Contacts of the helix formed by residues 42 - 69 (chain C) in PDB entry 3DVA
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 42 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLU* 5.5 1.2 + - - +
41C LEU* 1.3 76.3 - - - +
43C ASP* 1.3 65.5 + - - +
44C GLU* 3.6 8.8 + - - +
45C GLN* 3.0 33.9 + - - +
46C LEU* 2.9 21.6 + - - +
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Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU 5.0 0.9 - - - +
42C SER* 1.3 74.9 - - - +
44C GLU* 1.3 60.1 + - - +
46C LEU* 3.5 8.8 + - - +
47C LYS* 3.1 32.0 + - - +
306C LYS* 5.4 3.3 + - - -
308C LEU* 3.5 45.5 - - + +
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C SER* 3.1 8.8 + - - +
43C ASP* 1.3 81.1 - - - +
45C GLN* 1.3 58.9 + - + +
47C LYS* 3.6 19.9 + - - +
48C GLU* 3.1 25.5 + - - +
51C ARG* 3.9 14.1 + - - +
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Residues in contact with GLN 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLU 4.1 2.6 - - - +
41C LEU* 3.4 23.9 - - + +
42C SER* 3.0 35.4 + - - +
44C GLU* 1.3 78.6 - - + +
46C LEU* 1.3 65.2 + - - +
48C GLU* 3.3 2.1 + - - -
49C LEU* 2.9 22.5 + - - +
90C PHE* 3.5 31.0 - - + -
242C TYR* 5.5 2.0 + - - -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MET* 5.1 6.5 - - + -
41C LEU* 3.8 41.7 - - + +
42C SER 2.9 14.5 + - - +
43C ASP* 3.7 11.9 - - - +
45C GLN* 1.3 77.6 - - - +
47C LYS* 1.3 62.1 + - - +
49C LEU* 3.4 2.5 + - + +
50C MET* 3.1 17.8 + - - +
239C LEU* 4.1 9.4 - - + -
299C PHE* 3.5 29.3 - - + -
302C PHE* 4.2 20.4 - - + -
303C LEU* 3.8 13.0 - - + -
306C LYS* 4.5 8.7 - - + +
308C LEU* 4.1 21.1 - - + -
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASP* 3.1 22.8 + - - +
44C GLU* 3.7 19.7 - - - +
46C LEU* 1.3 76.9 - - - +
48C GLU* 1.3 57.5 + - - +
50C MET* 3.0 9.0 + - - +
51C ARG* 2.8 53.9 + - - +
303C LEU* 4.8 2.2 - - + -
308C LEU* 2.6 52.6 + - + +
309C TRP* 4.0 8.0 - - + -
313C GLU* 2.8 31.6 + - - +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU 3.1 14.9 + - - +
45C GLN* 3.6 6.7 - - - +
47C LYS* 1.3 78.6 - - - +
49C LEU* 1.3 63.5 + - - +
51C ARG* 3.2 33.3 + - - +
52C ARG* 2.9 62.0 + - - +
90C PHE* 3.7 22.7 - - + -
110C TRP* 5.0 2.6 - - - -
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 5.0 7.6 - - + -
45C GLN 2.9 16.1 + - - +
46C LEU* 3.7 5.8 - - - +
47C LYS 3.2 0.2 - - - -
48C GLU* 1.3 75.7 - - - +
50C MET* 1.3 63.8 + - - +
52C ARG* 3.4 2.8 + - - +
53C MET* 3.1 38.2 + - + +
86C ILE* 4.0 13.0 - - + -
87C ALA* 3.8 31.0 - - + +
90C PHE* 3.9 32.2 - - + -
238C PRO* 4.0 25.1 - - + +
239C LEU* 4.9 7.2 - - + -
242C TYR* 5.3 3.1 - - + -
299C PHE* 4.1 12.1 - - + -
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Residues in contact with MET 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU 3.1 5.2 + - - +
47C LYS 3.0 9.5 + - - +
49C LEU* 1.3 73.2 - - - +
51C ARG* 1.3 65.9 + - - +
53C MET* 3.1 14.7 + - - +
54C VAL* 2.9 46.7 + - + +
296C LEU* 3.8 25.6 - - + +
299C PHE* 3.6 23.3 - - + -
300C ARG* 3.8 22.4 - - + +
303C LEU* 3.5 24.2 - - + -
309C TRP* 3.6 36.3 - - + +
314C GLU* 4.0 4.7 - - - +
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Residues in contact with ARG 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 3.9 18.8 + - - +
47C LYS* 2.8 39.0 + - - +
48C GLU* 3.2 51.5 + - - +
50C MET* 1.3 77.2 - - - +
52C ARG* 1.3 53.2 + - + +
