Contacts of the helix formed by residues 59 - 86 (chain B) in PDB entry 1TAD
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 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 1.3 71.9 - - - +
60B GLU* 1.3 81.3 + - - +
62B CYS* 3.1 4.6 + - - +
63B LEU* 3.0 43.2 + - + +
164B VAL* 3.9 29.6 - - + -
353B CAC 4.0 17.8 - - + +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 3.2 12.1 + - - +
59B LEU* 1.3 102.0 + - - +
61B GLU* 1.3 61.3 + - + +
63B LEU* 3.5 21.5 + - + +
64B GLU* 3.4 22.4 + - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PRO* 5.1 10.6 - - - +
50B LYS* 2.9 35.5 + - - -
56B GLY 3.7 1.0 - - - +
57B TYR* 4.0 12.1 - - + -
58B SER* 3.0 35.5 + - - +
60B GLU* 1.3 76.7 - - + +
62B CYS* 1.3 63.5 + - - +
64B GLU* 3.2 20.9 + - - +
65B PHE* 3.2 18.5 - - + -
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Residues in contact with CYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 3.7 18.8 - - - -
58B SER 3.0 10.7 + - - -
59B LEU 3.5 4.7 - - - +
61B GLU* 1.3 77.0 - - - +
63B LEU* 1.3 61.9 + - - +
65B PHE* 3.0 27.2 + - - +
164B VAL* 4.7 0.2 - - + -
165B PRO* 3.5 18.8 - - + +
167B GLU* 6.0 0.4 - - - -
170B VAL* 4.6 8.7 - - - -
353B CAC 2.2 64.6 - - + -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.0 35.6 + - + +
60B GLU* 3.7 18.6 - - + +
61B GLU 3.3 0.2 - - - -
62B CYS* 1.3 74.9 - - - +
64B GLU* 1.3 63.6 + - - +
66B ILE* 3.1 44.9 + - + +
67B ALA 4.6 0.9 + - - -
164B VAL* 4.1 30.1 - - + -
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 3.4 18.1 - - - +
61B GLU* 3.2 14.3 + - - +
63B LEU* 1.3 80.2 - - - +
65B PHE* 1.3 65.0 + - + +
66B ILE 3.5 0.5 + - - -
67B ALA* 4.0 9.7 + - - +
68B ILE* 3.9 12.9 + - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 4.0 12.6 - - - -
57B TYR* 3.8 20.0 - + - -
61B GLU* 3.2 27.8 - - + -
62B CYS* 3.0 13.7 + - - +
64B GLU* 1.3 81.0 - - + +
66B ILE* 1.3 57.4 + - - +
67B ALA 3.3 0.2 - - - -
68B ILE* 3.1 14.3 + - + +
69B ILE* 2.8 45.8 + - + +
165B PRO* 4.4 0.2 - - + -
170B VAL* 3.6 39.0 - - + -
173B SER* 3.4 30.1 - - - -
175B VAL* 6.0 2.7 - - + -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.1 36.9 + - + +
65B PHE* 1.3 77.6 - - - +
67B ALA* 1.3 60.3 + - - +
69B ILE* 3.2 3.9 + - - +
70B TYR* 2.9 63.0 + - + +
113B GLY 5.1 0.4 - - - +
163B TYR* 3.6 26.5 - - + +
165B PRO* 3.6 24.0 - - + -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU 4.6 0.8 + - - -
64B GLU 4.0 8.1 + - - +
65B PHE 3.3 0.4 - - - -
66B ILE* 1.3 79.8 - - - +
68B ILE* 1.3 60.9 - - + +
71B GLY* 3.0 22.9 + - - -
112B GLU 5.3 0.7 - - - +
113B GLY* 3.5 34.4 - - - +
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU 3.9 16.6 - - - +
