Contacts of the helix formed by residues 42 - 69 (chain G) in PDB entry 1W88
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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G LEU* 1.3 77.4 - - - +
43G ASP* 1.3 60.0 + - - +
44G GLU* 3.1 19.2 + - - +
45G GLN* 3.1 32.0 + - - +
46G LEU* 3.0 27.6 + - - +
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Residues in contact with ASP 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G LEU 5.2 0.5 - - - +
42G SER* 1.3 73.5 - - - +
44G GLU* 1.3 60.7 + - - +
46G LEU* 3.6 10.1 + - - +
47G LYS* 3.1 27.7 + - - +
306G LYS* 4.1 10.4 + - - -
308G LEU* 3.6 41.6 - - + +
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Residues in contact with GLU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G SER* 3.1 8.5 + - - +
43G ASP* 1.3 78.7 - - - +
45G GLN* 1.3 60.6 + - + +
47G LYS* 3.3 6.5 + - - +
48G GLU* 2.8 30.1 + - + +
51G ARG* 2.8 32.4 + - - +
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Residues in contact with GLN 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G GLU 4.6 1.7 - - - +
41G LEU* 3.5 20.5 - - + +
42G SER* 3.1 35.5 + - - +
44G GLU* 1.3 76.4 - - + +
46G LEU* 1.3 65.6 + - - +
48G GLU* 3.2 2.9 + - - -
49G LEU* 2.9 26.9 + - - +
90G PHE* 3.6 28.6 - - + -
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G MET* 6.4 0.2 - - - -
41G LEU* 3.8 34.3 - - + +
42G SER 3.0 25.2 + - - +
43G ASP* 3.8 11.7 - - - +
45G GLN* 1.3 75.9 - - - +
47G LYS* 1.3 61.3 + - - +
49G LEU* 3.8 1.7 - - - +
50G MET* 3.4 7.4 + - - +
239G LEU* 4.0 10.1 - - + -
299G PHE* 3.3 43.1 - - + -
302G PHE* 4.0 24.7 - - + -
303G LEU* 3.7 13.3 - - + +
306G LYS* 4.5 6.7 - - - +
308G LEU* 4.2 18.2 - - + -
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Residues in contact with LYS 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ASP 3.1 18.4 + - - +
44G GLU* 3.6 9.0 - - - +
46G LEU* 1.3 75.9 - - - +
48G GLU* 1.3 59.5 + - - +
50G MET* 3.1 7.7 + - - +
51G ARG* 2.9 50.1 + - - +
303G LEU* 4.7 5.8 - - - +
308G LEU* 4.4 17.3 - - + +
309G TRP* 3.9 5.5 - - + -
313G GLU* 4.9 2.0 - - - +
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Residues in contact with GLU 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 2.8 22.5 + - + +
45G GLN* 3.7 8.1 - - - +
47G LYS* 1.3 70.5 - - - +
49G LEU* 1.3 57.3 + - - +
51G ARG* 3.2 35.2 + - - +
52G ARG* 2.9 65.5 + - - +
90G PHE* 3.9 11.2 - - + -
110G TRP* 5.3 2.8 - - - -
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G LEU* 4.9 13.7 - - + -
45G GLN 2.9 16.2 + - - +
46G LEU* 3.8 5.8 - - - +
48G GLU* 1.3 75.8 - - - +
50G MET* 1.3 56.9 + - - +
52G ARG* 3.4 3.6 + - - +
53G MET* 3.0 46.6 + - + +
86G ILE* 4.0 14.4 - - + -
87G ALA* 3.9 17.9 - - + +
90G PHE* 3.8 43.2 - - + -
238G PRO* 4.3 27.1 - - + +
239G LEU* 5.5 0.9 - - + -
242G TYR* 5.2 2.5 - - + -
299G PHE* 4.3 10.8 - - + -
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Residues in contact with MET 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LEU 3.4 2.9 + - - +
47G LYS 3.1 8.5 + - - +
49G LEU* 1.3 75.5 - - - +
51G ARG* 1.3 67.2 + - - +
53G MET* 3.3 8.8 + - - +
54G VAL* 2.8 49.5 + - + +
296G LEU* 3.7 34.3 - - + +
299G PHE* 4.0 19.5 - - + -
300G ARG* 3.9 23.6 - - + +
303G LEU* 3.6 22.9 - - + -
309G TRP* 3.7 24.0 - - + +
314G GLU* 3.9 14.4 - - - +
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Residues in contact with ARG 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 2.8 28.9 + - - -
47G LYS* 2.9 27.2 + - - +
48G GLU* 3.2 51.7 + - - +
50G MET* 1.3 77.6 - - - +
52G ARG* 1.3 51.2 + - - +
55G TYR* 2.8 36.4 + - - +
309G TRP* 3.8 11.4 - - + -
313G GLU* 3.2 23.8 + - - -
317G VAL* 3.4 35.5 - - + +
320G GLN* 6.2 0.4 - - - -
