Contacts of the helix formed by residues 65 - 93 (chain A) in PDB entry 1GGZ
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 PHE 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.0 18.8 - - + -
12A PHE* 3.7 8.1 - - + -
13A LYS* 3.5 52.5 - - + -
16A PHE* 3.5 40.7 - + + -
25A GLY 4.0 1.8 + - - +
64A ASP* 1.3 76.9 - - - +
66A PRO* 1.3 70.0 - - + +
68A PHE* 3.1 5.6 + + - -
69A LEU* 2.7 59.6 + - + +
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Residues in contact with PRO 66 (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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64A ASP* 3.3 19.1 - - + +
65A PHE* 1.3 98.2 - - + +
67A GLU* 1.3 58.3 + - + +
69A LEU* 3.7 8.4 - - + +
70A GLY* 2.9 25.1 + - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.8 16.8 - - - +
56A ASP* 3.6 2.6 - - - +
57A ARG* 3.5 24.6 - - + +
58A ASP* 3.0 28.6 + - - +
62A THR 3.1 9.7 - - - +
63A VAL* 3.3 13.1 - - + -
64A ASP* 3.0 22.4 + - - +
66A PRO* 1.3 73.5 - - + +
68A PHE* 1.3 65.4 + - - +
70A GLY* 3.2 2.5 + - - +
71A MET* 3.0 22.7 + - - +
74A ARG* 4.7 1.6 + - - -
150A CA 2.4 30.4 - - - -
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.5 27.1 - - + -
15A ALA* 4.0 12.8 - - + -
16A PHE* 3.6 29.4 - + + -
19A PHE* 4.0 30.5 - + - -
27A ILE* 3.9 18.4 - - + -
55A ILE* 4.6 2.2 - - + -
63A VAL* 3.9 9.3 - - + +
64A ASP 2.9 14.3 + - - +
65A PHE* 3.5 11.0 - + - +
67A GLU* 1.3 76.5 - - - +
69A LEU* 1.3 64.0 + - - +
71A MET* 3.2 26.3 + - + +
72A MET* 3.0 50.1 + - + +
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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
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4A LEU* 3.5 32.1 - - + -
9A VAL* 4.4 15.9 - - + -
12A PHE* 3.6 31.0 - - + -
65A PHE* 2.7 45.2 + - + +
66A PRO* 3.7 8.3 - - + +
68A PHE* 1.3 73.9 - - - +
70A GLY* 1.3 57.8 + - - +
72A MET* 3.2 3.1 + - - +
73A ALA* 2.9 30.0 + - + +
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Residues in contact with GLY 70 (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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66A PRO 2.9 15.7 + - - -
67A GLU* 3.2 4.0 + - - -
68A PHE 3.2 0.2 - - - -
69A LEU* 1.3 76.8 - - - +
71A MET* 1.3 54.6 + - - +
73A ALA* 3.4 6.0 + - - +
74A ARG* 2.9 51.4 + - - +
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Residues in contact with MET 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.9 41.1 - - + -
67A GLU 3.0 12.3 + - - +
68A PHE* 3.4 30.3 - - + +
70A GLY* 1.3 73.6 - - - +
72A MET* 1.3 77.8 + - - +
74A ARG* 3.3 21.2 + - - +
75A LYS* 3.0 63.1 + - - +
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Residues in contact with MET 72 (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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12A PHE* 3.5 57.9 - - + -
15A ALA* 5.1 5.6 - - + -
68A PHE* 3.0 37.0 + - + +
69A LEU 3.2 6.0 + - - +
71A MET* 1.3 98.1 - - - +
73A ALA* 1.3 59.4 + - - +
75A LYS* 3.1 11.6 + - - +
76A MET* 2.9 36.0 + - - +
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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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4A LEU* 4.4 25.6 - - + -
12A PHE* 5.0 0.8 - - - -
69A LEU* 2.9 16.2 + - + +
70A GLY* 3.8 7.2 - - - +
72A MET* 1.3 75.2 - - - +
74A ARG* 1.3 58.6 + - + +
76A MET* 3.3 7.0 + - - +
77A LYS* 2.9 29.6 + - - +
