Contacts of the helix formed by residues 39 - 63 (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 ASN 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.5 19.1 - - + +
38A LYS* 1.3 74.3 - - - +
40A THR* 1.3 59.5 + - - +
41A SER* 3.1 14.5 + - - -
42A LEU* 2.8 50.5 + - + +
43A ILE* 3.6 2.9 + - - +
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Residues in contact with THR 40 (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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32A LEU* 4.5 21.8 - - + -
37A LEU* 5.5 2.7 - - + -
38A LYS 3.4 10.4 + - - +
39A ASN* 1.3 70.1 + - - +
41A SER* 1.3 66.0 + - - +
42A LEU 3.2 1.8 - - - -
43A ILE* 3.3 15.1 + - + +
44A LYS* 3.1 21.9 + - - +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 3.1 10.9 + - - -
40A THR* 1.3 74.6 + - - +
42A LEU* 1.3 66.6 + - - +
44A LYS* 3.0 9.9 + - - +
45A LEU* 3.0 38.6 + - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 6.1 0.9 - - - +
28A LEU* 4.8 15.7 - - + -
37A LEU* 5.2 6.5 - - + -
39A ASN* 2.8 32.6 + - + +
40A THR 3.2 0.2 - - - -
41A SER* 1.3 77.3 - - - +
43A ILE* 1.3 55.3 + - - +
45A LEU* 3.4 7.5 + - + +
46A THR* 2.7 56.2 + - - +
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Residues in contact with ILE 43 (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* 3.3 34.8 - - + +
28A LEU* 3.5 26.0 - - + -
29A ARG* 3.8 11.0 - - + +
37A LEU* 3.5 27.1 - - + -
39A ASN 3.6 3.0 + - - -
40A THR* 3.3 21.3 + - + +
42A LEU* 1.3 77.9 - - - +
44A LYS* 1.3 55.7 + - + +
46A THR* 3.0 6.8 + - + -
47A LYS* 2.8 45.5 + - + +
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Residues in contact with LYS 44 (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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40A THR 3.1 13.3 + - - +
41A SER* 3.0 12.5 + - - +
43A ILE* 1.3 80.0 - - + +
45A LEU* 1.3 71.7 + - + +
47A LYS* 3.5 16.7 - - - +
48A ARG* 3.2 44.9 - - - +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.0 34.9 + - - +
42A LEU* 3.5 9.6 - - + +
44A LYS* 1.3 85.8 - - + +
46A THR* 1.3 67.5 + - - +
48A ARG* 3.0 36.5 + - - +
49A ASP* 3.4 11.6 + - - +
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Residues in contact with THR 46 (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* 5.0 10.0 + - - +
24A GLN* 4.5 10.1 + - - +
25A LEU* 4.3 11.0 - - + +
28A LEU* 4.0 22.1 - - + +
42A LEU* 2.7 46.4 + - - +
43A ILE* 3.3 9.4 - - - +
45A LEU* 1.3 74.3 - - - +
47A LYS* 1.3 49.0 + - - +
49A ASP* 3.2 3.9 + - - +
50A ILE* 2.7 58.5 + - + +
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Residues in contact with LYS 47 (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* 3.3 34.2 - - + +
43A ILE* 2.8 28.2 + - + +
44A LYS* 3.5 15.3 - - + +
46A THR* 1.3 73.1 - - - +
48A ARG* 1.3 57.9 + - + +
50A ILE* 3.7 10.1 - - + +
51A ALA* 2.8 31.2 + - - +
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Residues in contact with ARG 48 (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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44A LYS* 3.2 43.0 - - - +
45A LEU* 3.0 24.0 + - - +
47A LYS* 1.3 76.1 - - + +
49A ASP* 1.3 58.1 + - - +
51A ALA* 3.3 5.7 + - - +
52A ARG* 2.9 25.7 + - - +
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Residues in contact with ASP 49 (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* 3.9 16.9 + - - +
45A LEU 3.4 7.4 + - - +
46A THR* 3.2 6.9 + - - +
47A LYS 3.2 0.2 - - - -
48A ARG* 1.3 77.7 - - + +
50A ILE* 1.3 56.3 + - - +
51A ALA 3.2 1.1 - - - -
52A ARG* 2.8 36.9 + - - +
53A ILE* 2.7 60.1 + - + +
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Residues in contact with ILE 50 (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* 2.9 53.2 - - + +
22A LYS* 3.7 6.7 - - + +
24A GLN* 4.8 0.2 - - + -
25A LEU* 3.5 25.4 - - + -
46A THR* 2.7 57.6 + - + +
47A LYS* 3.7 8.5 - - + +
49A ASP* 1.3 69.0 - - - +
51A ALA* 1.3 59.7 + - + +
54A LYS* 2.7 50.1 + - + +
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Residues in contact with ALA 51 (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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47A LYS 2.8 18.4 + - - +
48A ARG* 3.5 5.6 - - - +
50A ILE* 1.3 77.4 - - + +
52A ARG* 1.3 56.7 + - - +
54A LYS* 3.7 14.3 - - - +
55A THR* 2.9 36.7 + - - +
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Residues in contact with ARG 52 (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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1A MET 4.6 18.9 + - - +
2A LYS* 2.8 31.7 + - - +
3A ALA* 4.2 5.7 + - - +
5A GLU* 4.9 8.1 + - - -
6A LEU* 3.3 36.1 - - - +
