Contacts of the helix formed by residues 86 - 112 (chain D) in PDB entry 1BL8
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 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C PRO 5.9 3.1 - - - +
84D VAL 3.6 3.8 + - - -
85D THR* 1.3 75.6 - - + +
87D TRP* 1.3 89.6 + - + +
89D ARG* 3.2 24.2 + - + +
90D CYS* 3.2 9.4 + - - +
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Residues in contact with TRP 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU* 6.3 3.4 - - + -
50D ALA* 4.4 13.7 - - + -
85D THR* 3.1 7.8 - - + +
86D LEU* 1.3 106.4 - - + +
88D GLY* 1.3 58.2 + - - +
89D ARG 2.9 1.6 - - - -
90D CYS* 2.5 43.0 + - + +
91D VAL* 3.0 17.0 + - + +
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Residues in contact with GLY 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA* 4.8 4.3 - - - -
50D ALA* 4.0 13.2 - - - +
51D GLU* 4.4 4.0 - - - -
68D TRP* 4.2 2.9 - - - -
83D PRO* 3.2 27.3 - - - +
85D THR* 2.9 19.5 + - - -
87D TRP* 1.3 79.7 - - - +
89D ARG* 1.3 58.6 + - - +
91D VAL* 3.6 9.6 + - - +
92D ALA* 3.2 13.7 + - - +
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Residues in contact with ARG 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 5.7 4.6 - - - +
64C ARG* 5.7 5.1 - - - +
67C TRP* 3.1 69.3 - - + +
80C ASP* 4.2 7.7 + - - -
81C LEU* 5.6 2.8 - - - +
82D TYR* 4.5 5.9 - - - -
83D PRO* 2.9 36.1 + - - +
84D VAL* 3.6 26.9 + - - +
85D THR 2.8 28.0 + - - +
86D LEU* 3.2 17.3 - - + +
88D GLY* 1.3 73.7 - - - +
90D CYS* 1.3 67.5 + - - +
92D ALA* 3.1 14.6 - - - +
93D VAL* 3.1 8.1 + - - +
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Residues in contact with CYS 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LEU* 3.2 10.5 + - - -
87D TRP* 2.5 32.9 + - + +
89D ARG* 1.3 69.1 - - - +
91D VAL* 1.3 68.7 + - + +
92D ALA 2.9 1.1 - - - -
93D VAL* 2.7 23.1 + - - +
94D VAL* 3.0 14.4 + - + +
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Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLY* 3.5 39.9 - - - +
46D LEU* 3.4 30.7 - - + +
47D ALA* 4.0 16.6 - - + +
50D ALA* 5.5 0.7 - - + -
68D TRP* 4.2 4.7 - - + -
87D TRP* 3.0 14.5 + - + +
88D GLY* 3.7 7.9 - - - +
90D CYS* 1.3 76.3 - - + +
92D ALA* 1.3 60.6 + - - +
94D VAL* 3.5 9.9 + - + +
95D VAL* 2.9 25.5 + - - +
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TRP* 3.5 26.9 - - + -
78C TYR* 4.8 2.0 - - - +
68D TRP* 3.5 21.3 - - + -
83D PRO* 3.8 0.2 - - + -
88D GLY 3.2 9.4 + - - +
89D ARG 3.1 12.5 + - - +
90D CYS 2.7 1.2 + - - -
91D VAL* 1.3 73.6 - - - +
93D VAL* 1.3 67.9 + - - +
95D VAL* 2.7 28.4 - - - +
96D MET* 2.8 16.8 + - - +
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Residues in contact with VAL 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TRP* 4.8 3.1 - - + -
70C VAL* 3.3 37.9 - - + -
89D ARG 3.1 9.0 + - - +
90D CYS* 2.7 16.8 + - - +
92D ALA* 1.3 74.3 - - - +
94D VAL* 1.3 72.5 + - + +
96D MET* 2.8 26.7 + - - +
97D VAL* 3.0 17.9 + - + +
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 4.1 17.0 - - + -
43D GLY* 6.4 1.3 - - - -
90D CYS* 3.0 10.7 + - + +
91D VAL* 3.6 13.9 - - + +
93D VAL* 1.3 88.4 - - + +
95D VAL* 1.3 59.8 + - - +
96D MET 2.6 11.8 + - - -
97D VAL* 3.1 9.7 + - + +
98D ALA* 3.1 21.2 + - + +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 3.8 21.3 - - + +
40D LEU* 3.9 16.4 - - + -
43D GLY* 5.4 1.8 - - - -
