Contacts of the helix formed by residues 34 - 61 (chain C) in PDB entry 1UMD
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 GLU 34 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASP 4.1 7.4 - - - +
33C LEU* 1.3 77.6 - - - +
35C GLY* 1.3 67.3 + - - +
36C GLU* 3.9 21.5 - - - +
37C LYS* 2.9 46.7 + - + +
38C LEU* 3.0 10.4 + - - +
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Residues in contact with GLY 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU 3.7 0.8 + - - -
34C GLU* 1.3 73.6 - - - +
36C GLU* 1.3 62.5 + - - +
38C LEU* 3.2 6.1 + - - +
39C ARG* 3.0 28.5 + - - +
309C LEU* 3.8 32.8 - - - +
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 3.1 21.8 + - + +
35C GLY* 1.3 75.3 + - - +
37C LYS* 1.3 65.1 + - + +
39C ARG* 3.4 11.8 + - - +
40C ARG* 3.1 21.4 + - - +
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.1 23.3 - - + -
34C GLU* 2.9 46.0 + - + +
36C GLU* 1.3 76.3 - - + +
38C LEU* 1.3 65.2 + - - +
40C ARG* 3.1 9.8 + - - +
41C LEU* 3.1 27.7 + - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.1 21.3 - - + -
33C LEU* 3.9 32.3 - - + +
34C GLU 3.0 14.3 + - - +
35C GLY* 3.5 7.9 - - - +
37C LYS* 1.3 75.6 - - - +
39C ARG* 1.3 61.7 + - - +
41C LEU* 3.3 8.9 + - + +
42C TYR 3.3 0.2 + - - -
241C LEU* 3.9 28.0 - - + -
300C PHE* 3.1 33.1 - - + -
303C PHE* 4.3 12.1 - - + -
304C LEU* 3.8 13.5 - - + -
307C ARG* 4.9 3.4 - - - +
309C LEU* 3.7 21.8 - - + -
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLY 3.0 22.6 + - - +
36C GLU* 3.7 8.7 - - - +
38C LEU* 1.3 74.4 - - - +
40C ARG* 1.3 60.8 + - - +
42C TYR* 3.3 5.3 + - - +
43C ARG* 2.9 29.4 + - - +
304C LEU* 4.6 2.5 - - + -
308C GLY 5.3 0.6 + - - -
309C LEU* 2.8 64.5 + - + +
310C TRP* 4.6 0.6 - - - +
311C ASN* 5.9 2.2 - - - +
314C TRP* 2.9 63.0 - - + +
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Residues in contact with ARG 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU 3.1 14.3 + - - +
37C LYS* 3.1 13.0 + - - +
39C ARG* 1.3 74.7 - - - +
41C LEU* 1.3 60.2 + - - +
43C ARG* 3.5 33.2 - - - +
44C ASP* 2.9 53.5 + - - -
82C HIS* 3.9 22.5 - - + -
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.2 14.8 - - + -
37C LYS* 3.1 18.5 + - + +
38C LEU* 3.5 8.3 - - - +
39C ARG 3.3 0.4 - - - -
40C ARG* 1.3 75.6 - - - +
42C TYR* 1.3 62.4 + - - +
44C ASP* 3.5 0.6 + - - -
45C MET* 3.1 29.7 + - - +
78C VAL* 3.7 15.2 - - + +
79C ALA* 5.1 2.2 - - - -
82C HIS* 3.6 39.7 - - + +
240C VAL* 4.4 18.4 - - + +
241C LEU* 4.0 27.8 - - + -
244C TYR* 5.2 8.3 - - + -
300C PHE* 3.9 12.8 - - + -
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Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU 3.3 2.2 + - - +
39C ARG 3.3 6.6 + - - +
40C ARG 3.2 0.2 - - - -
41C LEU* 1.3 77.8 - - - +
43C ARG* 1.3 63.2 + - - +
45C MET* 3.1 10.0 + - + +
46C LEU* 3.0 47.3 + - + +
297C ILE* 3.4 37.9 - - + +
300C PHE* 3.7 22.8 - + + -
301C ARG* 3.3 27.4 + - + -
304C LEU* 3.5 24.0 - - + -
310C TRP* 3.8 11.0 - + - -
314C TRP* 3.5 24.0 - + - -
315C GLU* 2.7 30.6 + - - -
318C VAL* 5.9 0.2 - - + -
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG 2.9 18.6 + - - +
40C ARG* 3.5 36.2 - - - +
42C TYR* 1.3 77.8 - - - +
44C ASP* 1.3 61.3 + - - +
46C LEU* 3.3 5.0 + - - +
47C ALA* 2.9 32.0 + - - +
314C TRP* 4.9 5.6 - - + -
318C VAL* 3.8 33.3 - - + +
321C GLU* 3.3 32.9 + - - +
322C ILE* 3.9 14.4 - - - +
325C GLU* 2.8 43.0 + - - -
