Contacts of the helix formed by residues 65 - 89 (chain C) in PDB entry 2IT0
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 THR 65 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLY* 2.8 30.4 + - - +
53C LEU 3.2 7.0 + - - -
54C LEU* 3.7 24.2 - - - +
55C ARG* 3.9 21.1 - - + +
63C GLU 3.7 0.2 + - - -
64C LEU* 1.3 76.6 - - - +
66C GLU* 1.3 55.5 + - - +
67C LYS* 3.6 3.2 + - - -
68C GLY 3.0 12.1 + - - -
69C ARG* 2.7 32.7 + - - +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C THR* 1.3 72.9 - - - +
67C LYS* 1.3 65.0 + - - +
69C ARG* 3.9 5.5 - - - +
70C ALA* 3.0 24.6 + - - +
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ASP* 3.6 17.6 + - - +
52C GLY* 3.5 24.2 - - - +
53C LEU* 3.7 17.8 - - + +
65C THR* 3.1 2.1 - - - +
66C GLU* 1.3 82.0 - - - +
68C GLY* 1.3 62.1 + - - +
70C ALA* 3.3 12.9 + - - +
71C LEU* 3.3 23.6 + - + +
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Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 10.0 - - - +
53C LEU* 3.3 33.4 - - - -
64C LEU* 4.3 5.4 - - - -
65C THR* 3.0 7.9 + - - -
67C LYS* 1.3 76.9 - - - +
69C ARG* 1.3 61.0 + - - +
71C LEU* 3.2 4.9 + - - +
72C ALA* 2.9 29.3 + - - +
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 3.3 34.6 - - - -
19C GLU* 3.0 36.2 + - - -
64C LEU* 3.6 36.9 + - + +
65C THR 2.7 21.8 + - - +
66C GLU* 3.9 5.8 - - - +
68C GLY* 1.3 72.2 - - - -
70C ALA* 1.3 63.6 + - - +
72C ALA* 3.8 0.3 - - - +
73C ILE* 3.0 38.8 + - + +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLU 3.0 13.4 + - - +
67C LYS* 3.4 11.9 - - - +
69C ARG* 1.3 79.8 - - - +
71C LEU* 1.3 67.6 + - + +
73C ILE* 3.4 8.4 + - - +
74C ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C THR* 6.0 0.7 - - + -
9C GLU* 6.2 2.5 - - + -
12C LEU* 4.1 15.9 - - + -
53C LEU* 3.9 28.9 - - + -
67C LYS* 3.4 22.7 - - + +
68C GLY 3.2 6.1 + - - +
70C ALA* 1.3 80.5 - - + +
72C ALA* 1.3 62.6 + - - +
74C ALA* 3.1 10.6 + - + +
75C VAL* 3.1 27.9 + - + +
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 32.5 - - + +
13C ARG* 4.9 3.5 - - - +
16C TYR* 4.3 13.8 - - + -
64C LEU* 3.9 17.5 - - + -
68C GLY 2.9 16.9 + - - +
69C ARG 3.8 4.0 - - - +
71C LEU* 1.3 76.5 - - - +
73C ILE* 1.3 63.4 + - - +
75C VAL* 3.2 6.9 + - - +
76C MET* 3.0 23.0 + - - +
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Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TYR* 4.1 20.2 - - + +
69C ARG* 3.0 44.0 + - + +
70C ALA* 3.6 7.0 - - - +
72C ALA* 1.3 72.7 - - - +
74C ALA* 1.3 56.8 + - - +
75C VAL 3.1 0.3 + - - -
76C MET* 3.1 4.9 + - - +
77C ARG* 2.8 40.6 + - - +
133C PRO* 3.7 26.6 - - + +
134C GLY* 3.9 20.0 - - - +
137C GLU* 5.5 8.1 - - + +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA 3.1 10.6 + - - +
71C LEU* 3.1 14.6 + - + +
73C ILE* 1.3 77.5 - - - +
75C VAL* 1.3 58.3 + - + +
77C ARG* 3.4 30.0 + - - +
78C LYS* 3.1 44.5 + - - +
110C GLU* 4.8 4.3 - - - +
113C GLU* 4.2 0.7 - - - +
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 3.8 38.1 - - + +
12C LEU* 6.0 0.4 - - + -
13C ARG* 4.0 17.0 - - + -
