Contacts of the helix formed by residues 21 - 45 (chain P) in PDB entry 1JY3
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 21 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45N ASN* 4.9 5.2 + - - +
48N CYS* 3.9 9.4 - - - -
86O GLY* 5.1 0.2 - - - -
20P PRO* 1.3 78.5 - - - +
22P THR* 1.3 60.9 + - - +
23P CYS* 3.1 18.7 + - - +
24P GLY* 3.1 12.5 + - - +
25P ILE* 3.1 25.2 + - - +
85R THR* 3.9 21.1 - - + +
15S PHE 4.8 0.6 + - - -
17S SER* 4.1 10.9 + - - +
19S CYS* 3.6 32.1 - - + -
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Residues in contact with THR 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N CYS* 3.0 18.9 - - - +
49N PRO* 2.6 36.3 + - - +
51N GLY* 4.0 12.3 - - - +
54N MET* 4.0 9.7 - - + +
84O PRO 5.2 1.3 - - - +
86O GLY* 5.2 4.9 - - - +
89O LEU* 3.8 27.6 - - + -
21P THR* 1.3 72.0 - - - +
23P CYS* 1.3 60.2 + - - +
25P ILE* 3.6 7.4 - - + +
26P ALA* 2.8 29.1 + - - +
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Residues in contact with CYS 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N TRP* 3.5 25.4 - - + -
45N ASN* 3.3 33.9 - - - +
47N LYS 3.3 12.3 - - - -
48N CYS* 2.0 47.4 - - - +
21P THR* 3.1 6.5 + - - +
22P THR* 1.3 75.9 - - - +
24P GLY* 1.3 60.1 + - - +
26P ALA 3.3 0.2 + - - -
27P ASP* 2.8 37.4 + - - -
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Residues in contact with GLY 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P THR* 3.1 14.1 + - - -
23P CYS* 1.3 77.7 - - - +
25P ILE* 1.3 62.0 + - - +
27P ASP* 4.0 5.4 - - - +
28P PHE* 2.9 26.0 + - - +
14S ARG 5.1 0.7 - - - +
15S PHE* 3.4 29.9 - - - +
16S GLY* 5.1 2.2 - - - -
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Residues in contact with ILE 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N MET* 4.2 14.1 - - + -
58N ILE* 3.8 28.7 - - + -
86O GLY* 3.5 25.1 - - - +
89O LEU* 3.8 16.4 - - + -
90O GLN* 3.7 16.6 - - + +
93O LEU* 4.0 5.6 - - + +
20P PRO* 4.2 6.1 - - + -
21P THR 3.1 15.0 + - - +
22P THR* 3.6 13.7 - - - +
23P CYS 3.2 0.2 - - - -
24P GLY* 1.3 77.5 - - - +
26P ALA* 1.3 56.6 + - - +
28P PHE* 3.3 1.9 + - - +
29P LEU* 2.9 27.9 + - - +
15S PHE* 3.8 22.9 - - + -
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Residues in contact with ALA 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N TRP* 3.8 24.0 - - + -
49N PRO* 4.5 0.4 - - + -
54N MET* 3.6 27.8 - - + -
22P THR 2.8 22.6 + - - +
23P CYS 3.8 0.2 - - - +
25P ILE* 1.3 73.1 - - - +
27P ASP* 1.3 59.6 + - - +
29P LEU* 3.4 3.0 + - - +
30P ASN* 2.9 29.8 + - - +
79R LEU* 4.4 10.3 - - + -
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Residues in contact with ASP 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N TRP* 3.0 35.9 + - - -
45N ASN* 4.5 4.0 + - - -
23P CYS 2.8 22.6 + - - +
24P GLY* 4.0 5.5 - - - +
26P ALA* 1.3 70.7 - - - +
28P PHE* 1.3 65.8 + - - +
30P ASN* 3.4 7.6 + - - +
31P ASN* 3.2 22.3 + - - +
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Residues in contact with PHE 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O LEU* 4.0 21.5 - - + -
94O VAL* 6.0 0.2 - - + -
97O GLU* 3.7 29.4 - - + -
24P GLY 2.9 19.0 + - - +
25P ILE 3.7 3.1 - - - +
27P ASP* 1.3 77.2 - - - +
29P LEU* 1.3 66.0 + - - +