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ARG* 2.9 46.3 + - - +
43C ARG* 1.3 78.7 + - - +
45C MET* 1.3 59.3 + - - +
47C ALA* 3.3 7.2 + - - +
48C ALA* 2.9 28.8 + - - +
78C VAL* 3.6 23.4 - - + +
82C HIS* 2.5 32.4 + - - -
99C GLY 5.6 0.2 - - - +
102C LEU* 5.3 0.7 - - - +
103C ALA* 4.1 22.6 - - + +
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Residues in contact with MET 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU 3.1 19.1 + - - +
42C TYR* 3.1 10.5 + - + +
44C ASP* 1.3 75.9 - - - +
46C LEU* 1.3 58.6 + - - +
48C ALA* 3.3 0.7 + - - -
49C ARG* 2.9 30.0 + - - +
74C GLU* 3.6 18.5 - - + +
75C ALA* 3.6 28.9 - - - -
78C VAL* 3.6 22.4 - - + -
240C VAL* 3.9 14.4 - - + -
296C PRO* 4.3 15.3 - - - +
297C ILE* 3.7 11.4 - - + +
300C PHE* 3.4 45.1 - - + -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 3.0 43.6 + - + +
43C ARG 3.6 6.7 - - - +
45C MET* 1.3 77.2 - - - +
47C ALA* 1.3 57.7 + - - +
49C ARG* 3.3 3.6 + - + +
50C MET* 2.9 34.7 + - - +
297C ILE* 3.9 25.8 - - + -
315C GLU* 3.9 14.1 - - - +
318C VAL* 3.8 23.3 - - + -
319C ARG* 3.5 39.3 - - + +
322C ILE* 3.8 10.3 - - + -
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 2.9 26.2 + - - +
44C ASP* 3.6 10.3 - - - +
45C MET 3.3 0.2 - - - -
46C LEU* 1.3 77.2 - - - +
48C ALA* 1.3 57.4 + - - +
50C MET* 3.3 1.6 + - - +
51C LEU* 2.8 30.7 + - - +
102C LEU* 3.7 19.3 - - + +
322C ILE* 3.4 27.1 - - + +
325C GLU* 5.5 1.1 - - - +
326C LEU* 5.5 0.7 - - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ASP 2.9 17.6 + - - +
45C MET* 3.6 5.8 - - - +
46C LEU 3.3 0.2 - - - -
47C ALA* 1.3 76.0 - - - +
49C ARG* 1.3 62.0 + - - +
51C LEU* 3.2 5.0 + - - +
52C ASP* 3.0 22.9 + - - +
74C GLU* 3.7 17.9 - - + -
77C GLN* 6.2 0.2 - - + -
78C VAL* 4.7 4.7 - - + -
98C HIS* 5.0 3.3 - - - -
99C GLY* 3.8 29.6 - - - +
102C LEU* 4.0 9.8 - - + +
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C MET 2.9 17.7 + - - +
46C LEU* 3.6 5.6 - - + +
48C ALA* 1.3 76.4 - - - +
50C MET* 1.3 60.2 + - + +
52C ASP* 3.2 5.9 + - - +
53C GLU* 3.0 54.7 + - - +
71C ALA* 3.9 18.2 - - - +
72C GLY 3.7 8.8 - - - +
74C GLU* 2.7 44.4 + - - +
270C TYR* 4.1 6.0 - - - -
292C ARG* 4.3 12.4 - - - +
295C ASP* 2.9 41.8 + - - -
296C PRO* 4.2 2.2 - - - +
297C ILE* 3.5 26.2 - - + +
319C ARG* 5.9 4.0 - - - +
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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* 2.9 20.3 + - + +
47C ALA 3.9 0.2 - - - +
49C ARG* 1.3 75.6 - - + +
51C LEU* 1.3 60.7 + - - +
53C GLU* 3.3 19.5 + - - +
54C ARG* 3.0 27.7 + - - +
319C ARG* 3.4 58.6 - - + +
322C ILE* 3.8 29.8 - - + -
323C ARG* 4.0 22.9 - - + +
326C LEU* 3.7 10.0 - - + +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA 2.8 18.5 + - - +
48C ALA 3.5 5.4 - - - +
49C ARG 3.2 0.2 - - - -
50C MET* 1.3 75.8 - - - +
52C ASP* 1.3 64.6 + - - +
54C ARG* 3.1 5.1 + - + +
55C TYR* 3.0 56.4 + - + +
98C HIS* 3.9 39.9 - - + +
99C GLY* 4.9 1.1 - - - +
102C LEU* 4.0 19.7 - - + -
108C LEU* 3.8 22.0 - - + -
111C LEU* 4.3 8.7 - - + -
112C LEU* 4.6 6.5 - - + -
326C LEU* 3.9 16.1 - - + +
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Residues in contact with ASP 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ALA 3.0 13.4 + - - +
49C ARG* 3.2 13.2 + - - +
51C LEU* 1.3 77.8 - - - +
53C GLU* 1.3 62.1 + - + +
55C TYR* 3.2 15.9 + - - +
56C THR* 3.3 16.7 + - - -
67C ILE* 5.1 0.9 - - - +
