Contacts of the helix formed by residues 10 - 35 (chain A) in PDB entry 1R73
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 THR 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ASN 5.2 1.8 - - - +
9A TYR* 1.3 73.7 - - - +
11A ASP* 1.3 56.0 + - - +
12A GLU* 4.0 7.1 + - - +
13A GLU* 2.7 42.0 + - - +
14A LEU* 2.8 31.3 + - - +
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Residues in contact with ASP 11 (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* 1.3 71.9 - - - +
12A GLU* 1.3 55.3 + - - +
14A LEU* 3.7 9.5 - - - +
15A LYS* 3.2 27.5 + - - +
60A ARG* 2.8 33.8 + - - -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.1 7.8 - - - +
11A ASP* 1.3 76.6 - - - +
13A GLU* 1.3 63.8 + - + +
15A LYS* 2.7 54.7 + - - +
16A ASN* 3.3 8.3 - - - +
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.6 28.3 - - + -
10A THR* 2.7 46.2 + - - +
12A GLU* 1.3 75.9 - - + +
14A LEU* 1.3 64.9 + - - +
16A ASN* 2.9 9.3 + - - +
17A LEU* 2.9 34.0 + - + +
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Residues in contact with LEU 14 (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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6A LEU 3.0 28.9 - - - +
7A ARG* 3.7 12.3 - - - +
9A TYR* 3.0 45.1 - - + +
10A THR 2.8 28.8 + - - +
11A ASP* 3.7 7.2 - - - +
13A GLU* 1.3 72.2 - - - +
15A LYS* 1.3 64.1 + - - +
17A LEU* 3.1 0.6 + - - -
18A LEU* 2.9 36.0 + - + +
60A ARG* 3.5 41.5 - - - +
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Residues in contact with LYS 15 (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 ASP 3.2 20.2 + - - +
12A GLU* 2.7 42.3 + - - +
14A LEU* 1.3 76.2 - - - +
16A ASN* 1.3 68.7 + - + +
17A LEU 3.0 0.3 + - - -
19A GLU* 2.8 42.7 + - + +
57A LEU* 4.8 15.5 - - + -
60A ARG* 4.3 4.7 - - - +
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Residues in contact with ASN 16 (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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12A GLU 3.3 16.8 - - - +
13A GLU* 2.9 8.2 + - - +
15A LYS* 1.3 87.8 - - + +
17A LEU* 1.3 66.5 + - - +
19A GLU* 3.6 25.5 - - - +
20A GLU* 3.7 11.6 + - - +
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Residues in contact with LEU 17 (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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6A LEU* 5.1 6.1 - - + -
9A TYR* 3.7 37.2 - - + +
13A GLU* 2.9 29.5 + - + +
14A LEU* 4.8 0.7 - - - -
16A ASN* 1.3 89.2 - - - +
18A LEU* 1.3 74.5 + - + +
19A GLU 3.3 1.1 - - - -
20A GLU* 3.0 28.1 + - - +
21A LYS* 3.2 14.7 + - - +
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Residues in contact with LEU 18 (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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6A LEU* 3.6 35.7 - - + +
9A TYR* 5.6 0.4 - - + -
14A LEU* 2.9 28.5 + - + +
17A LEU* 1.3 83.0 - - + +
19A GLU* 1.3 64.8 + - - +
21A LYS 3.7 0.3 + - - -
22A LYS* 3.1 23.4 + - - +
53A ILE* 3.2 42.5 - - + +
54A LYS* 5.0 2.7 - - - +
56A ILE* 3.4 28.0 - - + -
57A LEU* 3.7 27.1 - - + +
60A ARG* 4.6 4.7 - - - +
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Residues in contact with GLU 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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15A LYS* 2.8 27.6 + - + +
16A ASN* 3.6 21.3 - - - +
18A LEU* 1.3 76.8 - - - +
20A GLU* 1.3 73.9 + - - +
22A LYS* 3.2 14.9 + - - +
23A ARG* 2.8 61.9 + - - +
57A LEU* 4.9 6.0 - - + +
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Residues in contact with GLU 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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16A ASN* 3.7 13.6 + - - +
17A LEU* 3.0 16.3 + - - +
19A GLU* 1.3 91.2 - - - +
21A LYS* 1.3 59.5 + - + +
23A ARG* 3.1 12.7 - - - +
24A GLN* 2.8 52.7 + - + +
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Residues in contact with LYS 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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6A LEU* 6.0 0.4 - - + -
17A LEU* 3.2 11.9 + - + +
20A GLU* 1.3 79.8 - - + +
22A LYS* 1.3 63.7 + - - +
24A GLN* 3.0 25.7 + - + +
25A LEU 3.1 4.5 + - - -
46A THR* 5.0 11.3 + - - +
49A ASP* 3.9 19.9 + - - +
50A ILE* 2.9 34.4 - - + +
53A ILE* 3.7 49.6 - - + -
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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 LEU 3.1 19.1 + - - +
19A GLU* 3.2 11.0 + - - +
21A LYS* 1.3 74.9 - - - +
23A ARG* 1.3 64.2 + - - +
25A LEU* 3.8 3.6 + - - +
26A MET* 3.5 42.7 + - + +
50A ILE* 3.7 12.1 - - + +
54A LYS* 4.4 25.7 - - + +
57A LEU* 5.9 5.4 - - + +