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Residues in contact with ARG 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G GLU* 2.9 51.5 + - - +
49G LEU 3.6 1.8 - - - +
51G ARG* 1.3 70.7 - - - +
53G MET* 1.3 57.8 + - - +
55G TYR* 3.3 2.4 + - - +
56G THR* 2.8 34.6 + - - -
86G ILE* 3.4 26.2 - - + +
89G HIS* 3.7 29.5 + - - -
90G PHE* 3.8 28.6 - - - +
110G TRP* 3.9 49.3 + - + +
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Residues in contact with MET 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU* 3.0 30.5 + - + +
50G MET* 3.7 10.1 - - - +
52G ARG* 1.3 74.6 - - - +
54G VAL* 1.3 58.0 + - - +
56G THR 3.3 0.5 + - - -
57G ARG* 2.9 27.4 + - - +
82G GLU* 3.5 21.3 - - + +
83G ALA* 4.2 15.7 - - - -
86G ILE* 4.0 20.9 - - + -
87G ALA 5.4 0.2 - - - -
238G PRO* 3.6 32.3 - - + -
295G PRO* 4.8 4.0 - - - +
296G LEU* 3.7 17.0 - - + -
299G PHE* 3.5 38.8 - - + -
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Residues in contact with VAL 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G MET* 2.8 53.4 + - + +
51G ARG 3.5 3.4 - - - +
53G MET* 1.3 70.6 - - - +
55G TYR* 1.3 62.2 + - - +
57G ARG* 3.5 5.9 + - - +
58G ILE* 3.1 24.3 + - + +
296G LEU* 4.0 11.2 - - + -
309G TRP* 4.0 12.8 - - + -
314G GLU* 4.3 15.3 - - + +
317G VAL* 4.1 16.4 - - + -
318G ILE* 3.9 29.2 - - + +
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Residues in contact with TYR 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ARG 2.8 21.1 + - - +
52G ARG* 3.4 5.4 - - - +
54G VAL* 1.3 70.5 - - - +
56G THR* 1.3 63.4 + - - +
58G ILE* 3.2 5.1 + - - +
59G LEU* 2.8 43.8 + - + -
109G ILE* 5.8 4.9 - - + -
110G TRP* 3.7 33.7 - + + -
115G LEU* 3.9 16.5 - - + +
317G VAL* 4.1 10.1 - - + +
320G GLN* 4.3 15.3 - - - -
321G ALA* 3.5 39.1 + - + +
324G GLU* 2.9 40.4 + - - +
325G ILE* 4.7 1.5 - - + +
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Residues in contact with THR 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ARG 2.8 23.2 + - - -
53G MET 3.7 4.0 - - - -
55G TYR* 1.3 72.8 - - - +
57G ARG* 1.3 65.5 + - - +
59G LEU* 3.1 12.8 + - + +
60G ASP* 2.9 22.3 + - - +
78G THR* 4.4 8.1 - - - +
82G GLU* 4.1 11.9 - - + -
85G GLN* 4.8 3.4 - - - +
86G ILE* 3.3 15.3 - - + +
106G PRO* 3.8 31.9 - - + -
110G TRP* 3.1 22.5 + - - -
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Residues in contact with ARG 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G MET 2.9 17.5 + - - +
54G VAL 3.5 6.3 - - - +
56G THR* 1.3 74.2 - - - +
58G ILE* 1.3 65.2 + - + +
60G ASP* 3.2 6.4 + - - +
61G GLN* 3.0 46.2 + - - +
79G ALA* 4.0 17.9 - - - +
80G GLY* 3.8 11.7 - - - +
82G GLU* 2.7 45.0 + - - +
294G ASP* 2.7 45.4 + - - -
295G PRO* 4.1 2.0 - - - +
296G LEU* 3.6 28.4 - - + +
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Residues in contact with ILE 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G VAL* 3.1 17.1 + - + +
55G TYR 3.5 6.5 - - - +
57G ARG* 1.3 76.2 - - + +
59G LEU* 1.3 61.6 + - - +
61G GLN* 3.1 26.1 + - + +
62G ARG* 2.8 30.9 + - + +
318G ILE* 3.8 43.3 - - + -
321G ALA* 3.8 20.6 - - + -
322G LYS* 4.0 28.3 - - + +
325G ILE* 4.5 4.9 - - + -
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Residues in contact with LEU 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G TYR* 2.8 27.3 + - + +
56G THR* 3.3 15.3 - - + +
58G ILE* 1.3 72.7 - - - +
60G ASP* 1.3 51.1 + - - +
62G ARG* 3.4 0.9 + - - +
63G SER* 2.8 44.7 + - - +
75G TYR* 5.8 1.6 - - + +
105G VAL* 6.4 0.2 - - + -
106G PRO* 4.8 16.8 - - + -
109G ILE* 3.9 27.4 - - + -
110G TRP* 6.3 0.9 - - - +
115G LEU* 3.6 24.2 - - + -
119G PHE* 3.8 23.1 - - + -
325G ILE* 3.7 21.7 - - + +