31P ASN* 3.2 9.1 + - + +
32P TYR* 2.9 37.7 + + + +
14S ARG* 3.6 46.0 + - + +
15S PHE* 3.4 44.2 - + + -
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Residues in contact with LEU 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N MET* 4.0 22.0 - - + -
57N LEU* 4.1 18.8 - - + +
58N ILE* 4.0 19.5 - - + +
61N VAL* 4.2 27.1 - - + -
93O LEU* 4.1 25.1 - - + -
25P ILE 2.9 17.7 + - - +
26P ALA* 3.6 4.9 - - - +
27P ASP 3.3 0.2 - - - -
28P PHE* 1.3 82.5 - - - +
30P ASN* 1.3 58.0 + - - +
32P TYR* 4.2 11.4 - - + -
33P GLN* 2.8 36.9 + - + +
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Residues in contact with ASN 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P ALA 2.9 18.5 + - - +
27P ASP* 3.7 8.7 - - - +
28P PHE 3.2 0.2 - - - -
29P LEU* 1.3 77.8 - - - +
31P ASN* 1.3 62.5 + - - +
33P GLN* 4.1 3.0 + - - +
34P THR* 2.9 40.4 + - - -
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Residues in contact with ASN 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O ARG* 4.6 9.1 - - - +
27P ASP 3.2 11.6 + - - +
28P PHE* 3.7 10.0 + - - +
30P ASN* 1.3 81.9 + - - +
32P TYR* 1.3 63.0 + - - +
34P THR* 3.9 4.3 - - - -
35P SER* 3.0 32.6 + - - -
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Residues in contact with TYR 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N VAL* 4.3 9.0 - - + -
62N ASP* 4.8 2.8 + - - -
65N PHE* 4.3 13.8 - + - -
93O LEU* 4.3 17.7 - - + -
96O GLN* 3.9 6.9 + - - +
97O GLU* 3.7 40.0 + - + +
100O ILE* 3.3 36.6 - - + +
101O ARG* 4.0 21.5 - - + +
28P PHE* 2.9 30.8 + + + +
29P LEU* 3.8 16.6 - - + +
31P ASN* 1.3 79.9 - - - +
33P GLN* 1.3 64.8 + - - +
35P SER* 3.8 0.5 - - - -
36P VAL* 3.0 46.9 + - + +
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Residues in contact with GLN 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N VAL* 3.7 33.1 - - + +
64N ASP* 5.0 3.1 - - - +
65N PHE* 3.4 27.6 - - + -
68N ARG* 5.0 0.5 + - - -
29P LEU* 2.8 23.9 + - + +
30P ASN* 4.1 3.8 - - - +
32P TYR* 1.3 75.0 - - - +
34P THR* 1.3 69.3 + - - +
37P ASP* 2.9 41.0 + - - +
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Residues in contact with THR 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P ASN* 2.9 33.4 + - - -
31P ASN* 3.9 4.3 - - - -
33P GLN* 1.3 86.7 + - - +
35P SER* 1.3 63.6 + - - +
37P ASP* 3.8 3.5 - - - +
38P LYS* 3.1 24.7 + - + +
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Residues in contact with SER 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O ARG* 2.9 32.2 + - - -
31P ASN* 3.0 22.9 + - - -
32P TYR 3.8 0.4 - - - -
34P THR* 1.3 75.7 - - - +
36P VAL* 1.3 64.2 + - - +
38P LYS* 3.3 9.3 + - - +
39P ASP* 3.2 26.3 + - - +
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Residues in contact with VAL 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N PHE* 3.5 31.0 - - + -
100O ILE* 4.0 7.6 - - + -
101O ARG* 3.7 25.6 - - - +
104O ILE* 3.3 23.8 - - + -
32P TYR* 3.0 41.9 + - + +
35P SER* 1.3 73.5 - - - +
37P ASP* 1.3 66.3 + - - +
39P ASP* 3.1 7.8 + - - +
40P LEU* 2.9 29.4 + - + +
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Residues in contact with ASP 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65N PHE* 3.8 8.7 - - + -
