Contacts of the helix formed by residues 64 - 95 (chain A) in PDB entry 4DAJ
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 ILE 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 1.3 63.2 + - - +
66A GLN* 3.5 3.6 - - - +
67A VAL* 3.4 17.6 - - - +
68A VAL* 3.0 28.2 + - - +
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Residues in contact with TRP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 1.3 75.8 - - - +
66A GLN* 1.3 61.3 + - - +
68A VAL* 3.2 6.7 + - - +
69A PHE* 2.9 27.8 + - - +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE 4.5 2.6 - - - +
65A TRP* 1.3 77.8 - - - +
67A VAL* 1.3 63.4 + - - +
69A PHE* 3.2 8.3 + - + +
70A ILE* 2.9 37.3 + - + +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 3.4 22.0 + - - +
66A GLN* 1.3 80.7 - - - +
68A VAL* 1.3 57.8 + - - +
70A ILE* 3.3 4.7 + - - +
71A ALA* 2.9 28.5 + - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE 3.0 16.8 + - - +
65A TRP* 3.6 6.1 - - - +
67A VAL* 1.3 75.1 - - - +
69A PHE* 1.3 64.3 + - - +
71A ALA* 3.1 23.1 + - - +
72A PHE* 3.9 5.2 + - - +
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP 2.9 14.1 + - - +
66A GLN* 3.2 13.4 + - + +
68A VAL* 1.3 77.5 - - - +
70A ILE* 1.3 65.8 + - + +
72A PHE* 4.2 10.2 + - - +
73A LEU 5.1 0.5 + - - -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLN* 2.9 32.7 + - + +
67A VAL* 3.9 4.9 - - - +
69A PHE* 1.3 80.8 - - + +
71A ALA* 1.3 66.2 + - - +
72A PHE 3.2 1.3 - - - -
73A LEU* 3.1 34.7 + - + +
74A THR* 5.4 0.5 - - - +
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL 2.9 13.6 + - - +
68A VAL* 3.1 18.3 + - - +
70A ILE* 1.3 77.7 - - - +
72A PHE* 1.3 55.8 + - - +
73A LEU 3.1 1.0 + - - -
74A THR* 2.8 36.5 + - - +
125A THR* 4.5 8.7 - - + +
129A ILE* 5.7 9.4 - - + -
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL 3.9 4.4 + - - +
69A PHE 4.5 8.7 - - - +
70A ILE 3.1 1.4 + - - -
71A ALA* 1.3 75.1 - - - +
73A LEU* 1.3 64.8 + - - +
74A THR* 3.1 0.7 - - - -
75A GLY* 2.8 16.6 + - - +
76A PHE* 2.9 12.0 + - - +
125A THR* 6.0 0.9 - - - -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE 5.1 0.6 + - - -
70A ILE* 3.1 29.2 + - + +
72A PHE* 1.3 76.8 - - - +
74A THR* 1.3 64.2 + - + +
76A PHE* 3.1 25.7 + - + +
77A LEU* 3.0 22.0 + - + +
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE 5.4 0.4 - - - +
71A ALA* 2.8 21.1 + - - +
73A LEU* 1.3 79.3 - - + +
75A GLY* 1.3 70.2 + - - +
77A LEU* 3.0 10.8 + - - +
78A ALA* 2.9 22.7 + - - +
121A MET* 4.6 2.1 - - - +
125A THR* 3.1 23.7 + - + +
128A ILE* 5.9 0.7 - - + -
530A TRP* 3.4 47.0 - - + +
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Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 2.8 14.5 + - - +
74A THR* 1.3 79.0 + - - +
76A PHE* 1.3 61.3 + - - -
78A ALA* 3.1 8.8 + - - +
79A LEU* 2.9 24.5 + - - +
122A ASN* 5.9 0.2 - - - -
125A THR* 5.2 4.9 - - - -
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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
----------------------------------------------------------
72A PHE 2.9 10.7 + - - +
73A LEU* 3.1 27.1 - - + +
75A GLY* 1.3 74.4 - - - +
77A LEU* 1.3 62.8 + - + +