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Residues in contact with ARG 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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54A GLU 4.8 5.5 + - - -
55A ILE* 5.0 4.6 + - - +
57A ARG* 3.2 34.1 - - - +
67A GLU 4.7 2.8 + - - -
70A GLY* 2.9 33.6 + - - +
71A MET* 3.4 28.6 - - - +
73A ALA* 1.3 76.2 - - + +
75A LYS* 1.3 59.2 + - + +
77A LYS* 3.3 6.0 + - - +
78A ASP* 2.9 37.6 + - - +
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Residues in contact with LYS 75 (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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71A MET* 3.0 49.0 + - + +
72A MET* 3.6 13.7 - - - +
74A ARG* 1.3 76.4 - - + +
76A MET* 1.3 64.9 + - + +
78A ASP* 3.2 7.5 + - - +
79A THR* 3.0 27.5 + - - +
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Residues in contact with MET 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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4A LEU* 4.1 15.3 - - + -
8A GLN* 3.3 27.8 - - + +
12A PHE* 3.5 35.2 - - + -
72A MET 2.9 17.6 + - - +
73A ALA* 3.7 4.9 - - - +
75A LYS* 1.3 77.4 - - + +
77A LYS* 1.3 57.7 + - - +
79A THR* 3.3 6.5 + - - -
80A ASP* 2.8 41.7 + - - +
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Residues in contact with LYS 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 2.9 17.5 + - - +
74A ARG* 3.7 7.9 - - - +
75A LYS 3.2 0.2 - - - -
76A MET* 1.3 75.7 - - - +
78A ASP* 1.3 60.5 + - - +
80A ASP* 3.2 12.5 + - + +
81A ASN* 2.8 56.9 + - - +
84A GLU* 4.7 7.3 + - - -
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Residues in contact with ASP 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 ARG* 2.9 21.5 + - - +
75A LYS* 3.2 7.2 + - - +
77A LYS* 1.3 76.8 - - - +
79A THR* 1.3 65.1 + - - +
81A ASN* 3.3 11.8 + - - +
82A GLU* 3.1 35.8 + - + +
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Residues in contact with THR 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 LYS* 3.0 14.8 + - - +
76A MET* 3.7 9.4 - - - -
78A ASP* 1.3 76.9 - - - +
80A ASP* 1.3 69.1 + - - +
82A GLU* 3.2 13.8 + - - +
83A GLU* 3.0 25.2 + - + +
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Residues in contact with ASP 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 MET* 2.8 29.1 + - - +
77A LYS* 3.5 12.8 - - + +
79A THR* 1.3 82.2 - - - +
81A ASN* 1.3 58.5 + - - +
83A GLU* 3.3 7.1 + - - +
84A GLU* 2.8 43.2 + - + +
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Residues in contact with ASN 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 LYS* 2.8 57.0 + - - +
78A ASP* 3.7 12.1 + - - +
79A THR 3.3 0.2 - - - -
80A ASP* 1.3 72.7 - - - +
82A GLU* 1.3 65.1 + - + +
84A GLU* 3.3 18.4 + - - +
85A ILE* 3.0 34.6 + - + +
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Residues in contact with GLU 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 ASP* 3.1 25.1 + - + +
79A THR* 3.6 12.3 + - - +
80A ASP 3.2 0.2 - - - -
81A ASN* 1.3 79.7 - - + +
83A GLU* 1.3 60.9 + - - +
85A ILE* 3.4 10.7 + - + +
86A ARG* 3.0 23.0 + - - +
138A TYR* 4.6 5.0 + - - +
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Residues in contact with GLU 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 THR* 3.0 19.5 + - + +
80A ASP* 3.7 7.6 - - - +
82A GLU* 1.3 72.7 - - - +
84A GLU* 1.3 60.6 + - + +
86A ARG* 3.0 38.8 + - - -
87A GLU* 2.5 62.8 + - - +
