Contacts of the helix formed by residues 85 - 109 (chain A) in PDB entry 1FX8
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 LYS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.2 36.0 - - + +
10A GLN* 2.7 33.8 + - - +
81A PHE* 3.8 21.5 - - + -
82A ASP* 3.0 41.6 + - + +
84A ARG* 1.3 79.6 - - + +
86A VAL* 1.3 62.5 + - - +
88A PRO* 3.3 9.4 - - - +
89A PHE* 3.0 33.1 + - + +
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Residues in contact with VAL 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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72A THR* 3.9 13.7 - - + -
73A ILE* 4.5 10.5 - - + -
76A TRP* 3.8 34.3 - - + -
81A PHE* 4.0 6.7 - - + -
82A ASP 3.8 3.4 - - - +
83A LYS* 3.4 30.2 + - + +
85A LYS* 1.3 78.6 - - - +
87A ILE* 1.3 65.1 + - + +
89A PHE* 3.6 1.6 - - - +
90A ILE* 3.0 50.6 + - + +
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Residues in contact with ILE 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 LYS 4.6 2.8 + - - +
86A VAL* 1.3 78.7 - - + +
88A PRO* 1.3 74.9 - - + +
90A ILE* 3.8 7.7 - - + +
91A VAL* 3.0 36.8 + - + +
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Residues in contact with PRO 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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7A LEU* 4.3 16.8 - - + -
11A CYS* 3.6 21.1 - - - -
84A ARG 3.3 18.8 - - - +
85A LYS* 3.3 17.0 - - - +
87A ILE* 1.3 96.5 - - + +
89A PHE* 1.3 54.5 + - - +
91A VAL* 4.1 5.5 - - + +
92A SER* 2.7 33.3 + - - -
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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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7A LEU* 4.1 9.0 - - + -
10A GLN* 3.7 41.5 - - + -
11A CYS* 4.4 6.5 - - - -
14A GLU* 3.8 26.9 - - + +
63A SER* 3.8 27.4 - - - -
66A HIS* 3.5 25.6 - + - -
72A THR* 4.1 5.4 - - + +
81A PHE* 3.6 24.2 - + - -
85A LYS* 3.0 23.6 + - + +
86A VAL 3.6 4.5 - - - +
88A PRO* 1.3 79.9 - - - +
90A ILE* 1.3 57.9 + - - +
92A SER* 3.2 7.1 + - - -
93A GLN* 2.9 40.6 + - - +
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Residues in contact with ILE 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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69A PRO* 4.1 25.6 - - + +
72A THR* 4.4 6.1 - - + -
73A ILE* 4.0 24.5 - - + -
86A VAL* 3.0 36.3 + - + +
87A ILE* 3.3 8.7 + - + +
89A PHE* 1.3 76.1 - - - +
91A VAL* 1.3 61.6 + - + +
93A GLN* 3.4 14.9 + - - +
94A VAL* 3.0 39.7 + - + +
474A BOG 5.5 7.4 - - + -
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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
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87A ILE* 3.0 35.7 + - + +
88A PRO* 4.1 4.7 - - + +
90A ILE* 1.3 79.0 - - + +
92A SER* 1.3 58.1 + - - +
94A VAL* 4.0 5.2 - - - +
95A ALA* 3.0 30.7 + - + +
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Residues in contact with SER 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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11A CYS* 3.1 41.9 + - - +
14A GLU* 4.1 7.6 - - - -
15A PHE* 3.5 17.3 - - - -
88A PRO 2.7 17.8 + - - -
89A PHE 3.2 9.7 + - - -
91A VAL* 1.3 77.6 - - - +
93A GLN* 1.3 65.4 + - - +
95A ALA* 3.4 4.0 + - - -
96A GLY 3.0 18.9 + - - -
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Residues in contact with GLN 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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14A GLU* 2.7 32.3 + - + +
18A THR* 3.2 31.2 - - + +
66A HIS* 3.6 1.0 - - - +
68A ASN 3.5 16.3 - - - +
69A PRO* 3.0 29.9 - - + +
72A THR* 3.1 23.6 + - - -
89A PHE* 2.9 24.5 + - - +
90A ILE* 3.5 9.5 - - - +
92A SER* 1.3 77.6 - - - +
94A VAL* 1.3 63.3 + - - +
96A GLY 3.3 0.2 + - - -
97A ALA* 3.1 19.6 + - - +