71C LEU* 3.1 17.7 + - + +
72C ALA* 3.6 9.2 - - - +
73C ILE 3.1 0.4 - - - -
74C ALA* 1.3 74.8 - - + +
76C MET* 1.3 61.7 + - - +
77C ARG 3.1 1.3 - - - -
78C LYS* 3.1 12.0 + - - +
79C HIS* 2.7 26.9 + - - +
105C GLU* 3.6 36.3 - - + +
106C HIS* 4.5 6.7 - - + +
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Residues in contact with MET 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 4.1 16.8 - - + +
16C TYR* 3.4 34.8 - - + -
17C ASP* 3.5 24.7 - - - +
20C GLU* 4.0 2.7 - - - +
72C ALA 3.0 12.9 + - - +
73C ILE* 3.7 2.7 - - - +
75C VAL* 1.3 76.8 - - - +
77C ARG* 1.3 57.4 + - - +
79C HIS* 3.4 15.9 - - - +
80C ARG* 2.9 74.9 + - - +
133C PRO* 3.5 21.8 - - + -
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Residues in contact with ARG 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 2.8 20.1 + - - +
74C ALA* 3.5 22.7 - - - +
76C MET* 1.3 76.2 - - - +
78C LYS* 1.3 58.7 + - - +
80C ARG 3.9 0.3 - - - -
81C LEU* 3.0 36.3 + - + +
110C GLU* 3.0 29.3 + - - +
113C GLU* 2.6 32.7 + - - +
132C ILE* 3.8 19.3 - - + +
133C PRO* 3.3 24.0 + - - +
134C GLY* 3.1 25.1 + - - -
135C LEU* 4.5 4.7 - - + +
137C GLU* 4.5 7.3 - - - +
138C LEU* 3.6 31.3 - - - +
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 6.2 0.2 - - - -
74C ALA* 3.1 32.9 + - - +
75C VAL* 3.6 9.0 - - - +
77C ARG* 1.3 73.2 - - - +
79C HIS* 1.3 68.0 + - - +
81C LEU* 3.2 1.7 + - - +
82C ALA* 2.7 26.1 + - - +
105C GLU* 3.2 33.0 - - - +
106C HIS 5.7 0.2 - - - -
108C MET* 2.9 43.9 + - + +
109C SER* 3.9 3.6 - - - +
110C GLU* 3.8 16.2 - - - +
113C GLU* 2.9 39.7 + - + +
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Residues in contact with HIS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG* 3.6 12.9 + - - -
75C VAL 2.7 13.1 + - - +
76C MET* 3.4 19.1 - - - +
78C LYS* 1.3 78.6 - - - +
80C ARG* 1.3 65.5 + - + +
82C ALA* 3.0 6.6 + - - +
83C GLU* 2.7 36.4 + - - +
98C HIS* 3.3 15.4 - + - -
101C ALA* 3.7 22.1 - - + +
102C CYS 3.9 5.2 - - - -
105C GLU* 3.1 32.5 + - - +
1001C NI 2.0 45.1 - - + +
2001C ACT 4.0 2.9 - - - -
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Residues in contact with ARG 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TYR* 5.0 0.6 - - - -
17C ASP* 4.6 4.6 + - - -
20C GLU* 2.8 33.8 + - - -
76C MET* 2.9 57.7 + - - +
77C ARG 4.3 0.7 - - - +
79C HIS* 1.3 75.2 - - + +
81C LEU* 1.3 66.6 + - - +
83C GLU* 3.5 12.6 + - - +
84C ARG* 3.1 26.0 + - - +
126C SER* 3.3 23.4 - - - -
127C PRO* 4.4 1.7 - - - +
130C ASN* 3.7 18.9 - - - +
131C PRO* 3.2 28.3 + - - +
132C ILE* 3.8 20.4 - - + -
133C PRO* 4.6 1.7 - - - +
2001C ACT 3.7 22.4 + - - +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 3.0 24.3 + - + +
78C LYS* 3.7 5.4 - - - +
80C ARG* 1.3 72.5 - - - +
82C ALA* 1.3 65.9 + - - +
84C ARG* 3.3 6.3 + - + +
85C LEU* 3.0 24.6 + - - +
108C MET* 4.5 1.3 - - + -
113C GLU* 3.5 50.3 - - + +
116C LEU* 3.9 23.6 - - + +
117C VAL* 4.4 9.4 - - + -
120C LEU* 4.2 1.6 - - + +
123C PRO* 4.4 15.5 - - + -
132C ILE* 3.8 30.1 - - + -
135C LEU* 4.8 6.5 - - + -
