Contacts of the helix formed by residues 66 - 88 (chain A) in PDB entry 1DPR
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 PRO 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A THR* 1.4 87.8 - - + +
67A THR* 1.3 62.9 + - - +
69A ARG* 4.1 6.2 - - + +
70A THR* 3.7 21.5 + - - +
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Residues in contact with THR 67 (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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51A ASP 5.9 0.7 - - - +
52A GLY 5.2 4.0 - - - +
53A LEU* 4.3 9.9 - - + -
65A THR* 2.9 5.4 + - - +
66A PRO* 1.3 82.2 - - - +
68A GLY* 1.3 59.0 + - - +
69A ARG 3.2 1.3 - - - -
70A THR* 2.5 35.0 + - - +
71A LEU* 3.0 16.0 - - + +
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Residues in contact with GLY 68 (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 LEU* 3.4 11.9 - - - +
53A LEU* 3.5 38.3 - - - +
64A MET* 3.6 8.3 - - - -
65A THR* 3.2 11.7 + - - -
67A THR* 1.3 71.2 - - - +
69A ARG* 1.3 57.4 + - - +
71A LEU* 2.7 22.0 + - - -
72A ALA 2.9 10.0 + - - -
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Residues in contact with ARG 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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16A TYR* 3.8 18.4 - - - -
19A GLU* 4.2 25.3 + - - +
64A MET* 3.1 49.6 + - + +
65A THR 3.0 18.5 + - - +
66A PRO* 4.1 6.7 - - + +
68A GLY* 1.3 76.4 - - - +
70A THR* 1.3 59.5 + - - +
72A ALA* 3.8 1.7 - - + +
73A THR* 3.2 29.5 + - - +
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Residues in contact with THR 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 3.7 14.1 - - - +
67A THR* 2.5 31.9 + - - +
69A ARG* 1.3 71.3 - - - +
71A LEU* 1.3 71.3 + - - +
72A ALA 3.1 5.7 + - - -
73A THR* 3.4 13.3 + - - -
74A ALA* 3.5 15.4 + - - +
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Residues in contact with LEU 71 (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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8A THR* 5.6 2.2 - - - +
9A GLU* 4.5 10.3 - - + +
12A LEU* 3.5 25.8 - - + +
53A LEU* 4.3 14.1 - - + -
67A THR* 3.0 22.9 + - + +
68A GLY 2.7 8.7 + - - +
70A THR* 1.3 107.9 + - - +
72A ALA* 1.4 54.5 + - - -
74A ALA* 4.6 4.3 - - + -
75A VAL* 3.7 24.3 - - + +
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Residues in contact with ALA 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 LEU* 3.3 38.8 - - + +
13A ARG* 5.1 2.3 - - - +
16A TYR* 3.7 17.6 - - + -
64A MET* 4.0 8.1 - - - -
68A GLY 2.9 8.8 + - - +
69A ARG* 3.9 5.2 - - - +
70A THR 3.1 0.2 - - - -
71A LEU* 1.4 77.1 - - - +
73A THR* 1.3 59.7 + - - +
74A ALA 3.1 2.7 - - - -
75A VAL* 3.7 3.1 + - - +
76A MET* 3.0 29.9 + - - +
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Residues in contact with THR 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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16A TYR* 3.9 19.7 - - - -
69A ARG* 3.2 23.8 + - - +
70A THR* 3.4 6.0 + - - -
72A ALA* 1.3 76.6 - - - +
74A ALA* 1.3 56.3 + - - +
76A MET* 3.8 5.1 + - - -
77A ARG* 3.1 27.8 + - - +
133A PRO* 3.8 13.3 - - + +
134A GLY* 3.6 25.7 + - - +
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Residues in contact with ALA 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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70A THR 3.5 15.1 + - - +
71A LEU* 4.7 4.0 - - + -
73A THR* 1.3 73.9 - - - +
75A VAL* 1.3 63.0 + - + +
