Contacts of the helix formed by residues 68 - 96 (chain A) in PDB entry 5HLB
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 LEU 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A TRP* 1.4 81.8 + - - +
69A LEU* 1.3 58.3 + - - +
70A LEU* 3.1 6.5 - - + +
71A LYS* 3.3 50.4 - - + +
72A LEU* 3.3 18.2 - - + +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 4.1 10.8 - - + +
68A LEU* 1.3 72.7 - - - +
70A LEU* 1.3 54.9 - - + +
72A LEU* 4.5 17.3 - - + -
73A ALA* 2.2 45.6 + - + +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 5.0 16.6 - - + +
68A LEU* 3.1 1.3 - - + -
69A LEU* 1.3 83.0 - - + +
71A LYS* 1.3 60.2 + - - +
72A LEU 3.3 0.2 - - - -
73A ALA* 3.8 3.8 - - + -
74A ILE* 2.4 47.2 + - + +
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.3 51.1 + - + +
70A LEU* 1.3 76.8 - - - +
72A LEU* 1.3 93.3 + - + +
74A ILE* 2.7 28.1 - - - +
75A VAL* 3.2 22.1 + - - +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.3 29.8 - - + +
69A LEU* 4.5 20.6 - - + -
71A LYS* 1.3 102.4 - - + +
73A ALA* 1.4 62.2 + - - +
74A ILE 3.2 2.0 - - - -
75A VAL* 3.1 10.7 + - + +
76A PHE* 3.0 23.6 + - - +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 2.2 40.9 + - + +
70A LEU* 3.7 4.5 - - + +
72A LEU* 1.4 77.8 - - - +
74A ILE* 1.4 59.8 + - - +
76A PHE* 3.4 21.0 - - - +
77A ALA* 3.6 6.4 + - - +
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 2.4 37.3 + - + +
71A LYS* 2.7 30.1 - - - +
73A ALA* 1.4 68.1 - - - +
75A VAL* 1.4 65.1 + - + +
76A PHE 3.2 0.2 - - - -
77A ALA* 3.1 29.0 + - + +
78A VAL* 3.3 15.2 + - + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 3.2 25.8 + - - +
72A LEU* 3.1 17.6 + - + +
74A ILE* 1.4 75.7 - - + +
76A PHE* 1.4 62.4 + - - +
78A VAL* 3.5 16.5 + - + +
79A LEU* 3.2 30.4 - - + +
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU 3.0 11.0 + - - +
73A ALA* 3.4 15.7 - - - +
74A ILE 3.2 0.4 - - - -
75A VAL* 1.4 78.1 - - - +
77A ALA* 1.4 64.1 + - - +
78A VAL 3.4 0.2 + - - -
79A LEU* 3.5 13.9 - - + +
80A ILE* 3.4 56.0 - - + +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA 3.6 6.4 + - - +
74A ILE* 3.1 23.5 + - + +
76A PHE* 1.4 80.6 - - - +
78A VAL* 1.3 65.0 + - + +
80A ILE* 3.3 13.1 - - - +
81A ALA* 3.3 22.1 + - - +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.3 22.2 + - + +
75A VAL* 3.7 12.8 - - + +
76A PHE 3.4 0.4 - - - -
77A ALA* 1.3 77.7 - - + +
79A LEU* 1.4 66.7 + - + +
81A ALA* 3.2 6.0 + - - +
82A ILE* 3.2 35.6 + - + +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 3.2 35.4 - - + +
76A PHE* 3.5 24.7 - - + +
78A VAL* 1.4 79.2 - - + +
80A ILE* 1.3 66.4 + - + +
81A ALA 3.4 0.2 - - - -
82A ILE* 3.4 23.1 - - + +
83A TYR* 3.0 25.6 + - - +
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PHE* 3.4 53.1 + - + +
77A ALA* 3.3 19.7 - - - +
79A LEU* 1.3 83.6 - - + +
81A ALA* 1.4 57.0 + - + +
83A TYR* 3.4 12.0 - - + +
84A GLY 3.1 16.8 + - - -
292A TYR* 2.8 51.5 + - + +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA 3.3 11.7 + - - +
78A VAL* 3.2 11.3 + - - +
80A ILE* 1.4 75.4 - - + +
82A ILE* 1.4 60.9 + - + +
83A TYR 3.3 0.4 - - - -
84A GLY* 3.2 4.1 + - - +
85A VAL* 3.0 30.7 + - + +
292A TYR* 3.7 9.0 - - - +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 3.2 23.2 + - + +
79A LEU* 3.4 33.0 - - + +
81A ALA* 1.4 74.9 - - + +
83A TYR* 1.4 59.4 + - - +
84A GLY 3.2 0.7 - - - -
85A VAL* 3.3 11.2 + - + +
86A TYR* 3.1 24.9 + - - +
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU 3.0 19.3 + - - +
80A ILE* 3.4 17.0 - - + +
82A ILE* 1.4 75.0 - - - +
84A GLY* 1.3 56.1 + - - +
86A TYR* 3.1 33.8 + + - +
87A LEU* 3.0 51.7 + - + +
289A ASN* 2.6 41.5 + - - -
292A TYR* 4.6 13.5 - + - -
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE 3.1 14.2 + - - -
81A ALA 3.2 8.4 + - - -
83A TYR* 1.3 77.2 - - - +
85A VAL* 1.4 56.1 + - - +