138C LEU* 4.5 4.0 - - + -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LYS 2.7 13.2 + - - +
79C HIS* 3.0 11.4 + - - +
81C LEU* 1.3 73.8 - - - +
83C GLU* 1.3 67.4 + - - +
84C ARG 3.1 0.5 + - - -
85C LEU* 3.2 8.7 + - - +
86C LEU* 2.9 32.3 + - + +
101C ALA* 3.7 20.2 - - + -
104C TRP* 4.2 20.4 - - + -
108C MET* 4.2 10.7 - - - -
116C LEU* 5.3 0.2 - - - -
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C HIS* 2.7 17.5 + - - +
80C ARG* 3.5 19.2 - - - +
81C LEU 3.4 0.2 - - - -
82C ALA* 1.3 76.2 - - - +
84C ARG* 1.3 64.4 + - - +
86C LEU* 3.3 9.4 + - - +
87C VAL* 3.2 26.2 + - - +
97C VAL* 4.2 12.6 - - + +
98C HIS* 3.2 7.4 + - - +
101C ALA* 3.7 12.8 - - + -
126C SER* 3.3 18.0 + - - -
127C PRO* 3.5 14.8 - - + -
128C PHE* 4.3 11.6 - - + -
1001C NI 1.9 44.6 - - - +
2001C ACT 3.3 2.2 - - - +
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ARG 3.1 15.4 + - - +
81C LEU* 3.4 10.5 - - - +
82C ALA 3.1 0.2 - - - -
83C GLU* 1.3 75.2 - - - +
85C LEU* 1.3 64.9 + - - +
87C VAL* 2.9 4.8 + - - +
88C ASP* 2.8 68.3 + - - +
120C LEU* 4.0 13.9 - - + -
123C PRO* 3.8 29.1 - - + +
125C THR* 3.1 39.5 + - - +
126C SER 4.2 1.2 + - - -
127C PRO* 3.5 32.8 - - + +
132C ILE* 4.8 3.1 - - + -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU 3.0 10.5 + - - +
82C ALA* 3.4 9.0 - - - +
84C ARG* 1.3 78.4 - - - +
86C LEU* 1.3 57.3 + - - +
89C VAL* 3.4 25.9 + - + -
90C ILE* 3.1 34.8 + - + +
104C TRP* 4.0 27.6 - - + -
108C MET* 5.8 0.9 - - - -
116C LEU* 4.4 24.2 - - + -
119C VAL* 6.0 1.6 - - + -
120C LEU* 3.8 18.0 - - + +
85D LEU* 4.8 5.4 - - + -
89D VAL* 5.3 2.0 - - + -
90D ILE* 4.2 27.6 - - + -
104D TRP* 4.6 4.5 - - + -
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ALA* 2.9 28.0 + - + +
83C GLU* 3.6 6.3 - - - +
85C LEU* 1.3 77.4 - - - +
87C VAL* 1.3 60.7 + - - +
90C ILE* 3.7 25.6 - - + +
91C GLY 2.9 7.3 + - - -
92C LEU* 2.8 36.4 + - + +
97C VAL* 3.6 37.5 - - + +
100C GLU* 4.0 17.3 - - + -
101C ALA* 4.2 5.8 - - + +
104C TRP* 4.1 15.9 - - + -
112D VAL* 4.0 22.0 - - + -
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLU 3.3 16.2 - - - +
84C ARG* 2.9 4.5 + - - +
86C LEU* 1.3 79.8 - - - +
88C ASP* 1.3 72.9 + - - +
89C VAL 3.4 0.5 + - - -
91C GLY* 3.7 12.6 + - - -
92C LEU 4.5 7.2 - - - +
94C TRP* 4.3 26.7 - - + -
97C VAL* 3.4 28.7 - - + -
127C PRO* 4.0 20.0 - - + -
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Residues in contact with ASP 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ARG* 2.8 61.3 + - - +
87C VAL* 1.3 79.5 - - - +
89C VAL* 1.3 62.1 + - + +
120C LEU* 4.1 22.6 - - + +
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 3.4 21.7 + - + +
87C VAL 3.3 0.4 - - - -
88C ASP* 1.3 84.5 - - + +
90C ILE* 1.3 70.6 + - + +
91C GLY 3.3 1.5 + - - -
119C VAL* 5.0 9.4 - - + -
120C LEU* 3.7 26.9 - - + -
85D LEU* 5.1 2.0 - - + -
89D VAL* 3.9 26.5 - - + -
115D ARG* 4.9 0.5 + - - -
119D VAL* 3.8 25.0 - - + +
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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