76A MET 3.2 0.9 - - - -
77A ARG* 2.8 41.5 + - - +
78A LYS* 2.8 31.1 + - + +
110A ASP* 6.0 1.6 - - - +
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Residues in contact with VAL 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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9A GLU* 3.0 69.5 - - + +
13A ARG* 4.3 7.6 - - + +
71A LEU* 3.7 17.7 - - + +
72A ALA* 4.1 3.4 - - - +
74A ALA* 1.3 78.6 - - + +
76A MET* 1.3 56.1 + - - +
78A LYS* 3.6 15.7 - - - +
79A HIS* 3.0 24.3 + - - +
105A GLU* 3.4 30.9 - - + +
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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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13A ARG* 3.6 18.3 - - + +
16A TYR* 3.6 28.0 - - + -
17A GLU* 3.6 35.2 - - + +
20A GLU* 4.1 0.7 - - - +
72A ALA 3.0 19.3 + - - +
75A VAL* 1.3 77.1 - - - +
77A ARG* 1.3 57.9 + - - +
79A HIS* 3.2 32.7 - - - +
80A ARG* 2.9 66.4 + - - +
133A PRO* 3.5 18.8 - - + -
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Residues in contact with ARG 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 THR* 3.1 10.1 + - - +
74A ALA* 2.8 34.0 + - - +
76A MET* 1.3 68.9 - - - +
78A LYS* 1.3 59.3 + - - +
79A HIS 3.0 4.7 - - - -
80A ARG* 4.8 0.2 - - - -
81A LEU* 3.2 32.4 + - + +
110A ASP* 5.5 5.1 + - - -
113A GLU* 3.3 29.8 + - - -
132A ILE* 3.6 15.6 - - + +
133A PRO 3.0 26.0 - - - +
134A GLY* 3.7 13.9 - - - -
135A LEU* 2.6 43.5 - - + +
136A ASP* 3.3 29.6 + - - +
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Residues in contact with LYS 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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9A GLU* 4.3 3.8 + - - -
74A ALA* 2.8 39.8 + - + +
75A VAL* 3.5 12.5 - - - +
77A ARG* 1.3 72.2 - - - +
79A HIS* 1.3 57.9 + - - +
81A LEU 4.2 0.4 - - - -
82A ALA* 3.2 24.4 + - - +
105A GLU* 3.5 31.5 + - - +
106A HIS 5.6 0.4 - - - -
107A VAL 4.2 7.4 - - - -
108A MET* 2.9 49.3 - - + +
109A SER* 4.2 4.5 - - - +
110A ASP* 4.6 11.4 - - - +
113A GLU* 3.2 32.3 - - + +
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Residues in contact with HIS 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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13A ARG* 3.4 17.5 + - - -
17A GLU* 5.6 0.4 + - - -
75A VAL 3.0 22.1 + - - +
76A MET* 3.2 31.9 - - - +
77A ARG 3.0 0.2 - - - -
78A LYS* 1.3 78.8 - - - +
80A ARG* 1.3 69.1 + - - +
81A LEU 3.5 0.2 + - - -
82A ALA* 3.6 5.3 + - - +
83A GLU* 3.1 37.8 + - - +
98A HIS* 3.5 19.8 + - - -
101A ALA* 3.4 19.5 + - + +
102A CYS* 3.6 26.0 - - - -
105A GLU* 3.7 9.3 + - - +
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Residues in contact with ARG 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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20A GLU* 2.8 42.7 + - - -
76A MET* 2.9 50.8 + - - +
77A ARG 3.6 0.4 + - - -
79A HIS* 1.3 76.2 - - - +
81A LEU* 1.3 58.0 + - - +
83A GLU* 3.0 31.6 + - - +
84A ARG* 3.1 16.9 - - + +
125A ARG 5.1 4.9 - - - +
126A SER* 4.3 12.3 - - - +
127A PRO* 4.8 0.4 - - - +
130A ASN* 3.2 32.7 + - - +
131A PRO* 2.6 29.4 + - - +
132A ILE* 3.5 30.1 - - + +
133A PRO* 3.4 3.1 - - + +
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Residues in contact with LEU 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 ARG* 3.2 29.5 + - + +
80A ARG* 1.3 77.0 - - - +
82A ALA* 1.3 56.9 + - - +
84A ARG* 3.6 8.1 - - + +
85A LEU* 3.0 23.6 + - - +