54C VAL* 3.3 0.4 + - - -
55C TYR* 2.8 36.6 + - - +
309C TRP* 3.7 15.4 - - + -
313C GLU* 5.0 7.6 + - - -
317C VAL* 3.5 37.3 - - + +
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLU* 2.9 46.0 + - - +
49C LEU 3.8 2.0 - - - +
50C MET 3.2 0.2 - - - -
51C ARG* 1.3 76.4 - - + +
53C MET* 1.3 54.2 + - - +
55C TYR* 3.6 1.2 - - - +
56C THR* 2.7 36.9 + - - -
86C ILE* 3.6 20.4 - - + -
89C HIS* 3.5 33.1 + - - -
90C PHE* 3.9 30.1 - - - +
110C TRP* 3.7 52.0 + - + +
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Residues in contact with MET 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 3.1 29.5 + - + +
50C MET* 3.1 9.1 + - - +
52C ARG* 1.3 73.9 - - - +
54C VAL* 1.3 64.8 + - - +
56C THR 3.6 0.3 + - - -
57C ARG* 3.2 18.4 + - - +
82C GLU* 3.4 25.6 - - + +
83C ALA* 4.2 17.5 - - - -
86C ILE* 3.9 21.5 - - + -
238C PRO* 3.8 31.9 - - + -
295C PRO* 4.8 6.5 - - - +
296C LEU* 3.7 15.1 - - + +
299C PHE* 3.5 37.2 - - + -
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Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C MET* 2.9 47.8 + - + +
51C ARG* 3.7 3.6 - - - +
53C MET* 1.3 73.2 - - - +
55C TYR* 1.3 68.0 + - - +
57C ARG* 3.1 10.5 + - - +
58C ILE* 3.0 25.9 - - + +
296C LEU* 3.9 12.1 - - + -
309C TRP* 4.4 2.7 - - + -
314C GLU* 4.1 23.8 - - + +
317C VAL* 4.2 13.7 - - + -
318C ILE* 3.8 30.5 - - + +
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Residues in contact with TYR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ARG 2.8 19.0 + - - +
52C ARG 3.6 5.6 - - - +
54C VAL* 1.3 79.0 - - - +
56C THR* 1.3 58.8 + - - +
58C ILE* 3.3 4.4 + - - +
59C LEU* 3.0 33.7 + - + -
109C ILE* 6.0 5.4 - - + -
110C TRP* 3.7 32.8 - + + -
115C LEU* 4.0 14.2 - - + +
317C VAL* 4.3 14.6 - - + -
320C GLN* 4.7 8.5 - - + -
321C ALA* 3.7 36.1 + - + +
324C GLU* 2.3 47.1 + - - +
325C ILE* 4.6 11.2 - - + -
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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
----------------------------------------------------------
52C ARG 2.7 22.9 + - - -
53C MET 3.9 4.5 - - - -
54C VAL 3.2 0.2 - - - -
55C TYR* 1.3 73.9 - - - +
57C ARG* 1.3 66.0 + - - +
59C LEU* 3.4 12.3 + - + +
60C ASP* 3.0 22.3 + - - +
78C THR* 4.1 10.4 + - - +
82C GLU* 4.3 9.6 - - + -
85C GLN* 4.7 3.6 - - - +
86C ILE* 3.3 14.9 - - + +
106C PRO* 3.8 31.4 - - + -
110C TRP* 3.3 20.6 + - - -
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C MET 3.2 12.4 + - - +
54C VAL 3.1 10.0 + - - +
56C THR* 1.3 76.7 - - - +
58C ILE* 1.3 67.0 + - + +
60C ASP* 3.2 7.5 + - - +
61C GLN* 3.0 42.8 + - - +
79C ALA* 3.9 16.5 - - - +
80C GLY* 3.7 10.9 - - - +
82C GLU* 2.5 43.7 + - - -
268C TYR* 4.2 8.0 - - - -
294C ASP* 2.9 42.0 + - - -
295C PRO* 4.3 0.2 - - - +
296C LEU* 3.5 25.5 - - + +
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.0 28.4 + - + +
55C TYR* 3.6 6.7 - - - +
57C ARG* 1.3 78.4 - - + +
59C LEU* 1.3 55.1 + - - +
61C GLN* 3.1 20.5 + - + +
62C ARG* 2.7 52.3 + - + +
318C ILE* 3.8 45.5 - - + -
321C ALA* 3.8 21.8 - - + -
322C LYS* 4.2 17.3 - - + +
325C ILE* 4.9 0.4 - - + -
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 3.0 23.2 + - + +
56C THR* 3.5 15.3 - - + +
58C ILE* 1.3 77.1 - - - +
60C ASP* 1.3 53.3 + - - +
62C ARG* 3.2 1.3 + - - -
63C SER* 2.7 53.9 + - - +
75C TYR* 5.3 2.9 - - + +
105C VAL* 5.8 3.8 - - + -
106C PRO* 5.0 18.4 - - + -
109C ILE* 5.0 13.2 - - + -