79A LEU* 3.3 11.6 + - + +
80A VAL* 3.0 54.6 + - + +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.0 12.2 + - + +
74A THR* 3.0 11.6 + - - +
76A PHE* 1.3 83.6 - - + +
78A ALA* 1.3 52.7 + - - +
80A VAL* 3.5 6.5 + - - +
81A THR* 2.6 37.8 + - - -
121A MET* 3.8 12.6 - - + -
530A TRP* 5.8 1.3 - - + -
534A ILE* 5.8 6.7 - - + -
537A THR* 3.9 8.9 + - + +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR 2.9 12.5 + - - +
75A GLY* 3.1 11.6 + - - +
77A LEU* 1.3 73.3 - - - +
79A LEU* 1.3 67.3 + - - +
81A THR* 3.2 3.5 + - - -
82A ILE* 2.9 30.6 + - + +
117A GLY 3.7 6.7 - - - +
121A MET* 3.6 23.5 - - + +
122A ASN* 3.4 26.0 - - - +
125A THR* 5.9 0.7 - - - +
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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
----------------------------------------------------------
75A GLY 2.9 12.1 + - - +
76A PHE* 3.5 13.7 - - + +
78A ALA* 1.3 75.4 - - - +
80A VAL* 1.3 66.1 + - + +
82A ILE* 2.9 40.5 - - + +
83A ILE* 2.9 25.2 + - + +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 3.0 53.3 + - + +
77A LEU* 3.6 6.5 - - - +
79A LEU* 1.3 75.9 - - + +
81A THR* 1.3 57.8 + - - +
83A ILE* 3.0 17.2 - - + +
84A GLY* 2.9 28.5 + - - -
537A THR* 4.1 17.1 - - + +
541A VAL* 5.8 6.3 - - + -
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 2.6 15.9 + - - -
78A ALA 3.3 8.1 - - - -
79A LEU 3.1 0.2 - - - -
80A VAL* 1.3 77.7 - - - +
82A ILE* 1.3 57.5 + - - +
84A GLY* 3.8 0.4 - - - -
85A ASN* 2.8 55.8 + - - +
113A ASP 3.6 12.3 - - - +
117A GLY* 4.0 9.6 - - - -
121A MET* 3.5 11.5 - - - -
536A SER* 3.7 18.8 - - - +
537A THR* 2.5 33.6 + - - +
540A PRO* 5.0 0.3 - - - +
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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
----------------------------------------------------------
78A ALA* 2.9 10.7 + - + +
79A LEU* 2.9 51.4 - - + +
81A THR* 1.3 77.0 - - - +
83A ILE* 1.3 61.3 + - + +
85A ASN* 4.1 5.0 - - - +
86A ILE* 2.9 31.6 + - - +
114A LEU* 4.3 11.3 - - + +
117A GLY* 3.3 35.9 - - - +
118A VAL* 3.3 24.5 - - + +
122A ASN* 5.8 3.1 - - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 2.9 29.3 + - + +
80A VAL* 3.0 37.9 - - + +
82A ILE* 1.3 80.6 - - + +
84A GLY* 1.3 64.4 + - - +
86A ILE* 2.8 27.8 - - + +
87A LEU* 2.9 18.6 + - + +
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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
----------------------------------------------------------
80A VAL 2.9 17.4 + - - -
81A THR* 3.8 0.7 - - - -
83A ILE* 1.3 77.3 - - - +
85A ASN* 1.3 62.6 + - - +
87A LEU* 3.1 15.1 + - - +
88A VAL* 3.0 22.2 + - - +
540A PRO* 4.0 17.4 - - - +
554A PHE* 4.7 1.0 - - - -
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Residues in contact with ASN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 2.8 32.8 + - - +
82A ILE 4.1 0.7 - - - +
84A GLY* 1.3 75.5 - - - +
86A ILE* 1.3 63.0 + - - +
88A VAL* 2.8 20.7 + - - +
89A ILE* 2.9 18.1 + - - +
110A ALA* 3.4 20.8 - - - +
113A ASP* 3.0 50.2 + - - +
114A LEU* 3.7 12.2 - - + +
536A SER 3.7 0.8 + - - -
540A PRO* 2.8 26.7 - - - +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE 2.9 19.6 + - - +
