Contacts of the helix formed by residues 50 - 75 (chain Q) 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 SER 50 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O LEU 4.9 1.0 + - - -
81O VAL 4.0 10.0 + - - -
83O CYS* 6.6 0.2 - - - -
49Q PRO* 1.3 75.1 - - - +
51Q GLY* 1.3 60.5 + - - +
52Q CYS* 3.1 20.6 + - - +
53Q ARG* 3.1 15.3 + - - +
54Q MET* 3.0 27.0 + - - +
68R ASP* 5.8 0.4 - - - -
83R CYS* 3.6 8.5 - - - -
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Residues in contact with GLY 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49Q PRO 3.6 2.6 + - - -
50Q SER* 1.3 73.5 + - - +
52Q CYS* 1.3 56.6 + - - +
54Q MET* 3.5 2.2 + - - +
55Q LYS* 3.0 28.1 + - - +
83R CYS* 3.8 11.1 - - - +
84R PRO* 3.6 27.2 - - - +
89R LEU* 3.9 6.4 - - - +
22S THR* 4.0 14.8 - - - +
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Residues in contact with CYS 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N TRP* 4.6 9.6 - - + -
50Q SER* 3.1 6.2 + - - +
51Q GLY* 1.3 74.5 - - - +
53Q ARG* 1.3 66.3 + - - +
56Q GLY 3.1 9.7 + - - -
68R ASP* 3.5 6.5 - - + +
69R ALA 2.9 41.4 + - - +
71R GLY* 3.4 29.8 - - - -
81R VAL* 4.4 3.4 - - - -
83R CYS* 2.0 45.5 - - - +
84R PRO* 4.2 0.9 - - - -
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Residues in contact with ARG 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77O PRO 3.8 2.8 + - - -
78O ASP 3.0 34.6 + - - +
79O LEU* 4.0 11.7 - - - +
80O GLY* 3.7 17.2 - - - +
49Q PRO* 5.1 0.2 - - + -
50Q SER* 3.1 23.2 + - - +
52Q CYS* 1.3 79.2 - - - +
54Q MET* 1.3 67.6 + - - +
56Q GLY* 3.1 2.9 + - - -
57Q LEU* 3.0 33.7 + - + +
66R PRO* 3.5 27.6 + - - +
67R PRO 3.1 16.9 + - - -
68R ASP* 2.9 40.7 + - - +
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Residues in contact with MET 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79O LEU* 4.1 4.9 - - + -
49Q PRO* 3.7 26.2 - - + -
50Q SER 3.0 19.6 + - - +
51Q GLY 3.8 4.7 - - - +
52Q CYS 3.3 0.2 - - - -
53Q ARG* 1.3 77.7 - - - +
55Q LYS* 1.3 56.0 + - - +
57Q LEU* 3.2 25.9 + - + +
58Q ILE* 2.8 35.4 + - - +
89R LEU* 4.2 13.2 - - + -
22S THR* 4.0 23.1 - - + +
25S ILE* 4.3 11.4 - - + -
26S ALA* 3.5 33.4 - - + +
29S LEU* 4.2 17.3 - - + -
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Residues in contact with LYS 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q GLY 3.0 18.1 + - - +
54Q MET* 1.3 75.5 - - - +
56Q GLY* 1.3 58.0 + - - +
58Q ILE* 4.2 5.2 - - + -
59Q ASP* 2.9 57.8 + - - +
69R ALA* 3.9 14.1 - - + +
70R ASP* 3.0 39.5 + - + +
84R PRO* 4.3 7.2 - - + -
88R LYS* 4.7 8.5 - - - +
89R LEU* 3.9 18.5 - - + +
92R THR* 4.1 30.7 - - + -
95R ARG* 5.9 1.0 - - - +
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Residues in contact with GLY 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Q CYS 3.1 9.5 + - - -
53Q ARG 3.1 7.6 + - - -
55Q LYS* 1.3 77.6 - - - +
57Q LEU* 1.3 60.3 + - - +
59Q ASP* 3.4 4.6 + - - +
60Q GLU* 3.1 18.9 + - - +
67R PRO* 3.6 33.9 - - - +
69R ALA* 3.9 14.5 - - - +
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Residues in contact with LEU 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O ASP* 3.9 35.7 - - + +
79O LEU* 3.9 27.1 - - + -
53Q ARG* 3.0 22.4 + - + +
54Q MET* 3.7 20.0 - - + +
56Q GLY* 1.3 72.6 - - - +
58Q ILE* 1.3 65.1 + - - +
60Q GLU* 3.3 20.3 + - - +
61Q VAL* 3.1 27.6 + - + +
67R PRO* 4.2 16.2 - - + -
29S LEU* 4.0 14.8 - - + -