68D TRP* 4.0 11.0 - - + -
69D SER* 3.5 37.7 - - - +
72D THR* 3.4 13.9 - - + -
73D ALA* 3.4 15.3 - - - +
91D VAL* 2.9 20.3 + - + +
92D ALA* 2.7 30.7 - - - +
94D VAL* 1.3 75.6 - - - +
96D MET* 1.3 61.2 + - - +
98D ALA* 3.9 3.0 - - - +
99D GLY 3.8 4.0 + - - -
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Residues in contact with MET 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TRP* 5.5 3.8 - - + -
70C VAL* 3.9 8.1 - - + +
71C GLU* 3.8 17.9 - - + -
74C THR* 2.9 49.6 - - + +
76C VAL* 3.2 17.0 - - + -
78C TYR* 5.4 4.3 - - + -
72D THR* 3.6 30.9 - - + +
73D ALA 4.3 1.9 - - - +
75D THR* 5.3 0.2 - - - -
92D ALA* 2.8 26.3 + - - +
93D VAL* 2.8 16.6 + - - +
94D VAL 2.6 5.3 + - - -
95D VAL* 1.3 70.6 - - - +
97D VAL* 1.3 56.4 + - + +
98D ALA 3.1 0.9 - - - -
99D GLY* 2.7 26.3 + - - -
100D ILE* 3.1 13.6 + - - +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 4.7 18.6 - - + -
93D VAL* 3.0 24.2 + - + +
94D VAL* 3.6 10.5 - - + +
96D MET* 1.3 73.7 - - + +
98D ALA* 1.3 81.3 + - + +
99D GLY 2.7 0.7 + - - -
100D ILE* 2.8 13.3 + - + +
101D THR* 2.6 34.6 + - + +
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Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 3.4 18.8 - - + -
39D VAL* 3.6 30.3 - - + -
94D VAL* 3.1 13.8 + - + +
95D VAL 3.9 3.4 - - - +
97D VAL* 1.3 85.1 - - + +
99D GLY* 1.3 53.7 + - - +
101D THR* 4.2 5.3 - - - +
102D SER* 2.6 39.0 + - - -
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Residues in contact with GLY 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 3.5 13.3 - - - +
73D ALA 3.4 21.3 - - - -
75D THR* 5.5 0.7 - - - -
95D VAL 3.8 1.6 + - - -
96D MET 2.7 16.2 + - - -
98D ALA* 1.3 71.5 - - - +
100D ILE* 1.3 64.2 + - - -
101D THR 2.9 1.3 - - - -
103D PHE* 3.0 36.6 + - - +
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Residues in contact with ILE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C THR* 3.2 37.9 - - + +
103C PHE* 3.4 62.8 - - + -
107C THR* 5.1 1.4 + - - -
73D ALA 4.3 1.2 + - - -
75D THR* 4.5 13.0 - - + +
96D MET* 3.1 10.0 + - + +
97D VAL* 2.8 14.4 + - + +
99D GLY* 1.3 70.4 - - - +
101D THR* 1.3 56.6 + - - +
103D PHE* 4.4 2.1 - - - +
104D GLY* 3.3 19.6 + - - -
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Residues in contact with THR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C PHE* 4.9 10.0 - - - -
106C VAL* 4.9 13.3 - - - +
110C LEU* 5.3 2.3 - - + +
97D VAL* 2.6 28.4 + - + +
98D ALA* 4.2 4.7 - - - +
100D ILE* 1.3 71.7 - - - +
102D SER* 1.3 64.6 + - - +
103D PHE 2.9 1.8 - - - -
104D GLY* 2.6 25.2 + - - +
105D LEU* 3.2 24.1 + - + +
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ALA* 5.1 10.1 - - - +
33D THR* 4.5 15.6 - - - +
36D LEU* 3.4 39.5 - - - +
98D ALA 2.6 25.7 + - - -
99D GLY 4.3 0.4 - - - -
101D THR* 1.3 77.3 - - - +
103D PHE* 1.3 66.0 + - - +
105D LEU* 3.9 10.1 + - - +
106D VAL* 3.6 19.2 + - - +
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Residues in contact with PHE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 4.7 19.1 - - + -
100A ILE* 3.5 54.7 - - + -
101A THR* 5.0 8.5 - - - -
36D LEU* 4.6 16.6 - - + -
73D ALA* 4.8 9.4 - - + -
74D THR* 5.1 4.5 - - + -
99D GLY* 3.0 28.0 + - - +
100D ILE* 4.4 2.0 - - - +
101D THR 2.7 4.2 + - - -
102D SER* 1.3 80.4 + - - +
104D GLY* 1.3 64.0 + - - +
106D VAL* 3.2 19.2 + - + +