205A ALA* 3.7 14.8 - - + -
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Residues in contact with VAL 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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69A PRO* 4.8 1.3 - - + -
90A ILE* 3.0 28.6 + - + +
91A VAL* 4.0 5.4 - - - +
93A GLN* 1.3 75.3 - - - +
95A ALA* 1.3 62.0 + - - +
97A ALA* 3.5 2.5 + - - +
98A PHE* 3.1 23.8 + - + +
204A PRO 5.5 0.7 - - - +
205A ALA* 3.9 22.7 - - + +
208A PHE* 4.4 15.9 - - + -
209A GLY* 4.1 20.9 - - - +
474A BOG 4.8 14.4 - - + -
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Residues in contact with ALA 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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15A PHE* 3.5 19.7 - - + -
91A VAL* 3.0 22.8 + - + +
92A SER* 3.8 2.0 - - - +
94A VAL* 1.3 77.6 - - - +
96A GLY* 1.3 62.3 + - - +
98A PHE* 3.4 6.0 + - - +
99A CYS* 3.0 31.1 + - - -
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Residues in contact with GLY 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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15A PHE* 3.3 38.5 - - - -
19A GLY* 3.3 17.2 - - - -
92A SER 3.0 13.1 + - - -
93A GLN 3.8 1.1 - - - -
95A ALA* 1.3 75.8 - - - +
97A ALA* 1.3 63.7 + - - +
99A CYS* 3.4 1.4 + - - +
100A ALA 3.0 18.7 + - - -
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Residues in contact with ALA 97 (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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18A THR* 4.0 4.5 - - + +
22A ILE* 3.7 32.5 - - + +
93A GLN 3.1 15.7 + - - +
94A VAL 3.8 3.1 - - - +
95A ALA 3.3 0.2 - - - -
96A GLY* 1.3 75.2 - - - +
98A PHE* 1.3 64.2 + - - +
101A ALA* 3.1 24.4 + - - +
205A ALA 3.3 30.3 - - - +
210A PRO* 3.9 9.3 - - + +
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Residues in contact with PHE 98 (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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94A VAL* 3.1 18.5 + - + +
95A ALA* 3.6 6.3 - - - +
97A ALA* 1.3 76.9 - - - +
99A CYS* 1.3 75.8 + - - +
101A ALA* 3.3 5.9 + - - +
102A ALA* 3.1 18.9 + - - +
209A GLY* 3.4 30.2 - - - +
212A VAL* 4.1 11.4 - - + -
213A PHE* 3.7 30.3 - + + +
216A LEU* 3.8 24.7 - - + -
473A BOG 3.9 36.1 - - + -
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Residues in contact with CYS 99 (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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15A PHE* 3.7 25.6 - - + -
95A ALA* 3.0 26.0 + - - +
96A GLY 3.9 2.9 - - - +
98A PHE* 1.3 88.3 - - - +
100A ALA* 1.3 59.9 + - - +
102A ALA* 3.1 8.8 + - - +
103A LEU* 2.9 27.6 + - - +
473A BOG 5.2 9.0 - - + -
475A BOG 4.8 12.2 - - + +
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Residues in contact with ALA 100 (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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19A GLY* 3.0 31.2 - - - +
22A ILE* 3.3 18.2 - - + -
23A PHE* 4.0 7.1 - - + +
96A GLY 3.0 16.6 + - - +
99A CYS* 1.3 73.9 - - - +
101A ALA* 1.3 67.3 + - - +
103A LEU* 3.1 11.5 + - - +
104A VAL* 2.9 27.2 + - - +
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Residues in contact with ALA 101 (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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22A ILE* 3.6 7.0 - - + +
26A VAL* 5.0 2.2 - - + -
97A ALA 3.1 14.3 + - - +
98A PHE 3.5 10.1 - - - +
99A CYS 3.2 0.2 - - - -
100A ALA* 1.3 76.5 - - - +
102A ALA* 1.3 62.7 + - - +
104A VAL* 3.4 5.0 + - - +
105A TYR* 3.0 24.3 + - - +
135A PHE* 3.8 20.0 - - + -
210A PRO* 3.9 30.3 - - + -
213A PHE* 4.3 8.1 - - + -
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Residues in contact with ALA 102 (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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98A PHE* 3.1 9.3 + - + +