83A ILE* 2.8 33.7 - - + +
85A ASN* 1.3 75.7 - - - +
87A LEU* 1.3 60.7 + - + +
89A ILE* 3.4 9.8 + - + +
90A VAL* 3.0 45.5 + - + +
114A LEU* 3.6 23.9 - - + +
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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
----------------------------------------------------------
83A ILE* 2.9 22.6 + - + +
84A GLY* 3.1 15.0 - - - +
86A ILE* 1.3 78.9 - - + +
88A VAL* 1.3 66.2 + - - +
90A VAL* 4.0 8.4 - - + +
91A ALA* 2.9 28.8 + - - +
554A PHE* 3.3 44.7 - - + +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 3.0 15.1 + - - +
85A ASN* 2.8 11.3 + - - +
87A LEU* 1.3 75.9 - - - +
89A ILE* 1.3 64.9 + - - +
91A ALA* 3.8 1.4 - - - +
92A PHE* 3.0 26.1 + - + +
106A LEU* 4.3 3.6 - - + +
107A LEU* 4.7 7.2 - - - -
110A ALA* 3.4 25.6 - - + -
540A PRO* 3.8 23.1 - - + -
543A TYR* 3.9 22.9 - - + -
550A PHE* 5.0 12.1 - - + -
554A PHE* 3.8 17.9 - - + -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN 2.9 12.8 + - - +
86A ILE* 3.5 12.8 - - + +
88A VAL* 1.3 80.3 - - + +
90A VAL* 1.3 67.4 + - + +
92A PHE* 3.3 4.0 + - - +
93A LYS* 3.0 45.9 + - + +
107A LEU* 5.1 9.1 - - + +
110A ALA* 4.9 6.5 - - + -
111A CYS* 4.0 27.6 - - - -
114A LEU* 3.4 33.0 - - + -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 3.0 30.5 + - + +
87A LEU* 4.0 9.2 - - + +
89A ILE* 1.3 78.1 - - + +
91A ALA* 1.3 65.3 + - - +
93A LYS* 3.0 7.2 + - - +
94A VAL* 2.9 33.1 + - + +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 2.9 22.3 + - + +
88A VAL* 3.8 1.8 - - - +
90A VAL* 1.3 73.1 - - - +
92A PHE* 1.3 62.3 + - - +
94A VAL* 3.5 9.6 - - - +
95A ASN* 3.2 21.3 + - - +
98A LEU* 3.3 17.7 - - + +
550A PHE* 5.5 1.1 - - + -
553A THR* 3.4 24.5 - - + +
554A PHE* 3.6 20.9 - - + -
----------------------------------------------------------
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.0 20.6 + - + +
89A ILE 3.7 3.4 - - - +
91A ALA* 1.3 79.0 - - - +
93A LYS* 1.3 71.3 - - + +
95A ASN 3.4 15.4 - - - +
98A LEU* 3.0 37.6 - - + +
99A LYS* 3.5 39.1 - - + +
100A THR 4.1 3.8 - - - -
103A ASN* 3.2 34.8 - - + -
104A TYR* 4.0 24.7 - + - -
107A LEU* 3.5 28.3 - - + -
181A THR* 5.9 0.4 - - + -
550A PHE* 5.4 6.5 - + + -
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.0 35.6 + - + +
90A VAL* 3.0 6.0 + - - +
92A PHE* 1.3 84.9 - - + +
94A VAL* 1.3 60.3 + - - +
95A ASN 3.7 0.9 + - - -
99A LYS* 5.3 12.9 + - - +
104A TYR* 6.0 3.6 - - - -
107A LEU* 3.6 32.1 - - + +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 2.9 28.6 + - + +
91A ALA* 3.5 13.7 - - - +
93A LYS* 1.3 78.6 - - - +
95A ASN* 1.3 62.4 + - + +
96A LYS 4.2 0.8 + - - -
553A THR* 4.8 4.9 - - + -
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Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 3.2 16.2 + - - +
92A PHE 3.4 13.6 - - - +
93A LYS 3.5 1.6 - - - -
94A VAL* 1.3 81.3 - - + +
96A LYS* 1.3 65.5 + - - +
97A GLN* 2.8 43.7 + - - +
98A LEU* 3.0 18.9 + - + +
99A LYS* 3.6 3.5 + - - +
553A THR* 3.5 27.4 + - + +
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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