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Residues in contact with ASP 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G THR 2.9 11.2 + - - +
57G ARG* 3.5 10.1 - - - +
59G LEU* 1.3 73.7 - - - +
61G GLN* 1.3 59.6 + - - +
63G SER* 3.3 0.5 + - - -
64G ILE* 2.9 42.8 + - - +
75G TYR* 2.3 46.5 + - - +
77G PRO* 3.3 3.8 - - - +
78G THR* 3.3 25.4 + - - +
79G ALA* 2.8 36.9 + - + +
82G GLU* 5.2 0.2 - - - +
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Residues in contact with GLN 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G ARG* 3.0 44.4 + - - +
58G ILE* 3.1 27.6 + - + +
60G ASP* 1.3 75.8 - - + +
62G ARG* 1.3 60.8 + - - +
64G ILE* 3.7 10.7 + - + +
65G SER* 3.2 23.7 + - - -
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Residues in contact with ARG 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ILE* 2.8 19.5 + - + +
59G LEU 3.8 3.1 - - - +
61G GLN* 1.3 76.7 - - - +
63G SER* 1.3 54.2 + - - +
65G SER* 3.4 7.4 + - - -
66G LEU* 2.8 42.4 + - + +
322G LYS* 6.3 2.0 - - + -
325G ILE* 3.9 30.5 - - + -
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Residues in contact with SER 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G LEU* 2.8 33.6 + - - +
60G ASP 3.8 0.2 - - - -
62G ARG* 1.3 71.2 - - - +
64G ILE* 1.3 55.2 + - - +
66G LEU* 3.5 2.7 - - - +
67G ASN* 2.7 36.6 + - - +
72G LEU* 3.8 23.1 - - - +
75G TYR* 3.6 34.5 - - - -
119G PHE* 4.0 15.6 - - - -
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Residues in contact with ILE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G ASP* 2.9 53.2 + - - +
61G GLN* 4.0 10.3 - - + +
63G SER* 1.3 71.2 - - - +
65G SER* 1.3 63.9 + - - +
67G ASN* 3.3 3.9 + - - +
68G ARG* 3.0 63.3 + - + +
75G TYR* 3.8 14.1 - - + -
77G PRO* 4.5 14.8 - - + -
79G ALA* 5.7 1.1 - - + -
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Residues in contact with SER 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 4.0 18.6 + - - +
61G GLN 3.2 17.2 + - - -
62G ARG* 3.4 8.6 + - - -
64G ILE* 1.3 80.8 - - - +
66G LEU* 1.3 61.1 + - - +
68G ARG* 3.3 12.5 + - - +
69G GLN* 3.0 43.4 + - - +
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Residues in contact with LEU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ARG* 2.8 33.5 + - + +
63G SER* 3.1 8.0 + - - +
65G SER* 1.3 72.0 - - - +
67G ASN* 1.3 64.2 + - - +
69G GLN* 3.2 19.0 + - - +
71G ARG* 2.9 52.7 + - + +
72G LEU* 3.9 18.8 - - + -
119G PHE* 4.8 3.8 - - + -
325G ILE* 4.1 18.4 - - + -
329G ILE* 3.0 39.0 - - + -
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Residues in contact with ASN 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G SER 2.7 19.3 + - - +
64G ILE* 3.5 7.9 - - - +
66G LEU* 1.3 71.0 - - - +
68G ARG* 1.3 58.6 + - + +
70G GLY* 2.8 26.0 + - - -
72G LEU* 3.8 15.8 + - + +
73G GLY 2.4 30.9 + - - +
75G TYR* 3.3 30.6 + - + +
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Residues in contact with ARG 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 3.2 62.7 + - + +
69A GLN* 4.4 12.9 + - - +
70A GLY* 5.1 1.0 - - - +
64G ILE* 3.0 43.6 + - + +
65G SER* 3.5 11.1 - - - +
66G LEU 3.3 0.2 - - - -
67G ASN* 1.3 79.1 - - + +
69G GLN* 1.3 57.6 + - - +
70G GLY 3.1 3.0 + - - -
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Residues in contact with GLN 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.9 4.3 + - - -
65A SER* 3.4 24.2 + - - +
68A ARG* 5.0 10.8 + - - +
69A GLN* 3.4 27.6 + - + +
65G SER* 3.0 36.8 + - - +
66G LEU* 3.2 20.6 + - - +
68G ARG* 1.3 75.1 - - - +
70G GLY* 1.3 60.4 + - - +
71G ARG* 3.5 29.4 + - + +
----------------------------------------------------------
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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