Contacts of the helix formed by residues 58 - 89 (chain b) in PDB entry 5W97
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 ALA 58 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268a PHE* 3.6 30.1 - - + -
269a GLY* 4.3 16.4 - - - +
56b MET 4.7 2.5 - - - +
57b ASP* 1.3 76.2 + - - +
59b GLN* 1.3 68.9 + - - +
60b GLU* 2.9 17.0 + - - +
61b VAL* 3.0 14.7 + - - +
62b GLU* 3.5 9.9 + - + +
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Residues in contact with GLN 59 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C PEK 3.8 53.3 + - - +
57b ASP* 4.6 4.0 + - - +
58b ALA* 1.3 76.6 - - - +
60b GLU* 1.3 62.0 + - - +
61b VAL 3.4 0.2 - - - -
62b GLU* 3.4 9.3 + - - +
63b THR* 3.4 22.9 + - - -
301b CHD 2.7 57.5 + - + +
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Residues in contact with GLU 60 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57b ASP* 2.9 50.5 + - - +
58b ALA* 2.9 15.7 + - - +
59b GLN* 1.3 75.0 - - - +
61b VAL* 1.3 72.1 + - + +
63b THR* 3.7 17.2 + - - -
64b ILE* 4.5 7.0 - - - +
201e PSC 3.9 23.7 - - + +
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Residues in contact with VAL 61 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268a PHE* 4.1 9.4 - - + -
58b ALA 3.0 13.3 + - - +
60b GLU* 1.3 86.9 - - + +
62b GLU* 1.3 67.2 + - - +
63b THR 3.2 2.0 - - - -
64b ILE* 3.4 28.4 - - + +
65b TRP* 3.5 37.2 + - + -
201e PSC 3.4 59.5 - - + -
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Residues in contact with GLU 62 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268a PHE* 4.1 9.4 - - - -
269a GLY* 4.2 12.5 - - - -
272a GLY* 4.3 8.7 - - - -
318a VAL* 3.9 14.8 - - - +
322a SER* 4.0 15.1 + - - -
58b ALA* 3.7 21.9 - - + +
59b GLN* 3.6 11.9 - - - +
60b GLU 3.4 0.2 - - - -
61b VAL* 1.3 75.5 - - - +
63b THR* 1.3 62.7 + - - +
65b TRP* 3.5 28.6 + - + +
66b THR* 3.1 27.3 + - - +
301b CHD 2.8 39.2 + - + +
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Residues in contact with THR 63 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59b GLN 3.4 9.4 + - - -
60b GLU* 3.7 11.6 + - - -
61b VAL 3.2 0.6 - - - -
62b GLU* 1.3 79.5 - - - +
64b ILE* 1.3 54.6 + - + +
66b THR* 3.6 0.7 - - - -
67b ILE* 2.8 55.8 + - + +
301b CHD 2.8 26.1 + - - +
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Residues in contact with ILE 64 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60b GLU 4.5 4.7 - - - +
61b VAL* 3.4 35.4 + - + +
62b GLU 3.3 0.2 - - - -
63b THR* 1.3 77.4 - - + +
65b TRP* 1.3 59.6 + - + +
66b THR 3.0 0.3 + - - -
67b ILE* 5.0 2.2 - - - -
68b LEU* 2.9 47.7 + - + +
201e PSC 3.9 39.3 - - + -
25i PHE* 6.1 1.8 - - + -
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Residues in contact with TRP 65 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268a PHE* 3.6 28.7 - + - -
314a ILE 4.7 1.9 - - - +
317a GLY 4.8 0.2 - - - -
318a VAL* 4.1 32.7 + - + +
321a PHE* 3.5 57.5 - + + -
322a SER* 4.3 3.6 - - - -
325a ALA* 4.0 6.7 - - + -
61b VAL* 3.5 33.4 + - + -
62b GLU* 3.5 35.9 + - + +
63b THR 3.4 0.8 - - - -
64b ILE* 1.3 77.5 - - - +
66b THR* 1.3 55.5 + - - +
69b PRO* 3.4 20.9 - - - +
201e PSC 4.0 51.4 - - + -
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Residues in contact with THR 66 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PEK 3.7 31.6 - - + -