68N ARG* 2.9 35.6 + - - +
33P GLN* 2.9 38.0 + - - +
34P THR* 3.8 4.7 - - - +
36P VAL* 1.3 77.4 - - - +
38P LYS* 1.3 58.4 + - - +
40P LEU* 3.3 0.8 + - - -
41P ARG* 2.8 52.0 + - - +
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Residues in contact with LYS 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P THR* 3.1 18.5 + - + +
35P SER* 3.6 7.2 - - - +
36P VAL 3.2 0.2 - - - -
37P ASP* 1.3 79.0 - - - +
39P ASP* 1.3 72.4 + - - +
41P ARG* 3.4 18.3 + - + +
42P THR* 3.2 29.2 + - - +
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Residues in contact with ASP 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O ARG* 4.4 12.1 + - - -
104O ILE* 4.0 23.6 - - + +
105O GLU* 5.0 2.9 - - - +
108O ARG* 2.7 36.1 + - - +
35P SER* 3.2 13.5 + - - +
36P VAL* 3.1 10.8 + - - +
38P LYS* 1.3 90.9 - - - +
40P LEU* 1.3 62.6 + - - +
42P THR* 3.4 6.9 + - - -
43P LEU* 3.2 26.6 + - - +
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Residues in contact with LEU 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N PHE* 3.5 38.1 - - + +
68N ARG* 3.4 37.2 - - + +
69N ILE* 4.0 19.3 - - + -
72N LEU* 3.7 26.0 - - + -
104O ILE* 4.0 17.0 - - + -
107O LEU* 5.0 0.7 - - + -
36P VAL* 2.9 22.4 + - + +
37P ASP 3.7 0.2 - - - +
39P ASP* 1.3 75.4 - - - +
41P ARG* 1.3 60.6 + - - +
43P LEU* 3.1 7.3 + - + +
44P GLU* 2.8 35.9 + - - +
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Residues in contact with ARG 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N ARG* 4.3 2.5 - - - +
37P ASP* 2.8 38.7 + - - +
38P LYS* 3.6 17.3 - - - +
39P ASP 3.3 0.2 - - - -
40P LEU* 1.3 76.6 - - - +
42P THR* 1.3 64.1 + - - +
44P GLU* 3.3 13.8 + - - +
45P GLY* 3.0 21.0 + - - -
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Residues in contact with THR 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O ARG* 6.1 2.5 - - - +
38P LYS* 3.2 18.7 + - - +
39P ASP* 3.7 10.0 - - - -
40P LEU 3.2 0.2 - - - -
41P ARG* 1.3 78.6 - - - +
43P LEU* 1.3 68.0 + - + +
45P GLY* 3.2 11.7 + - - -
46P ILE* 3.5 20.7 + - + +
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Residues in contact with LEU 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72N LEU* 3.9 25.1 - - + +
76N LEU* 6.3 0.2 - - + -
104O ILE* 4.3 20.2 - - + +
107O LEU* 4.0 30.7 - - + +
108O ARG* 4.2 24.5 - - + +
111O VAL* 4.0 30.2 - - + +
39P ASP 3.2 15.4 + - - +
40P LEU* 3.1 10.1 + - + +
42P THR* 1.3 81.1 - - + +
44P GLU* 1.3 61.1 + - - +
46P ILE* 3.3 28.6 + - + +
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Residues in contact with GLU 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68N ARG* 2.9 60.1 + - - +
71N LYS* 6.1 1.2 - - - +
72N LEU* 4.1 24.6 - - + +
40P LEU* 2.8 24.6 + - - +
41P ARG* 3.6 8.6 - - - +
42P THR 3.3 0.2 - - - -
43P LEU* 1.3 72.3 - - - +
45P GLY* 1.3 57.9 + - - +
46P ILE 3.3 5.0 - - - +
47P LEU* 5.8 1.6 - - - +
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Residues in contact with GLY 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P ARG 3.0 13.6 + - - -
42P THR 3.2 6.6 + - - -
44P GLU* 1.3 76.8 - - - +
46P ILE* 1.3 63.1 + - - +
47P LEU* 3.6 13.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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