107D THR* 3.2 18.4 + - - -
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Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C THR* 3.6 23.3 + - - +
110C LEU* 4.8 4.0 - - - -
100D ILE 3.3 11.7 + - - -
101D THR* 2.6 15.3 + - - -
103D PHE* 1.3 73.8 - - - +
105D LEU* 1.3 49.1 + - - -
107D THR* 2.8 12.5 + - - +
108D ALA* 2.7 33.3 + - - +
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.3 31.0 - - + +
113C TRP* 5.7 3.1 - - + -
114C PHE* 3.9 19.3 - - + -
28D ALA* 3.4 35.4 - - + +
29D ALA* 4.2 7.2 - - + +
32D ALA* 4.5 12.3 - - + -
101D THR* 3.2 27.2 + - + +
102D SER* 4.0 8.3 - - - +
104D GLY* 1.3 74.6 - - - +
106D VAL* 1.3 52.4 + - - +
108D ALA* 2.6 12.5 + - - +
109D ALA* 2.6 36.0 + - - +
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Residues in contact with VAL 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A THR* 5.0 11.7 - - - +
29D ALA* 4.3 14.8 - - + -
33D THR* 4.5 16.8 - - + -
102D SER 3.6 16.2 - - - +
103D PHE* 3.2 21.7 + - + +
105D LEU* 1.3 75.1 - - - +
107D THR* 1.3 59.8 + - - +
109D ALA* 3.6 6.9 - - + +
110D LEU* 2.9 47.2 + - + +
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Residues in contact with THR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ILE 5.2 1.4 + - - -
104A GLY* 3.7 25.5 - - - +
107A THR* 4.2 20.5 - - + +
108A ALA* 4.7 1.8 - - - +
107C THR* 4.0 23.6 - - + -
111C ALA* 5.9 0.4 - - + -
103D PHE 3.2 9.5 + - - -
104D GLY* 2.8 14.1 + - - +
106D VAL* 1.3 73.6 - - - +
108D ALA* 1.3 58.3 + - - +
110D LEU* 3.2 9.3 + - - +
111D ALA* 2.7 36.5 + - + +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C THR 4.5 1.6 - - - +
110C LEU* 3.7 40.2 - - + +
111C ALA* 3.7 10.3 - - - +
114C PHE* 3.7 9.6 - - + -
104D GLY 2.7 10.6 + - - +
105D LEU* 2.6 16.7 + - - +
107D THR* 1.3 73.9 - - - +
109D ALA* 1.3 67.1 + - - +
111D ALA* 2.8 15.3 + - - +
112D THR* 3.0 14.3 + - - +
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 3.4 6.8 - - + -
25D HIS* 2.9 39.0 + - - +
26D TRP* 3.4 20.6 - - + -
29D ALA* 4.1 12.1 - - + -
105D LEU 2.6 17.9 + - - +
106D VAL* 3.6 7.6 - - + +
108D ALA* 1.3 76.1 - - - +
110D LEU* 1.3 61.4 + - + +
113D TRP* 3.0 18.0 + - - +
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A THR* 5.4 2.9 - - + +
104A GLY* 5.0 1.3 - - - -
105A LEU* 3.4 48.0 - - + +
108A ALA* 3.9 10.8 - - + -
26D TRP* 3.5 30.7 - - + -
106D VAL* 2.9 35.2 + - + +
107D THR* 3.2 9.8 + - - +
108D ALA 3.2 0.4 - - - -
109D ALA* 1.3 78.7 - - + +
111D ALA* 1.3 63.5 + - - +
112D THR 3.3 0.5 + - - -
113D TRP* 3.4 10.2 + - + +
114D PHE* 3.3 29.1 + - + +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 6.0 0.2 - - + -
108A ALA* 3.8 15.6 - - - +
111A ALA* 4.3 18.9 - - + +
112A THR* 3.5 21.5 - - - +
111C ALA* 4.1 22.2 - - + +
115C VAL* 5.5 0.4 - - - -
107D THR* 2.7 20.4 + - + +
108D ALA* 2.8 12.6 + - - +
110D LEU* 1.3 73.0 - - - +
112D THR* 1.3 60.5 + - - +
115D VAL* 3.6 9.4 + - - +
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ALA 3.3 14.4 - - - +
114C PHE* 3.0 40.6 + - + -
115C VAL* 3.7 14.6 - - - -
25D HIS* 2.6 28.8 + - - -
108D ALA 3.0 14.6 - - - +
109D ALA 3.7 1.1 - - - +
111D ALA* 1.3 73.6 - - - +
113D TRP* 1.3 49.2 + - - +
114D PHE 2.8 5.8 - - - -
115D VAL* 2.5 29.4 + - - +
116D GLY* 2.6 16.5 + - - -
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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