Contacts of the helix formed by residues 54 - 81 (chain C) in PDB entry 2YMB
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 ASP 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C THR* 4.5 0.6 - - - +
53C LYS* 1.3 76.4 - - - +
55C ASN* 1.3 60.2 + - - +
56C THR* 3.0 16.3 + - - -
57C LYS* 2.8 59.1 + - + +
58C ARG* 2.8 32.4 + - - +
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Residues in contact with ASN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LYS 3.3 6.7 + - - -
54C ASP* 1.3 73.1 + - - +
56C THR* 1.3 61.1 + - - +
58C ARG* 3.8 23.4 + - - +
59C CYS* 3.5 19.9 + - - +
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ASP* 3.0 11.7 + - - -
55C ASN* 1.3 78.1 - - - +
57C LYS* 1.3 60.5 + - + +
58C ARG 3.2 0.2 - - - -
59C CYS* 3.2 6.1 + - - +
60C ASN* 3.0 47.0 + - - +
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Residues in contact with LYS 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C THR* 4.8 18.4 - - + -
54C ASP* 2.8 41.8 + - + +
56C THR* 1.3 71.3 - - + +
58C ARG* 1.3 65.8 + - - +
60C ASN* 3.2 12.2 + - - +
61C LEU* 3.0 35.5 + - + +
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Residues in contact with ARG 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 3.6 16.6 - - + +
52C THR* 3.5 34.7 + - - +
53C LYS* 3.7 13.7 - - - +
54C ASP 2.8 24.2 + - - +
55C ASN* 3.8 21.4 + - - +
56C THR 3.2 0.2 - - - -
57C LYS* 1.3 76.2 - - - +
59C CYS* 1.3 60.2 - - - +
62C ARG 3.7 4.7 + - - -
183F MET* 3.5 43.6 - - + +
184F GLU* 3.6 29.1 + - - +
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Residues in contact with CYS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ASN 3.5 10.9 + - - +
56C THR* 3.2 9.9 + - - +
57C LYS 3.2 0.4 - - - -
58C ARG* 1.3 77.8 - - - +
60C ASN* 1.3 66.5 + - - +
61C LEU 3.3 0.4 - - - -
62C ARG* 3.5 16.1 + - - +
63C GLU* 3.4 27.0 + - - +
183F MET* 5.3 2.2 - - - -
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Residues in contact with ASN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 3.0 40.1 + - - +
57C LYS* 3.2 12.6 + - - +
59C CYS* 1.3 78.7 - - - +
61C LEU* 1.3 65.9 + - + +
63C GLU* 3.4 22.3 + - - +
64C LYS* 3.4 14.3 + - + +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 4.3 16.6 - - + +
48C VAL* 4.0 17.5 - - + -
49C LEU* 3.7 48.5 - - + +
52C THR* 4.1 12.6 - - + +
57C LYS* 3.0 25.4 + - + +
59C CYS 3.3 0.2 - - - -
60C ASN* 1.3 81.8 - - + +
62C ARG* 1.3 59.0 + - - +
64C LYS* 3.3 12.3 + - + +
65C ILE* 2.8 40.4 + - + +
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 4.9 0.2 - - - +
58C ARG 3.7 3.7 + - - +
59C CYS* 3.5 16.1 + - - +
60C ASN 3.3 0.6 - - - -
61C LEU* 1.3 78.4 - - - +
63C GLU* 1.3 75.5 + - - +
65C ILE* 5.0 0.4 - - - -
66C SER* 2.7 66.1 + - - -
183F MET* 3.6 41.6 - - + +
187F LEU* 3.8 29.9 - - + +
190F ARG* 5.2 1.6 - - - +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C CYS* 3.4 24.3 - - - +
60C ASN* 3.4 13.2 + - - +
61C LEU 3.2 0.2 - - - -
62C ARG* 1.3 100.0 + - - +
64C LYS* 1.3 63.4 + - + +
