - - +
33A ARG* 1.3 78.8 + - - +
34A GLY 3.5 1.4 + - - -
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Residues in contact with ARG 33 (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 LEU 4.4 2.6 + - - -
11A THR* 2.9 63.5 + - + +
14A TYR* 2.9 29.9 + - - -
15A ASP* 4.4 8.5 + - - +
29A ILE* 2.9 38.8 + - - +
31A ARG 3.3 0.8 - - - -
32A ARG* 1.3 98.5 - - - +
34A GLY* 1.3 56.2 + - - +
35A LEU* 3.2 33.3 + - + +
45A PHE* 3.3 20.7 - - + -
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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