275a TRP* 5.2 0.6 - - + -
314a ILE* 4.0 21.9 - - + +
318a VAL* 3.7 19.6 - - - +
62b GLU 3.1 17.2 + - - -
63b THR* 3.2 2.9 + - - -
64b ILE 3.1 0.2 - - - -
65b TRP* 1.3 75.4 - - - +
67b ILE* 1.3 70.3 + - + +
68b LEU 3.4 1.1 - - - -
69b PRO* 3.7 4.3 - - - +
70b ALA* 3.4 20.3 + - - +
301b CHD 3.7 26.4 - - + +
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Residues in contact with ILE 67 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PEK 4.1 30.7 - - + -
63b THR* 2.8 41.0 + - + +
64b ILE* 4.4 2.9 - - - +
66b THR* 1.3 76.2 - - + +
68b LEU* 1.3 64.2 + - + +
70b ALA* 3.2 9.4 + - + +
71b ILE* 3.1 37.2 + - + +
301b CHD 6.1 1.3 - - - -
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Residues in contact with LEU 68 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64b ILE* 2.9 27.6 + - + +
65b TRP* 5.3 0.2 - - - -
67b ILE* 1.3 78.1 - - + +
69b PRO* 1.3 69.8 - - + +
71b ILE* 3.0 30.6 + - + +
72b ILE* 3.0 29.3 + - + +
201e PSC 5.0 12.3 - - + -
25i PHE* 4.9 19.5 - - + -
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Residues in contact with PRO 69 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313a ALA 5.4 0.4 - - - +
314a ILE* 4.5 17.7 - - + +
317a GLY* 5.9 0.7 - - - -
321a PHE* 4.8 9.0 - - + -
602a HEA 3.9 34.6 - - + +
64b ILE 3.6 8.1 - - - +
65b TRP* 3.4 26.5 - - - +
66b THR 3.7 4.9 - - - +
68b LEU* 1.3 93.2 - - + +
70b ALA* 1.3 60.8 + - - +
72b ILE* 3.2 7.4 + - + +
73b LEU* 3.0 30.9 + - + +
201e PSC 5.4 4.0 - - + -
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Residues in contact with ALA 70 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PEK 6.1 5.2 - - + -
101G CDL 4.9 5.0 - - + +
314a ILE* 4.2 21.7 - - + +
66b THR* 3.4 12.1 + - + +
67b ILE* 3.2 16.5 + - + +
68b LEU 3.1 0.8 - - - -
69b PRO* 1.3 77.7 - - - +
71b ILE* 1.3 63.5 + - + +
73b LEU* 3.4 5.7 + - - +
74b ILE* 3.3 30.4 + - + +
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Residues in contact with ILE 71 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67b ILE* 3.1 30.1 + - + +
68b LEU* 3.0 23.1 + - + +
70b ALA* 1.3 76.4 - - + +
72b ILE* 1.3 65.2 + - + +
74b ILE* 3.1 22.5 + - + +
75b LEU* 3.2 28.2 + - + +
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Residues in contact with ILE 72 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602a HEA 4.0 15.5 - - + -
30b ILE* 3.5 34.9 - - + +
33b LEU* 5.3 11.9 - - + -
34b ILE* 4.6 15.3 - - + -
68b LEU* 3.0 36.3 + - + +
69b PRO* 3.2 10.5 + - + +
71b ILE* 1.3 77.9 - - + +
73b LEU* 1.3 62.1 + - - +
75b LEU* 3.2 17.7 + - + +
76b ILE* 3.2 24.5 + - + +
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Residues in contact with LEU 73 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 4.8 11.4 - - + -
310a MET* 3.3 55.1 - - + +
311a ILE* 4.6 0.7 - - - -
313a ALA* 3.9 8.1 - - + -
314a ILE* 3.8 32.3 - - + -
356a ILE* 4.6 6.3 - - + -
602a HEA 4.0 28.0 - - + -
69b PRO 3.0 17.7 + - - +
70b ALA* 3.8 4.5 - - - +
71b ILE 3.2 0.2 - - - -
72b ILE* 1.3 73.2 - - - +
74b ILE* 1.3 55.5 + - - +
76b ILE* 3.3 7.9 + - + +
77b ALA* 2.7 37.7 + - - +
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Residues in contact with ILE 74 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LEU* 4.4 29.4 - - + -