86A TYR 3.3 0.4 - - - -
87A LEU* 3.5 15.6 + - - +
88A ASP* 3.0 27.0 + - - +
292A TYR* 4.6 9.2 - - - -
296A ILE* 3.7 11.9 - - - +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ALA 3.0 18.6 + - - +
82A ILE* 3.3 11.8 + - + +
83A TYR 3.3 0.4 - - - -
84A GLY* 1.4 74.9 - - - +
86A TYR* 1.4 58.8 - - - +
87A LEU 3.4 0.4 - - - -
88A ASP* 4.1 14.4 - - + +
89A GLN* 3.3 22.2 + - + +
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Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ILE 3.1 12.2 + - - +
83A TYR* 3.1 40.6 + + + +
85A VAL* 1.4 77.2 - - - +
87A LEU* 1.4 67.5 + - + +
89A GLN* 4.0 12.6 - - - +
90A LYS* 3.1 61.0 + - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TYR* 3.0 57.9 + - + +
84A GLY* 3.5 16.6 - - - +
86A TYR* 1.4 83.1 - - + +
88A ASP* 1.4 58.3 + - - +
90A LYS* 3.2 5.2 + - - +
91A ILE* 2.9 38.0 + - + +
289A ASN* 4.5 3.4 - - - +
292A TYR* 4.5 16.2 - - + -
293A MET* 3.8 34.3 - - + -
296A ILE* 3.6 18.4 - - + -
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLY 3.0 17.4 + - - +
85A VAL* 4.5 14.3 - - + +
87A LEU* 1.4 73.6 - - - +
89A GLN* 1.3 62.1 + - - +
91A ILE* 3.3 3.1 + - - +
92A ARG* 3.2 51.9 + - - +
296A ILE* 3.2 31.8 - - + +
300A ARG* 4.6 17.0 - - - +
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.3 21.7 + - + +
86A TYR* 4.0 13.5 - - - +
87A LEU 3.4 0.4 - - - -
88A ASP* 1.3 79.3 + - - +
90A LYS* 1.4 69.4 + - - +
92A ARG* 4.4 11.1 - - - +
93A SER* 3.7 17.7 + - - -
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TYR* 3.1 57.8 + - + +
87A LEU* 3.2 6.0 + - - +
88A ASP 3.2 0.6 - - - -
89A GLN* 1.4 88.9 - - - +
91A ILE* 1.4 61.5 + - - +
92A ARG 3.4 1.6 - - - -
93A SER* 3.6 19.8 - - - +
94A ARG* 3.6 9.0 + - - +
277A PHE* 4.3 5.2 - - - -
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU 2.9 25.3 + - - +
88A ASP* 3.3 6.0 + - - +
90A LYS* 1.4 73.3 - - + +
92A ARG* 1.4 64.4 + - + +
94A ARG* 3.3 5.5 + - - +
95A ILE* 3.1 42.3 + - + +
273A VAL* 5.5 1.6 - - + -
277A PHE* 3.8 26.5 - - + -
293A MET* 3.7 41.5 - - + +
296A ILE* 4.4 22.0 - - + -
297A MET* 4.4 14.4 - - + +
301A TYR* 4.5 9.2 - - + -
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ASP* 3.2 39.0 + - - +
89A GLN* 4.4 9.7 - - - +
91A ILE* 1.4 75.4 - - + +
93A SER* 1.4 59.0 + - - +
94A ARG 3.1 0.5 + - - -
95A ILE 3.1 0.2 + - - -
96A ASP* 2.6 55.5 + - + +
300A ARG* 5.2 17.2 - - - +
301A TYR* 4.1 15.0 - - + +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLN* 3.7 15.3 + - - -
90A LYS* 3.6 18.0 + - - +
91A ILE 3.4 0.2 - - - -
92A ARG* 1.4 76.5 - - - +
94A ARG* 1.3 60.8 + - - +
96A ASP* 4.4 8.8 - - - +
98A LYS 4.9 3.3 + - - +
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS 3.6 3.6 + - - +
91A ILE 3.3 9.3 + - - +
92A ARG 3.1 0.8 - - - -
93A SER* 1.3 79.5 - - - +
95A ILE* 1.3 64.9 + - + +
97A GLY 3.9 1.4 - - - +
98A LYS 3.1 32.6 + - - +
99A VAL* 2.8 39.2 + - + +
100A TRP* 4.0 16.2 - - - +
211A GLU* 5.5 3.0 + - - -
276A LEU* 3.3 35.1 + - + +
277A PHE* 3.6 32.3 - - + -
313A GLU* 5.2 0.8 + - - -
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 3.1 20.6 + - + +
94A ARG* 1.3 79.2 - - + +
96A ASP* 1.3 51.4 + - - +
97A GLY 2.6 28.2 + - - +
99A VAL* 3.9 6.6 - - + +
276A LEU* 4.9 4.3 - - + -
277A PHE* 4.9 3.6 - - + -
297A MET* 3.3 36.8 - - + -
301A TYR* 3.5 33.7 - - + +
305A ARG* 3.4 43.3 + - - +
309A LEU* 3.9 18.2 - - + -
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ARG* 2.6 47.2 + - - +
93A SER* 4.4 6.7 - - - +
94A ARG 4.6 1.3 - - - -
95A ILE* 1.3 65.8 - - - +
97A GLY* 1.3 56.2 + - - +
301A TYR* 2.8 28.4 + - - -
305A ARG* 5.4 0.9 + - - -
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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
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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