66C SER* 4.4 2.0 - - - -
67C LYS* 3.1 31.5 + - - +
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ALA* 5.7 6.9 - - - +
19C LEU* 5.1 4.0 - - - +
45C LEU* 4.2 29.3 - - + +
60C ASN* 3.4 13.4 + - + +
61C LEU* 3.3 15.8 + - + +
63C GLU* 1.3 76.8 - - + +
65C ILE* 1.3 63.4 + - - +
67C LYS* 3.2 10.1 + - - +
68C TYR* 3.0 48.6 + - + -
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 4.2 13.2 - - + +
45C LEU* 3.5 48.2 - - + +
46C LEU* 4.0 8.1 - - + +
49C LEU* 3.9 26.2 - - + -
61C LEU* 2.8 27.4 + - + +
62C ARG 4.0 2.0 - - - +
64C LYS* 1.3 73.0 - - - +
66C SER* 1.3 52.5 + - - +
68C TYR* 3.3 6.8 + - - +
69C MET* 2.7 57.3 + - + +
187F LEU* 3.6 20.9 - - + -
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 2.7 52.4 + - - -
63C GLU* 4.4 1.8 - - - -
65C ILE* 1.3 76.5 - - - +
67C LYS* 1.3 58.7 + - - +
69C MET* 3.7 7.5 - - - +
70C ASP* 2.9 37.2 + - - +
187F LEU* 4.5 4.3 - - - -
190F ARG* 3.2 19.5 + - - +
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 3.1 24.7 + - - +
64C LYS* 3.4 10.0 - - - +
65C ILE 3.1 0.2 - - - -
66C SER* 1.3 76.0 - - - +
68C TYR* 1.3 76.3 + - + +
70C ASP* 3.2 17.3 + - - +
71C ARG* 3.3 13.3 + - - +
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Residues in contact with TYR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.6 42.8 - - + +
23C VAL* 4.2 16.3 - - + +
38C TYR* 3.7 33.3 - + + -
42C ILE* 3.8 19.4 - - + +
45C LEU* 4.8 2.9 - - + -
64C LYS* 3.0 49.8 + - + +
65C ILE* 3.9 3.4 - - - +
67C LYS* 1.3 84.6 - - + +
69C MET* 1.3 59.6 + - - +
71C ARG* 3.4 6.2 + - + +
72C ALA* 2.9 31.2 + - - +
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Residues in contact with MET 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ILE* 3.6 39.0 - - + +
65C ILE* 2.7 33.4 + - + +
66C SER* 3.7 7.2 - - - +
67C LYS 3.2 0.2 - - - -
68C TYR* 1.3 77.4 - - - +
70C ASP* 1.3 55.5 - - - +
72C ALA* 3.9 1.0 - - - +
73C GLU* 3.0 42.3 + - - +
187F LEU* 3.3 31.4 - - + +
190F ARG* 3.4 51.6 - - + +
191F LEU 4.1 1.8 - - - +
194F LEU* 4.3 8.5 - - - -
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Residues in contact with ASP 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER* 2.9 25.8 + - - +
67C LYS* 3.2 10.8 + - - +
69C MET* 1.3 77.6 - - - +
71C ARG* 1.3 61.4 + - - +
73C GLU* 4.0 6.2 - - - +
74C ASN* 2.8 37.2 + - - +
190F ARG* 2.9 22.7 + - - -
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASP* 2.8 42.6 + - - +
31C TYR* 3.4 15.4 - - - -
38C TYR* 3.7 19.3 - - + +
67C LYS 3.3 8.9 + - - +
68C TYR* 3.4 10.7 + - + +
70C ASP* 1.3 80.4 - - - +
72C ALA* 1.3 61.5 + - - +
74C ASN* 3.3 12.3 + - - +
75C ILE* 3.1 39.8 + - - +
78C TYR* 4.6 6.1 - - - -
88C TYR* 3.1 30.0 + - - -
91C GLN* 3.1 32.9 + - - +
93C LYS* 5.9 6.2 - - - +
239C ASP* 3.8 2.6 + - - -
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.3 24.2 - - + +
38C TYR* 3.9 21.5 - - + -
42C ILE* 4.3 2.5 - - + -
68C TYR 2.9 17.7 + - - +
69C MET 3.9 2.0 - - - +
71C ARG* 1.3 77.1 - - - +
73C GLU* 1.3 62.7 + - - +
75C ILE* 3.2 3.0 + - - -