108A MET* 3.7 13.1 - - + +
113A GLU* 3.3 41.5 - - + +
116A LEU* 4.3 11.5 - - + +
117A VAL* 3.9 11.0 - - + -
120A LEU* 3.8 14.9 - - + +
123A VAL* 3.7 29.4 - - + -
132A ILE* 4.0 10.7 - - + +
135A LEU* 5.8 1.1 - - + -
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Residues in contact with ALA 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 LYS 3.2 19.0 + - - +
79A HIS 3.8 0.4 - - - +
80A ARG 3.2 0.8 - - - -
81A LEU* 1.3 77.4 - - - +
83A GLU* 1.3 54.2 + - - +
85A LEU* 3.3 7.4 + - - +
86A LEU* 2.8 39.5 + - - +
101A ALA* 3.7 24.7 - - + -
104A TRP* 4.0 21.9 - - + -
108A MET* 3.6 12.3 - - + +
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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 HIS* 3.1 42.7 + - - +
80A ARG* 3.2 12.6 - - - +
82A ALA* 1.3 73.3 - - - +
84A ARG* 1.3 61.5 + - - +
85A LEU 3.3 0.2 - - - -
86A LEU* 4.1 6.1 - - - -
87A THR* 2.9 38.7 + - - -
97A VAL* 4.2 8.3 - - + -
98A HIS* 3.7 23.7 + - - -
101A ALA* 3.9 8.2 - - + +
126A SER* 3.9 7.3 + - - -
127A PRO* 3.7 24.8 - - + +
128A PHE* 3.2 25.0 - - - +
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Residues in contact with ARG 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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80A ARG 3.1 19.1 - - - +
81A LEU* 3.6 10.8 - - - +
83A GLU* 1.3 73.6 - - - +
85A LEU* 1.3 64.5 + - - +
88A ASP* 2.7 64.4 + - - +
120A LEU* 3.3 24.6 - - + +
122A ASP* 3.1 31.3 + - - +
123A VAL* 4.4 8.7 - - - +
125A ARG* 3.2 52.1 + - - +
126A SER 3.5 13.3 - - - -
127A PRO* 3.7 9.4 - - + +
132A ILE* 5.9 1.3 - - - -
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Residues in contact with LEU 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 LEU 3.0 15.1 + - - +
82A ALA* 3.3 7.8 + - - +
83A GLU 3.3 0.2 - - - -
84A ARG* 1.3 79.7 - - - +
86A LEU* 1.3 55.0 + - - +
87A THR 2.7 14.8 + - - -
89A ILE* 3.0 39.4 + - + +
90A ILE* 3.5 25.3 + - + -
104A TRP* 3.6 24.0 - - + -
108A MET* 6.0 0.4 - - + -
116A LEU* 4.5 18.2 - - + -
120A LEU* 4.7 6.5 - - + -
85B LEU* 4.0 17.3 - - + -
89B ILE* 4.8 0.4 - - + -
90B ILE* 4.6 11.7 - - + -
104B TRP* 4.0 22.2 - - + -
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Residues in contact with LEU 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 ALA 2.8 25.9 + - - +
83A GLU* 3.3 6.3 + - - +
85A LEU* 1.3 69.4 - - - +
87A THR* 1.3 57.9 + - - +
90A ILE* 3.7 11.6 - - + +
91A GLY 2.7 23.4 + - - -
92A LEU* 3.1 18.9 + - + +
97A VAL* 3.5 32.3 - - + +
100A GLU* 3.5 31.6 - - + -
101A ALA 4.4 3.1 - - - +
104A TRP* 3.6 23.6 - - + -
112B VAL* 3.5 31.0 - - + -
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Residues in contact with THR 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 2.9 19.1 + - - -
85A LEU 2.7 4.8 + - - -
86A LEU* 1.3 75.4 - - - +
88A ASP* 1.4 70.6 + - - +
90A ILE 3.5 2.6 + - - +
91A GLY* 3.5 22.1 + - - +
92A LEU 5.0 0.4 - - - +
94A ILE* 4.2 16.5 - - + +
97A VAL* 3.5 22.3 - - - +
127A PRO* 4.6 8.1 - - + +
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Residues in contact with ASP 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 ARG* 2.7 69.4 + - - +
85A LEU 3.0 1.8 + - - -
87A THR* 1.4 84.3 - - - +
89A ILE* 1.4 59.1 + - + +
120A LEU* 4.3 15.9 - - + +
121A LYS* 5.1 9.4 + - + +
122A ASP* 4.6 3.5 - - - +
127A PRO* 5.4 0.7 - - - +
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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