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Residues in contact with ILE 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q MET* 2.8 20.7 + - - +
55Q LYS* 3.7 6.7 - - + +
57Q LEU* 1.3 76.0 - - - +
59Q ASP* 1.3 66.1 + - - +
61Q VAL* 3.3 3.6 + - - +
62Q ASP* 3.0 22.3 + - - +
89R LEU* 3.8 29.6 - - + +
92R THR* 4.0 14.4 - - + -
93R LEU* 3.9 32.8 - - + -
96R GLN* 3.3 27.0 + - - +
25S ILE* 3.9 12.1 - - + -
29S LEU* 4.1 21.3 - - + +
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Residues in contact with ASP 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Q LYS* 2.9 53.0 + - - +
56Q GLY* 3.6 6.1 - - - +
58Q ILE* 1.3 79.1 - - - +
60Q GLU* 1.3 56.3 + - - +
62Q ASP* 3.3 5.9 + - - +
63Q GLN* 2.9 31.5 + - - +
69R ALA* 4.0 15.1 - - + +
70R ASP* 4.9 1.2 - - - +
96R GLN* 4.2 9.9 - - - +
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Residues in contact with GLU 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Q GLY 3.1 12.6 + - - +
57Q LEU* 3.5 19.8 - - - +
58Q ILE 3.3 0.2 - - - -
59Q ASP* 1.3 77.2 - - - +
61Q VAL* 1.3 64.5 + - + +
63Q GLN* 3.4 6.8 + - - +
64Q ASP* 3.0 24.4 + - + +
64R ARG* 2.5 52.2 + - - -
67R PRO* 4.6 6.3 - - + +
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Residues in contact with VAL 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q LEU* 3.1 14.8 + - + +
58Q ILE 3.3 7.4 + - - +
60Q GLU* 1.3 80.5 - - + +
62Q ASP* 1.3 56.8 + - - +
64Q ASP* 3.3 7.0 + - - +
65Q PHE* 3.0 60.6 + - + -
29S LEU* 4.1 27.4 - - + -
32S TYR* 4.4 7.9 - - + -
33S GLN* 3.9 21.5 - - + -
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Residues in contact with ASP 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Q ILE 3.0 16.7 + - - +
59Q ASP* 3.8 5.6 - - - +
61Q VAL* 1.3 78.7 - - - +
63Q GLN* 1.3 58.8 + - - +
65Q PHE* 3.9 4.8 - - - +
66Q THR* 2.9 44.6 + - - -
96R GLN* 3.6 46.8 - - - +
100R ILE* 4.2 16.1 - - - +
32S TYR* 4.9 2.7 + - - -
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Residues in contact with GLN 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q ASP 2.9 18.1 + - - +
60Q GLU* 3.7 7.5 - - - +
62Q ASP* 1.3 78.3 - - - +
64Q ASP* 1.3 63.5 + - - +
66Q THR* 3.9 4.7 - - - -
67Q SER* 2.9 41.6 + - - -
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Residues in contact with ASP 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Q GLU* 3.0 15.8 + - + +
61Q VAL* 3.3 11.2 + - - +
63Q GLN* 1.3 83.7 + - - +
65Q PHE* 1.3 66.0 + - - +
67Q SER* 3.7 3.2 - - - -
68Q ARG* 2.9 72.1 + - - +
33S GLN* 4.9 3.5 - - - +
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Residues in contact with PHE 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Q VAL* 3.0 35.8 + - + +
62Q ASP* 4.0 4.7 - - - +
64Q ASP* 1.3 95.3 - - - +
66Q THR* 1.3 61.8 + - - +
68Q ARG* 3.3 12.9 + - - +
69Q ILE* 3.0 31.5 + - + +
100R ILE* 4.0 16.2 - - + -
32S TYR* 4.0 20.2 - + - -
33S GLN* 3.5 46.9 - - + -
36S VAL* 3.5 28.5 - - + -
37S ASP 4.1 3.6 - - - -
40S LEU* 3.5 22.4 - - + -
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Residues in contact with THR 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Q ASP* 2.9 33.3 + - - -
63Q GLN* 3.9 5.8 - - - +
65Q PHE* 1.3 75.1 - - - +
67Q SER* 1.3 63.8 + - - +
69Q ILE* 3.3 6.3 + - - +
70Q ASN* 3.0 39.3 + - - +
100R ILE* 4.2 14.4 - - - +