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Residues in contact with ARG 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 GLU* 2.8 46.9 + - - +
20A GLU* 3.1 27.4 - - + +
22A LYS* 1.3 71.0 - - - +
24A GLN* 1.3 59.3 - - + +
26A MET* 2.8 35.7 + - - +
27A GLU* 2.8 58.9 + - + +
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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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20A GLU* 2.8 42.3 + - + +
21A LYS* 3.0 19.0 + - + +
23A ARG* 1.3 72.9 - - + +
25A LEU* 1.3 59.2 + - - +
27A GLU* 3.0 7.5 + - - -
28A LEU* 2.8 67.4 + - + +
42A LEU* 6.1 0.9 - - - +
46A THR* 4.5 10.7 + - + +
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Residues in contact with LEU 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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21A LYS 3.1 4.4 + - - +
22A LYS 4.1 2.9 - - - +
23A ARG 3.0 0.2 + - - -
24A GLN* 1.3 76.9 - - - +
26A MET* 1.3 77.7 + - + +
28A LEU 3.5 0.2 + - - -
29A ARG* 3.1 35.6 + - + +
43A ILE* 3.3 32.0 - - + +
46A THR* 4.3 2.9 - - + -
47A LYS* 3.3 41.3 - - + +
50A ILE* 3.5 37.8 - - + +
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Residues in contact with MET 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* 3.5 45.1 - - + +
23A ARG* 2.8 16.2 + - - +
25A LEU* 1.3 85.7 - - + +
27A GLU* 1.3 57.2 + - + -
29A ARG* 3.2 26.0 - - - +
30A PHE* 3.3 11.6 + - - +
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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 ARG* 2.8 73.6 + - + +
24A GLN* 3.8 7.2 - - - +
26A MET* 1.3 76.2 - - + +
28A LEU* 1.3 66.7 + - + +
30A PHE* 3.1 17.8 + - + +
31A GLN* 2.8 33.4 + - + +
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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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24A GLN* 2.8 49.8 + - - +
27A GLU* 1.3 80.7 - - + +
29A ARG* 1.3 61.0 + - - +
31A GLN* 2.8 33.9 + - - +
32A LEU 3.1 3.1 + - - -
37A LEU* 3.0 31.7 - - + +
42A LEU* 4.8 15.3 - - + -
43A ILE* 3.5 18.4 - - + -
46A THR* 4.0 28.7 - - + +
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Residues in contact with ARG 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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25A LEU* 3.1 27.0 + - + +
26A MET* 3.2 27.1 - - - +
28A LEU* 1.3 74.1 - - - +
30A PHE* 1.3 56.2 + - - +
32A LEU* 3.4 7.5 + - - +
33A ALA* 3.0 31.0 + - - +
37A LEU* 4.8 0.4 - - - -
43A ILE* 3.8 11.6 - - + +
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Residues in contact with PHE 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 MET 3.3 17.1 + - - +
27A GLU* 3.1 23.9 + - + +
29A ARG* 1.3 77.4 - - + +
31A GLN* 1.3 65.0 + - + +
33A ALA* 4.0 7.3 - - + +
34A MET* 3.3 44.7 + - + +
36A GLN* 5.2 8.1 - - - -
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Residues in contact with GLN 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* 2.8 15.8 + - + +
28A LEU* 2.8 31.5 + - - +
30A PHE* 1.3 76.7 - - + +
32A LEU* 1.3 53.9 + - - +
34A MET* 3.5 1.2 + - - +
35A GLY 2.8 14.4 + - - -
36A GLN* 2.7 63.8 + - + +
37A LEU* 3.5 20.7 + - + +
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Residues in contact with LEU 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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28A LEU 3.1 9.6 + - - +
29A ARG* 3.6 10.5 - - - +
31A GLN* 1.3 72.3 - - - +
33A ALA* 1.3 65.9 + - - +
34A MET 3.0 8.0 + - - +
35A GLY* 3.1 14.8 + - - -
37A LEU* 3.2 40.5 - - + +
38A LYS* 4.4 6.5 - - - -
40A THR* 4.5 18.4 - - + -
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Residues in contact with ALA 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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29A ARG* 3.0 17.6 + - - +
30A PHE* 4.0 10.3 - - + +
32A LEU* 1.3 81.7 - - - +
34A MET* 1.3 61.2 + - + +
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Residues in contact with MET 34 (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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30A PHE* 3.3 39.3 + - + +
31A GLN 3.6 7.2 - - - +
32A LEU 3.0 3.3 + - - +
33A ALA* 1.3 80.3 - - - +
35A GLY* 1.3 58.2 + - - +
36A GLN* 4.2 20.9 - - + +
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Residues in contact with GLY 35 (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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31A GLN 2.8 9.3 + - - -
32A LEU* 3.1 9.8 + - - -
34A MET* 1.3 75.4 - - - +
36A GLN* 1.3 60.6 + - - +
37A LEU 4.6 2.9 - - - -
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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