110C TRP* 6.4 0.4 - - - +
115C LEU* 4.0 15.7 - - + -
119C PHE* 4.0 16.4 - - + -
325C ILE* 3.6 32.1 - - + +
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR 3.0 12.4 + - - +
57C ARG 3.3 10.1 - - - +
59C LEU* 1.3 77.3 - - - +
61C GLN* 1.3 65.0 + - - +
63C SER* 3.1 2.3 + - - -
64C ILE* 2.9 43.7 + - - +
75C TYR* 2.4 30.6 + - - +
77C PRO* 3.1 8.0 - - - +
78C THR* 2.8 23.5 + - - +
79C ALA* 3.0 35.8 + - + +
269C GLY* 5.8 0.7 + - - -
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Residues in contact with GLN 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ARG* 3.0 34.1 + - + +
58C ILE* 3.5 24.4 - - + +
60C ASP* 1.3 82.3 - - + +
62C ARG* 1.3 67.1 + - + +
64C ILE* 3.7 7.8 + - + +
65C SER* 3.3 22.0 + - - -
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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
----------------------------------------------------------
58C ILE* 2.7 40.7 + - + +
59C LEU 3.7 3.4 - - - +
61C GLN* 1.3 75.8 + - - +
63C SER* 1.3 59.3 + - - +
65C SER* 3.5 28.0 + - - -
66C LEU* 3.0 51.8 + - - +
69C GLN* 4.2 8.5 + - - -
322C LYS* 4.7 20.4 - - + +
325C ILE* 3.8 35.7 - - + +
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 2.7 42.4 + - - +
60C ASP 3.7 0.2 - - - -
62C ARG* 1.3 68.9 - - - +
64C ILE* 1.3 61.0 + - - +
66C LEU* 3.4 1.2 + - - -
67C ASN* 2.9 30.7 + - - +
72C LEU* 3.6 22.2 - - - +
75C TYR* 3.4 39.9 - - - -
119C PHE* 4.0 4.5 - - - -
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASP* 2.9 40.1 + - - +
61C GLN* 4.0 7.2 - - + +
63C SER* 1.3 74.7 - - - +
65C SER* 1.3 65.0 + - - +
67C ASN* 3.3 6.4 + - - +
68C ARG* 3.1 43.3 + - - +
75C TYR* 3.7 17.7 - - + -
77C PRO* 4.2 13.9 - - + -
269C GLY* 5.4 3.6 - - - -
270C PRO* 5.0 6.1 - - + -
273C MET* 3.8 28.3 - - + -
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLN 3.3 16.4 + - - -
62C ARG* 3.6 26.2 + - - -
64C ILE* 1.3 78.9 - - - +
66C LEU* 1.3 62.7 + - - +
68C ARG* 3.1 11.3 + - - +
69C GLN* 3.0 42.7 + - - +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 3.0 41.2 + - + +
63C SER* 3.7 4.0 - - - +
65C SER* 1.3 76.5 - - - +
67C ASN* 1.3 60.2 + - - +
69C GLN* 3.1 12.4 + - - +
70C GLY 3.1 4.0 + - - -
71C ARG* 2.8 60.3 + - + +
72C LEU* 3.7 23.8 - - + -
119C PHE* 4.6 3.1 - - + -
325C ILE* 4.0 25.1 - - + -
329C ILE* 4.2 22.2 - - + -
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Residues in contact with ASN 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C SER 2.9 18.6 + - - +
64C ILE 3.7 4.9 - - - +
65C SER 3.2 0.2 - - - -
66C LEU* 1.3 75.0 - - - +
68C ARG* 1.3 65.1 + - - +
70C GLY* 3.0 17.3 + - - -
72C LEU* 3.6 20.8 + - + +
73C GLY 2.6 28.1 + - - -
75C TYR* 4.3 4.9 - - + +
273C MET* 3.4 45.0 + - + +
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 3.1 25.4 + - - +
65C SER* 3.1 12.3 + - - +
67C ASN* 1.3 83.8 - - - +
69C GLN* 1.3 60.8 + - + +
70C GLY 3.2 1.4 + - - -
270C PRO* 5.2 6.7 - - - +
273C MET* 3.5 29.3 - - + +
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Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 4.2 9.9 + - - -
65C SER* 3.0 37.1 + - - +
66C LEU* 3.1 15.7 + - - +
68C ARG* 1.3 77.8 - - + +
70C GLY* 1.3 59.1 + - - +
71C ARG* 3.2 27.3 + - + +
----------------------------------------------------------
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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