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Residues in contact with SER 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q GLN* 2.9 37.0 + - - +
64Q ASP* 3.7 5.6 - - - -
66Q THR* 1.3 78.1 - - - +
68Q ARG* 1.3 59.1 + - - +
70Q ASN* 3.3 7.6 + - - +
71Q LYS* 2.9 55.3 + - - +
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Residues in contact with ARG 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Q ASP* 2.9 52.6 + - - +
65Q PHE* 3.9 15.8 - - - +
66Q THR 3.3 0.2 - - - -
67Q SER* 1.3 78.3 - - - +
69Q ILE* 1.3 62.8 + - - +
71Q LYS* 3.4 10.8 + - + +
72Q LEU* 3.1 29.3 + - + +
33S GLN* 5.2 0.6 + - - -
37S ASP* 2.9 34.1 + - - -
40S LEU* 3.4 31.6 - - + +
41S ARG* 3.9 5.7 - - - +
44S GLU* 2.9 41.7 + - - +
48S TYR* 4.3 1.1 + - - -
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Residues in contact with ILE 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65Q PHE* 3.0 16.7 + - + +
66Q THR* 3.7 5.8 - - - +
68Q ARG* 1.3 75.4 - - - +
70Q ASN* 1.3 65.6 + - - +
72Q LEU* 3.2 9.3 + - - +
73Q ARG* 3.0 53.5 + - - +
100R ILE* 3.7 42.6 - - + +
103R SER* 3.9 22.7 - - - +
104R ILE* 4.4 5.8 - - + -
107R LEU* 4.3 12.3 - - + +
40S LEU* 4.0 17.7 - - + -
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Residues in contact with ASN 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q THR* 3.0 35.2 + - - +
67Q SER* 3.7 6.3 - - - +
69Q ILE* 1.3 79.5 - - - +
71Q LYS* 1.3 62.0 + - + +
73Q ARG* 3.2 27.7 + - - +
74Q ASP* 3.0 30.4 + - - +
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Residues in contact with LYS 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Q SER* 2.9 37.8 + - - +
68Q ARG* 3.8 8.7 - - + +
70Q ASN* 1.3 76.1 - - + +
72Q LEU* 1.3 61.9 + - - +
74Q ASP* 3.2 14.7 + - - +
75Q SER* 3.0 25.3 + - - -
48S TYR* 3.3 17.5 - - + +
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Residues in contact with LEU 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Q ARG 3.1 21.2 + - - +
69Q ILE* 3.2 6.3 + - - +
71Q LYS* 1.3 76.8 - - - +
73Q ARG* 1.3 62.1 + - - +
75Q SER* 2.9 14.6 + - - -
76Q LEU* 3.3 14.8 + - - +
107R LEU* 3.8 21.3 - - + -
40S LEU* 3.9 23.8 - - + -
43S LEU* 3.6 48.9 - - + +
44S GLU* 3.7 17.5 - - + +
47S LEU* 4.2 11.8 - - + +
48S TYR* 3.7 19.7 - - + +
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Residues in contact with ARG 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q ILE* 3.0 29.2 + - + +
70Q ASN* 3.2 25.6 + - - +
72Q LEU* 1.3 76.8 - - - +
74Q ASP* 1.3 61.3 - - - +
75Q SER 3.1 0.9 + - - -
76Q LEU* 3.2 30.7 + - + +
77Q PHE 4.7 1.0 + - - -
103R SER* 3.6 31.9 + - - +
106R ASP* 6.2 1.0 - - - +
107R LEU* 4.2 17.3 - - + +
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Residues in contact with ASP 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Q ASN* 3.0 19.9 + - - +
71Q LYS* 3.5 17.7 - - - +
72Q LEU 3.2 0.2 - - - -
73Q ARG* 1.3 77.7 - - - +
75Q SER* 1.3 58.3 + - - +
76Q LEU 3.5 0.6 + - - -
77Q PHE 4.5 1.7 + - - -
78Q ASN 3.0 24.8 + - - +
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Residues in contact with SER 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71Q LYS 3.0 6.6 + - - -
72Q LEU 2.9 10.7 + - - -
74Q ASP* 1.3 77.4 - - - +
76Q LEU* 1.3 65.7 + - - +
77Q PHE 3.2 2.5 - - - -
78Q ASN* 3.2 16.8 + - - +
47S LEU* 4.0 25.3 - - - +
48S TYR* 2.9 37.1 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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