76C LYS 3.2 17.3 + - - -
194F LEU* 3.7 30.2 - - + +
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Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C MET* 3.0 24.2 + - + +
70C ASP* 4.0 5.0 - - - +
72C ALA* 1.3 76.6 - - - +
74C ASN* 1.3 62.5 + - - +
76C LYS* 3.4 4.7 + - - +
77C LYS* 3.1 35.7 + - + +
190F ARG* 2.9 58.8 + - - +
193F ALA* 6.0 1.4 - - - +
194F LEU* 3.8 19.1 - - + -
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Residues in contact with ASN 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ASP* 2.8 27.8 + - - +
71C ARG* 3.6 16.5 - - - +
73C GLU* 1.3 75.1 - - - +
75C ILE* 1.3 60.6 + - - +
77C LYS* 3.2 31.6 + - - +
78C TYR* 2.9 55.4 + - + -
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ASP* 3.8 11.4 - - - +
31C TYR* 3.9 29.8 - - + +
34C ALA* 4.9 3.8 - - + -
35C LEU* 4.2 12.6 - - + -
38C TYR* 3.8 21.1 - - + -
71C ARG* 3.1 47.9 + - - +
72C ALA* 3.2 7.8 + - - +
74C ASN* 1.3 75.3 - - - +
76C LYS* 1.3 58.8 + - - +
78C TYR* 3.3 8.9 + - - +
79C LEU* 3.0 48.1 + - + +
88C TYR* 4.6 3.8 - - + -
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 4.0 18.6 - - + +
72C ALA 3.2 12.1 + - - +
73C GLU* 3.6 10.1 - - - +
75C ILE* 1.3 77.8 - - - +
77C LYS* 1.3 63.5 + - + +
79C LEU* 3.3 4.3 + - - +
80C ASP* 2.8 50.3 + - - +
193F ALA 3.5 25.1 - - - +
194F LEU* 4.2 18.8 - - + +
196F ASN* 2.8 34.9 + - - +
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Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C GLU* 3.1 21.4 + - + +
74C ASN* 3.2 31.7 + - - +
76C LYS* 1.3 79.6 - - + +
78C TYR* 1.3 62.0 + - + +
80C ASP* 3.6 5.4 + - - +
81C GLN* 2.9 45.4 + - - +
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ARG* 4.6 2.0 - - - -
74C ASN* 2.9 40.7 + - + +
75C ILE* 3.6 5.2 - - - +
77C LYS* 1.3 83.5 - - + +
79C LEU* 1.3 61.3 + - - +
81C GLN* 3.1 28.0 + - + +
82C GLU* 3.6 9.2 + - - +
87C LYS 5.4 0.2 + - - -
88C TYR* 3.3 46.1 + + + -
206C LYS* 4.5 23.6 - - + +
239C ASP* 3.5 24.4 + - + +
241C PHE* 3.5 35.7 - + + -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 4.5 14.4 - - + -
32C PRO* 4.4 30.5 - - + -
35C LEU* 4.3 15.5 - - + -
75C ILE* 3.0 38.0 + - + +
76C LYS* 3.9 4.3 - - - +
78C TYR* 1.3 77.8 - - + +
80C ASP* 1.3 64.1 + - - +
82C GLU* 3.4 37.2 - - - +
87C LYS* 6.1 0.9 - - - +
88C TYR* 5.0 11.4 - - + -
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LYS* 2.8 42.3 + - - +
77C LYS* 3.9 7.0 - - - +
78C TYR 3.2 0.4 - - - -
79C LEU* 1.3 79.5 - - - +
81C GLN* 1.3 61.1 + - - +
82C GLU* 3.0 11.4 + - - +
83C LYS* 3.1 33.9 + - - +
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Residues in contact with GLN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LYS* 2.9 35.9 + - - +
78C TYR* 3.1 19.7 + - + +
80C ASP* 1.3 77.9 - - - +
82C GLU* 1.3 54.2 + - - +
83C LYS* 3.0 31.6 + - + +
85C ASP* 2.9 37.5 - - - +
86C GLY* 2.9 11.9 + - - -
206C LYS* 5.1 12.8 + - - +
241C PHE* 5.7 2.5 - - + -
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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