36G TRP* 6.5 0.7 - - + -
37G LEU* 5.6 8.1 - - + -
101G CDL 4.5 24.5 - - + -
70b ALA* 3.3 19.5 + - + +
71b ILE* 3.1 14.5 + - + +
73b LEU* 1.3 77.3 - - - +
75b LEU* 1.3 61.3 + - + +
77b ALA* 4.4 4.9 - - - +
78b LEU* 3.1 52.2 + - + +
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Residues in contact with LEU 75 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26b HIS* 2.9 31.1 + - + +
30b ILE* 4.8 7.6 - - + -
71b ILE* 3.2 27.7 + - + +
72b ILE* 3.2 19.9 + - + +
74b ILE* 1.3 81.8 - - + +
76b ILE* 1.3 58.0 + - - +
78b LEU* 5.3 4.0 - - + -
79b PRO* 3.2 16.2 - - - +
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Residues in contact with ILE 76 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310a MET* 3.8 11.2 - - + -
356a ILE* 4.2 20.6 - - + -
360a ASN* 3.6 28.5 - - - +
602a HEA 5.0 2.5 - - + -
23b PHE* 3.5 10.3 - - + -
26b HIS* 4.3 4.7 - - - +
27b THR* 4.3 17.9 - - + +
30b ILE* 3.9 35.7 - - + -
72b ILE* 3.2 20.1 + - + +
73b LEU* 3.7 13.0 - - + +
74b ILE 3.3 0.2 - - - -
75b LEU* 1.3 76.2 - - - +
77b ALA* 1.3 66.2 + - - +
78b LEU 3.3 0.2 - - - -
79b PRO* 3.3 6.4 - - - +
80b SER* 3.2 18.2 + - - -
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Residues in contact with ALA 77 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 3.9 31.6 - - + -
306a THR* 5.8 1.3 - - + -
307a SER* 5.6 1.8 - - - +
310a MET* 3.3 21.8 - - + -
73b LEU 2.7 21.1 + - - +
74b ILE 4.1 1.8 - - - +
76b ILE* 1.3 74.6 - - - +
78b LEU* 1.3 57.6 + - - +
80b SER* 3.4 4.2 + - - -
81b LEU* 2.9 42.1 + - + +
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Residues in contact with LEU 78 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LEU* 4.9 10.3 - - + -
101G CDL 3.3 53.5 - - + +
74b ILE* 3.1 40.0 + - + +
75b LEU* 5.4 4.7 - - + -
77b ALA* 1.3 74.0 - - - +
79b PRO* 1.3 74.5 - - + +
81b LEU* 3.4 3.3 + - - +
82b ARG* 3.0 21.8 + - - +
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Residues in contact with PRO 79 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23b PHE* 3.8 19.5 - - + -
26b HIS* 4.0 9.6 - - + +
75b LEU* 3.2 25.1 - - - +
76b ILE 3.3 10.5 - - - +
78b LEU* 1.3 92.3 - - + +
80b SER* 1.3 62.3 + - - +
82b ARG* 3.2 25.0 + - + +
83b ILE* 3.1 28.4 + - - +
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Residues in contact with SER 80 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306a THR* 4.2 7.9 - - - +
360a ASN* 2.6 45.3 + - - +
361a SER* 4.5 1.0 + - - -
362a SER* 2.6 31.3 + - - -
23b PHE* 3.4 14.9 - - - -
76b ILE 3.2 15.1 + - - -
77b ALA* 3.4 7.4 - - - -
79b PRO* 1.3 80.0 - - - +
81b LEU* 1.3 64.6 + - - +
83b ILE* 5.0 0.2 - - - -
84b LEU* 3.3 4.9 + - - +
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Residues in contact with LEU 81 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 3.8 55.0 - - + +
303a ALA* 3.7 38.8 - - + +
306a THR* 4.6 14.4 - - + -
307a SER* 3.9 16.6 - - - +
361a SER* 5.2 0.4 - - - +
77b ALA* 2.9 25.3 + - + +
78b LEU 3.9 3.4 - - - +
80b SER* 1.3 78.2 - - - +
82b ARG* 1.3 63.7 + - - +
84b LEU* 3.6 12.0 - - + +
85b TYR* 3.1 32.8 + - + -
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Residues in contact with ARG 82 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G CDL 4.3 27.6 - - + +