65B PHE* 3.1 20.3 + - + +
67B ALA* 1.3 79.0 - - + +
69B ILE* 1.3 54.9 + - - +
71B GLY* 3.2 2.3 + - - -
72B ASN* 2.8 47.1 + - - +
173B SER* 3.9 13.0 - - - -
174B ARG 3.7 11.7 - - - +
175B VAL* 3.7 33.9 - - + -
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 2.8 29.5 + - + +
66B ILE* 3.7 4.0 - - - +
68B ILE* 1.3 72.4 - - - +
70B TYR* 1.3 63.3 + - + +
72B ASN* 3.2 7.6 + - - +
73B THR* 2.8 33.7 + - - +
151B TYR* 3.6 38.6 - - + +
158B LEU* 4.0 16.4 - - + -
163B TYR* 3.5 25.8 - - + +
165B PRO* 3.8 21.5 - - + -
169B ASP* 3.9 16.4 - - + +
173B SER* 4.4 7.0 - - - -
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 2.9 34.1 + - + +
67B ALA 4.1 0.2 - - - +
69B ILE* 1.3 81.2 - - + +
71B GLY* 1.3 58.6 + - - +
73B THR* 3.5 7.0 + - - -
74B LEU* 2.9 30.1 + - - +
113B GLY* 3.3 31.2 - - - +
114B THR* 4.0 7.3 - - - +
115B MET* 3.7 40.9 - - + +
155B LEU* 5.9 1.1 - - + -
158B LEU* 2.7 42.6 + - + -
159B VAL* 4.1 8.4 - - + -
160B THR 5.3 0.2 + - - -
163B TYR* 3.6 18.4 - + - +
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA 3.0 15.7 + - - -
68B ILE* 3.5 3.1 - - - -
70B TYR* 1.3 75.8 - - - +
72B ASN* 1.3 61.0 + - - +
74B LEU* 3.4 5.6 + - - +
75B GLN* 2.9 39.7 + - - +
112B GLU* 6.2 0.2 - - - -
113B GLY* 4.6 8.5 - - - -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 2.8 24.3 + - - +
69B ILE 3.5 4.9 - - - +
71B GLY* 1.3 72.5 - - - +
73B THR* 1.3 58.0 - - - +
75B GLN* 3.3 2.4 + - - +
76B SER* 2.9 36.0 + - - +
145B ASN* 3.8 17.9 + - + +
151B TYR* 3.8 19.0 - - + -
172B ARG 4.5 0.3 - - - +
173B SER* 3.4 11.3 - - - -
174B ARG* 2.7 56.8 + - - +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ILE 2.8 23.2 + - - -
70B TYR* 3.7 9.1 - - - -
72B ASN* 1.3 76.7 - - - +
74B LEU* 1.3 62.7 + - - +
76B SER* 3.4 6.8 + - - -
77B ILE* 3.3 21.8 + - - +
115B MET* 4.1 10.1 - - + -
123B ILE* 5.0 4.3 - - + -
151B TYR* 3.4 25.0 - - + +
152B LEU* 3.6 24.8 - - + +
155B LEU* 3.9 25.8 - - + -
158B LEU* 3.9 7.1 - - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B TYR 2.9 18.2 + - - +
71B GLY* 3.8 5.6 - - - +
72B ASN 3.3 0.2 - - - -
73B THR* 1.3 77.1 - - - +
75B GLN* 1.3 73.0 + - - +
77B ILE* 3.2 9.3 - - + +
78B LEU* 3.1 47.1 + - + +
103B LEU* 4.2 13.5 - - + -
107B ALA* 4.3 15.0 - - + +
110B ILE* 3.8 29.6 - - + -
113B GLY 6.4 0.4 - - - +
114B THR 5.2 0.4 - - - +
115B MET* 4.2 9.2 - - + +
119B MET* 3.8 25.4 - - + -
123B ILE* 4.6 1.6 - - + -
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLY* 2.9 22.8 + - - +
72B ASN* 3.8 4.3 - - - +
74B LEU* 1.3 88.4 - - - +
76B SER* 1.3 63.6 + - - +
78B LEU* 3.4 25.6 + - - +
79B ALA* 3.0 23.6 + - - +
82B ARG* 5.0 6.9 + - - -