69C PRO* 3.6 12.8 - - - +
70C ALA* 2.7 22.1 + - + -
71C ALA* 3.3 29.4 + - + +
74C GLU* 4.9 1.1 - - - +
98C HIS* 2.7 33.2 + - - +
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 3.0 36.0 + - - +
50C MET* 3.8 24.4 - - - +
51C LEU 3.3 0.4 - - - -
52C ASP* 1.3 75.0 - - + +
54C ARG* 1.3 64.9 + - - +
56C THR* 3.3 18.4 + - - -
57C ILE* 3.4 18.6 + - + +
292C ARG* 5.7 2.1 + - - -
319C ARG* 5.0 5.0 + - - -
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Residues in contact with ARG 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C MET 3.0 14.5 + - - +
51C LEU* 3.1 10.3 + - + +
53C GLU* 1.3 73.8 - - - +
55C TYR* 1.3 67.1 + - + +
57C ILE* 3.1 27.8 + - - +
58C LEU* 2.9 39.4 + - + +
112C LEU* 5.1 9.4 - - + -
323C ARG* 4.3 12.9 - - - +
326C LEU* 4.1 36.4 + - + +
327C GLU* 2.6 43.6 + - - +
330C LEU* 3.8 20.5 - - + +
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Residues in contact with TYR 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.0 40.9 + - + +
52C ASP* 3.3 11.4 - - - +
53C GLU 3.2 0.2 - - - -
54C ARG* 1.3 78.4 - - + +
56C THR* 1.3 62.8 + - - +
58C LEU* 3.1 27.1 + - + +
59C ILE* 3.1 10.2 + - - +
67C ILE* 3.7 23.5 - - + +
98C HIS* 3.4 45.3 - + - +
111C LEU* 4.2 17.3 + - - +
112C LEU* 3.9 11.0 - - + -
115C MET* 3.5 38.2 - - + +
130C GLU* 3.5 24.9 + - - -
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ASP* 3.3 12.4 + - - -
53C GLU* 3.4 14.1 - - - -
54C ARG 3.2 0.4 - - - -
55C TYR* 1.3 76.9 - - - +
57C ILE* 1.3 61.9 + - - +
59C ILE* 3.3 5.4 + - - +
60C ARG* 3.2 57.5 + - + +
67C ILE* 3.9 16.9 - - + +
69C PRO* 5.7 2.1 - - - +
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Residues in contact with ILE 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLU* 3.6 13.5 - - + +
54C ARG* 3.1 29.9 + - - +
56C THR* 1.3 77.1 - - - +
58C LEU* 1.3 67.3 + - + +
60C ARG* 3.1 25.6 + - + +
61C THR* 3.0 35.1 + - + +
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 2.9 26.3 + - + +
55C TYR* 3.1 25.3 + - + +
57C ILE* 1.3 78.5 - - + +
59C ILE* 1.3 57.5 + - - +
61C THR* 3.4 4.4 + - - +
62C GLY 3.0 5.2 + - - -
63C LYS* 2.8 50.1 + - + -
64C THR* 3.3 19.5 + - + -
112C LEU* 3.9 26.9 - - + -
115C MET* 4.8 2.7 - - + -
116C LEU* 4.1 14.4 - - + -
330C LEU* 4.1 28.0 - - + -
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Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR 3.1 6.9 + - - +
56C THR* 3.5 9.0 - - - +
57C ILE 3.1 0.2 - - - -
58C LEU* 1.3 74.6 - - - +
60C ARG* 1.3 70.6 + - + +
62C GLY* 2.9 14.0 + - - -
64C THR* 3.6 21.2 - - + +
65C SER* 3.8 3.8 - - - +
66C PHE* 3.6 21.3 - - - +
67C ILE* 3.5 33.0 - - + -
275C SER* 3.7 25.6 - - - +
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Residues in contact with ARG 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 3.2 37.0 + - + +
57C ILE* 3.1 24.6 + - + +
59C ILE* 1.3 86.0 - - + +
61C THR* 1.3 62.0 + - + +
62C GLY 3.6 0.2 + - - -
----------------------------------------------------------
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Residues in contact with THR 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ILE* 3.0 28.6 + - + +
58C LEU* 3.4 5.5 + - - +
60C ARG* 1.3 79.8 - - + +
62C GLY* 1.3 60.7 + - - +
63C LYS* 3.3 29.7 + - - +
----------------------------------------------------------
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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