19b GLU* 3.4 30.1 + - - -
78b LEU 3.0 13.8 + - - +
79b PRO* 3.2 24.1 + - - +
81b LEU* 1.3 76.7 - - - +
83b ILE* 1.3 71.6 + - - +
85b TYR* 3.7 2.8 + - - +
86b MET* 3.2 51.2 + - + +
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Residues in contact with ILE 83 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362a SER* 3.4 15.7 - - - +
16b ILE* 5.1 5.4 - - + -
19b GLU* 3.8 33.9 - - + +
20b LEU* 3.6 23.1 - - + -
23b PHE* 3.5 35.7 - - + -
79b PRO 3.1 14.2 + - - +
80b SER 3.7 1.8 - - - +
82b ARG* 1.3 92.1 - - - +
84b LEU* 1.3 53.9 + - - +
86b MET* 3.1 8.8 + - - +
87b MET* 2.8 43.0 + - + +
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Residues in contact with LEU 84 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299a VAL* 3.8 20.9 - - + +
302a ARG* 3.4 26.4 + - + +
303a ALA* 3.7 33.2 - - + +
361a SER* 3.0 37.9 - - - +
362a SER* 3.1 22.7 + - - +
365a ILE* 6.2 0.4 - - + -
80b SER 3.3 4.2 + - - +
81b LEU* 3.4 15.5 + - + +
83b ILE* 1.3 75.6 - - - +
85b TYR* 1.3 63.2 + - + +
87b MET* 3.5 12.3 + - - +
88b ASP* 3.3 21.0 + - - +
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Residues in contact with TYR 85 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 3.6 70.9 + - + +
299a VAL* 3.7 27.1 - - + -
300a ASP* 2.6 30.0 + - - -
303a ALA* 3.5 31.6 - - + +
81b LEU* 3.1 28.2 + - + +
82b ARG 4.1 3.1 - - - +
83b ILE 3.2 0.2 - - - -
84b LEU* 1.3 81.1 - - + +
86b MET* 1.3 64.6 + - - +
88b ASP* 3.5 4.1 + - + +
89b GLU* 3.2 26.6 + - - +
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Residues in contact with MET 86 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16b ILE* 3.7 23.7 - - + +
19b GLU* 4.4 17.5 - - - +
82b ARG* 3.2 49.4 + - + +
83b ILE* 3.1 12.3 + - - +
85b TYR* 1.3 76.7 - - - +
87b MET* 1.3 62.7 + - - +
88b ASP 3.3 0.5 + - - -
89b GLU* 3.4 35.1 + - - +
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Residues in contact with MET 87 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302a ARG* 6.0 3.6 - - - +
361a SER 5.2 0.2 - - - +
362a SER* 3.4 35.0 - - - +
365a ILE* 4.1 21.1 - - + -
16b ILE* 3.7 26.9 - - + +
20b LEU* 3.6 30.3 - - + -
83b ILE* 2.8 22.8 + - + +
84b LEU* 3.5 14.4 - - - +
85b TYR 3.4 0.2 - - - -
86b MET* 1.3 71.6 - - - +
88b ASP* 1.3 61.7 + - - +
89b GLU 4.9 0.2 - - - +
169b GLY 4.4 9.9 - - - +
183b THR* 4.1 17.7 + - - +
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Residues in contact with ASP 88 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299a VAL* 3.6 38.1 + - + +
302a ARG* 3.8 13.9 + - - +
84b LEU 3.3 13.6 + - - +
85b TYR* 3.8 6.3 - - + +
86b MET 3.2 0.6 - - - -
87b MET* 1.3 80.2 - - - +
89b GLU* 1.3 70.0 + - - +
91b ASN* 3.9 6.6 + - - +
181b GLN* 5.9 1.0 + - - -
183b THR* 4.9 2.3 - - - +
21h PRO 4.2 15.6 - - - +
22h ASN* 4.9 3.3 + - - -
23h GLN* 4.6 15.6 + - - +
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Residues in contact with GLU 89 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85b TYR 3.2 14.6 + - - +
86b MET* 3.4 34.7 + - - +
87b MET 4.9 0.2 - - - +
88b ASP* 1.3 79.8 - - - +
90b ILE* 1.4 63.2 - - - +
91b ASN* 2.3 29.6 - - - +
183b THR* 4.8 0.3 - - - +
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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