48A ARG 2.9 11.7 + - - +
49A ASP* 2.8 56.4 + - - +
51A ALA* 1.3 74.9 - - - +
53A ILE* 1.3 62.2 + - - +
55A THR* 3.3 8.0 - - - +
56A ILE* 2.8 40.5 + - + +
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Residues in contact with ILE 53 (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* 3.5 30.3 - - + -
18A LEU* 3.2 50.0 - - + +
21A LYS* 3.7 33.0 - - + -
49A ASP* 2.7 60.7 + - + +
50A ILE 3.9 0.9 - - - +
52A ARG* 1.3 75.1 - - - +
54A LYS* 1.3 57.6 + - - +
56A ILE* 2.9 20.9 + - - +
57A LEU 3.1 10.2 + - - -
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Residues in contact with LYS 54 (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* 5.0 2.9 - - - +
22A LYS* 4.4 33.2 - - + -
50A ILE* 2.7 39.8 + - + +
51A ALA* 3.7 14.4 - - - +
53A ILE* 1.3 74.6 - - - +
55A THR* 1.3 66.2 + - - +
57A LEU* 3.5 9.9 + - - +
58A ARG* 3.1 20.9 + - + +
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Residues in contact with THR 55 (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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51A ALA* 2.9 24.0 + - - +
52A ARG* 3.3 8.5 - - - +
54A LYS* 1.3 83.6 + - - +
56A ILE* 1.3 57.4 + - + +
58A ARG* 2.9 10.0 + - + +
59A GLU* 2.8 57.7 + - + +
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Residues in contact with ILE 56 (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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1A MET 4.6 11.7 - - - +
2A LYS 5.4 0.4 - - - +
3A ALA* 3.6 28.7 - - + -
6A LEU* 3.5 26.0 - - + +
7A ARG* 4.6 5.6 - - + +
18A LEU* 3.4 19.5 - - + -
52A ARG* 2.8 26.9 + - + +
53A ILE* 2.9 11.9 + - - +
55A THR* 1.3 70.6 - - + +
57A LEU* 1.3 63.2 + - - +
59A GLU* 3.2 11.0 + - - +
60A ARG* 2.9 41.5 + - + +
65A ARG* 5.0 14.4 - - + +
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Residues in contact with LEU 57 (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* 4.8 15.9 - - + +
18A LEU* 3.7 23.3 - - + +
19A GLU* 4.9 7.0 - - + +
22A LYS* 5.9 5.2 - - + +
53A ILE 3.1 10.6 + - - +
54A LYS* 3.7 10.8 - - - +
55A THR 3.2 0.2 - - - -
56A ILE* 1.3 74.5 - - - +
58A ARG* 1.3 63.8 + - - +
60A ARG* 2.9 37.5 + - + +
61A GLU* 3.0 38.7 + - + +
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Residues in contact with ARG 58 (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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54A LYS* 3.1 14.9 + - + +
55A THR* 2.9 14.2 + - - +
57A LEU* 1.3 74.3 - - - +
59A GLU* 1.3 57.3 + - + +
61A GLU* 2.9 40.5 + - - +
62A LEU* 3.1 45.5 - - - +
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Residues in contact with GLU 59 (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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1A MET 5.7 1.2 - - - +
55A THR* 2.8 42.3 + - + +
56A ILE* 3.5 12.5 - - + +
58A ARG* 1.3 71.4 - - + +
60A ARG* 1.3 59.8 + - - +
62A LEU* 3.6 10.7 + - - +
63A GLY 3.5 2.9 + - - -
64A ILE* 2.9 59.2 + - + +
65A ARG* 3.9 24.1 + - + +
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Residues in contact with ARG 60 (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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7A ARG* 4.7 11.0 - - - +
11A ASP* 2.8 29.7 + - - -
14A LEU* 3.5 39.5 - - - +
15A LYS* 4.3 7.7 - - - +
18A LEU* 4.6 1.6 - - - +
56A ILE* 2.9 34.5 + - + +
57A LEU* 2.9 30.1 + - + +
59A GLU* 1.3 73.9 - - - +
61A GLU* 1.3 64.5 + - - +
63A GLY* 3.9 2.9 + - - -
65A ARG* 3.5 33.1 + - + +
66A ARG 3.9 14.6 - - - +
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Residues in contact with GLU 61 (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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57A LEU* 3.0 38.7 + - + +
58A ARG* 2.9 35.5 + - - +
60A ARG* 1.3 76.8 - - - +
62A LEU* 1.3 67.3 + - + +
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Residues in contact with LEU 62 (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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58A ARG* 3.1 66.0 + - - +
59A GLU* 3.8 2.2 - - - -
60A ARG 3.5 0.2 - - - -
61A GLU* 1.3 82.4 - - + +
63A GLY* 1.3 55.1 + - - +
64A ILE* 3.7 29.8 - - + -
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Residues in contact with GLY 63 (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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59A GLU 3.5 1.6 + - - -
60A ARG 3.9 4.9 + - - -
61A GLU 3.4 4.0 + - - -
62A LEU* 1.3 77.6 - - - +
64A ILE* 1.3 65.5 + - - +
65A ARG 3.2 3.9 + - - -
66A ARG* 3.8 17.6 + - - -
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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