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Residues in contact with GLU 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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77A LYS* 4.7 6.6 + - - -
80A ASP* 2.8 26.8 + - + +
81A ASN* 3.6 24.5 - - - +
83A GLU* 1.3 78.6 - - + +
85A ILE* 1.3 57.5 + - + +
87A GLU* 3.4 8.9 + - - +
88A ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 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 ASN* 3.0 26.8 + - + +
82A GLU* 3.8 7.2 - - + +
84A GLU* 1.3 74.1 - - + +
86A ARG* 1.3 60.6 + - - +
88A ALA* 3.2 4.4 + - - +
89A PHE* 2.9 25.3 + - - +
138A TYR* 4.7 2.0 - - + +
141A PHE* 3.6 9.9 - - + -
142A VAL* 3.7 32.5 - - + -
145A LEU* 3.1 46.4 - - + +
146A VAL* 4.4 18.4 - - + -
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Residues in contact with ARG 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 GLU 3.0 13.9 + - - +
83A GLU* 3.0 40.8 + - - +
85A ILE* 1.3 77.0 - - - +
87A GLU* 1.3 71.8 + - - +
89A PHE* 3.2 4.6 + - + +
90A ARG* 2.3 88.9 + - + +
138A TYR* 4.0 31.6 - - + +
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Residues in contact with GLU 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 GLU* 2.5 59.5 + - - +
84A GLU* 3.8 8.1 - - - +
86A ARG* 1.3 78.6 - - - +
88A ALA* 1.3 66.6 + - - +
90A ARG* 3.1 11.4 + - - +
91A VAL* 2.9 30.5 + - + +
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Residues in contact with ALA 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 GLU 2.9 17.9 + - - +
85A ILE* 3.2 7.4 + - - +
87A GLU* 1.3 77.4 - - - +
89A PHE* 1.4 58.0 + - - +
91A VAL* 3.1 7.1 + - - +
92A PHE* 2.8 43.7 + - + -
141A PHE* 4.1 14.4 - - + -
145A LEU* 5.2 4.3 - - + -
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Residues in contact with PHE 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 ILE 2.9 13.9 + - - +
86A ARG* 3.2 8.5 + - + +
88A ALA* 1.4 76.6 - - - +
90A ARG* 1.3 66.2 + - + +
92A PHE* 3.2 4.2 + - - +
93A ASP* 2.8 35.3 + - + +
98A GLY* 3.4 37.2 - - - -
99A PHE 4.6 0.2 - - - -
100A VAL* 3.6 16.4 - - + -
136A VAL 3.6 12.6 - - - -
137A ASN 3.6 9.4 - - - -
138A TYR* 3.4 47.6 - + + -
141A PHE* 3.6 38.0 - + + -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 2.3 67.9 + - + +
87A GLU* 3.1 8.7 + - - +
89A PHE* 1.3 85.9 - - + +
91A VAL* 1.3 64.2 + - + +
93A ASP* 3.3 27.2 + - - +
94A LYS* 4.9 0.5 - - - -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 2.9 21.2 + - + +
88A ALA* 3.1 10.7 + - - +
90A ARG* 1.3 79.8 - - + +
92A PHE* 1.3 64.8 + - + +
93A ASP 3.4 0.3 + - - -
94A LYS* 4.0 10.6 + - - +
108A VAL* 4.4 18.7 - - + +
112A LEU* 6.3 0.4 - - + -
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 2.8 33.2 + - + +
89A PHE* 3.6 8.1 - - - +
91A VAL* 1.3 76.2 - - + +
93A ASP* 1.3 56.6 + - - +
94A LYS* 2.9 10.6 + - - +
100A VAL* 3.7 20.0 - - + -
104A GLU* 3.5 23.7 - - - +
105A LEU* 3.6 29.2 - - + -
108A VAL* 3.6 36.6 - - + +
109A MET* 4.2 14.6 - - - -
112A LEU* 5.3 9.9 - - + -
141A PHE* 3.7 29.4 - + + -
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 2.8 25.3 + - + +
90A ARG* 3.3 18.8 - - - +
91A VAL 3.2 0.6 - - - -
92A PHE* 1.3 70.6 - - - +
94A LYS* 1.3 58.2 + - - +
95A ASP* 3.2 6.1 - - - +
96A GLY* 2.9 24.2 + - - -
97A ASN* 3.2 1.0 - - - +
98A GLY* 2.7 32.7 + - - -
99A PHE 3.6 8.5 - - - +
100A VAL* 3.9 7.8 - - + +
104A GLU* 3.9 6.1 - - - -
151A CA 2.3 31.4 - - - -
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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