99A CYS 3.1 10.0 + - - +
101A ALA* 1.3 79.4 - - - +
103A LEU* 1.3 56.8 + - - +
105A TYR* 3.3 2.9 + - - +
106A GLY* 2.9 24.4 + - - -
213A PHE* 3.6 31.3 - - + -
473A BOG 4.0 26.7 - - + -
475A BOG 3.7 18.1 - - - +
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Residues in contact with LEU 103 (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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23A PHE* 3.8 28.5 - - + -
99A CYS 2.9 14.2 + - - +
100A ALA* 3.5 11.4 - - - +
102A ALA* 1.3 77.2 - - - +
104A VAL* 1.3 62.7 + - - +
106A GLY* 3.1 1.7 + - - -
107A LEU* 3.0 43.1 + - + +
475A BOG 4.0 56.9 - - + +
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Residues in contact with VAL 104 (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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23A PHE* 3.6 43.7 - - + +
26A VAL* 3.8 27.8 - - + +
27A GLY* 3.8 19.1 - - - +
30A ALA* 4.4 4.7 - - + -
100A ALA 2.9 20.6 + - - +
101A ALA 3.8 4.5 - - - +
103A LEU* 1.3 75.0 - - - +
105A TYR* 1.3 63.9 + - - +
107A LEU* 3.2 7.3 + - - -
108A TYR* 3.0 37.4 + - + +
112A PHE* 5.8 0.4 - - + -
134A THR* 5.5 0.4 - - + -
135A PHE* 5.5 1.1 - - + -
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Residues in contact with TYR 105 (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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101A ALA 3.0 17.0 + - - +
102A ALA 3.6 2.0 - - - +
104A VAL* 1.3 76.6 - - - +
106A GLY* 1.3 53.9 + - - +
109A TYR* 2.7 54.9 + + - +
112A PHE* 3.9 30.3 - + + -
113A PHE* 3.2 11.8 - - - -
123A ARG* 2.9 33.0 + - - -
135A PHE* 4.0 18.1 - + + -
213A PHE* 3.5 18.8 - + + -
217A ALA* 4.5 2.0 - - + -
219A TRP* 4.3 6.1 - + - -
473A BOG 2.7 35.0 + - - -
475A BOG 3.2 29.4 - - - -
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Residues in contact with GLY 106 (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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102A ALA 2.9 11.0 + - - -
103A LEU 3.1 4.0 + - - -
105A TYR* 1.3 78.9 - - - +
107A LEU* 1.3 62.3 + - - +
109A TYR* 3.5 14.8 - - - +
475A BOG 3.4 40.1 + - - -
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Residues in contact with LEU 107 (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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23A PHE* 3.8 31.2 - - + -
103A LEU* 3.0 31.4 + - + +
104A VAL* 3.2 5.6 + - - +
106A GLY* 1.3 80.3 - - - +
108A TYR* 1.3 68.4 + - + +
109A TYR* 3.3 1.2 + - - +
111A LEU* 5.2 3.3 - - - +
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Residues in contact with TYR 108 (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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27A GLY* 3.4 28.6 + - - -
30A ALA* 4.0 5.2 - - + -
31A ALA* 3.4 29.9 - - - +
34A VAL* 4.0 17.7 - - + -
35A ALA* 4.1 11.6 - - + +
104A VAL* 3.0 33.9 + - + +
105A TYR 3.5 0.7 - - - -
107A LEU* 1.3 82.9 - - + +
109A TYR* 1.3 65.7 + - - +
110A ASN 3.4 2.0 - - - -
111A LEU* 2.9 34.1 + - + +
112A PHE* 3.3 25.7 + - + -
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Residues in contact with TYR 109 (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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105A TYR* 2.7 40.1 + + - +
106A GLY* 3.5 13.7 - - - +
107A LEU 3.3 1.8 - - - +
108A TYR* 1.3 70.5 - - - +
110A ASN* 1.3 83.0 + - - +
112A PHE* 3.1 17.2 + - - +
113A PHE* 3.4 52.1 - + + -
473A BOG 3.6 17.4 + - - -
475A BOG 3.9 21.1 - - - +
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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
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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