107B ALA* 6.1 0.2 - - - +
112B GLU* 5.2 7.9 + - - -
145B ASN* 4.4 14.7 - - - +
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 2.9 24.0 + - - +
73B THR* 3.6 7.1 - - - -
75B GLN* 1.3 77.1 - - - +
77B ILE* 1.3 63.5 + - - +
79B ALA* 3.1 6.4 + - - +
80B ILE* 3.1 25.1 + - - +
144B LEU* 3.4 10.1 - - - +
145B ASN* 3.5 16.6 + - - +
148B ALA* 3.4 35.6 - - - +
151B TYR* 5.6 1.2 - - - -
152B LEU* 3.9 9.6 - - - -
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR 3.3 11.3 + - - +
74B LEU* 3.2 16.6 - - + +
76B SER* 1.3 77.9 - - - +
78B LEU* 1.3 59.9 + - - +
80B ILE* 3.2 17.1 + - + +
81B VAL* 2.9 37.7 + - + +
103B LEU* 3.9 27.8 - - + -
123B ILE* 4.0 37.5 - - + +
126B LEU* 4.1 26.0 - - + -
127B TRP* 4.8 3.1 - - + +
132B ILE* 4.7 11.9 - - + -
152B LEU* 4.1 13.1 - - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.1 31.8 + - + +
75B GLN* 3.6 29.8 - - - +
76B SER 3.2 0.2 - - - -
77B ILE* 1.3 78.1 - - - +
79B ALA* 1.3 61.7 - - - +
81B VAL* 3.3 5.2 + - - +
82B ARG* 3.1 49.6 + - - +
103B LEU* 4.2 22.0 - - + -
104B MET* 3.5 30.3 - - + -
107B ALA* 3.9 28.5 - - + -
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN 3.0 13.8 + - - +
76B SER* 3.1 8.7 + - - +
78B LEU* 1.3 77.2 - - - +
80B ILE* 1.3 63.0 + - - +
82B ARG* 3.4 14.7 + - - +
83B ALA* 3.0 23.4 + - - +
142B TYR* 4.1 7.0 - - + -
143B GLN 3.8 22.9 - - - +
144B LEU* 3.9 11.4 - - + -
145B ASN* 5.4 1.6 - - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B SER 3.1 14.8 + - - +
77B ILE* 3.6 10.3 - - + +
79B ALA* 1.3 74.6 - - - +
81B VAL* 1.3 64.3 + - - +
83B ALA* 3.2 4.3 + - - +
84B MET* 3.1 20.4 + - - +
127B TRP* 4.0 19.1 - - + -
132B ILE* 3.8 37.7 - - + +
135B CYS* 3.5 11.3 - - - -
136B PHE* 3.9 26.5 - - + +
142B TYR* 3.8 18.6 - - - +
144B LEU* 3.9 12.3 - - + -
152B LEU* 4.1 12.3 - - + -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 2.9 28.9 + - + +
78B LEU* 3.5 6.5 - - - +
80B ILE* 1.3 75.3 - - - +
82B ARG* 1.3 64.8 + - + +
84B MET* 3.0 27.0 + - - +
85B THR* 3.9 4.3 + - - -
91B TYR* 3.9 10.3 - - - +
100B ALA* 3.9 23.6 - - + -
103B LEU* 4.3 18.4 - - + -
104B MET* 4.3 20.4 - - + -
126B LEU* 4.3 10.1 - - + -
132B ILE* 4.5 7.6 - - + -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 5.0 6.5 + - - -
78B LEU* 3.1 49.0 + - - +
79B ALA* 3.8 12.4 - - - +
81B VAL* 1.3 75.3 - - - +
83B ALA* 1.3 63.6 + - - +
85B THR* 3.0 21.1 + - - -
86B THR* 3.2 19.1 + - + +
104B MET* 3.8 31.1 - - + +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 3.0 17.5 + - - +
80B ILE 3.4 0.9 - - - +
82B ARG* 1.3 74.2 - - - +
84B MET* 1.3 58.2 + - - +
86B THR* 3.2 12.1 - - - +
87B LEU* 2.7 39.3 + - + +
135B CYS* 3.4 21.8 - - - -
142B TYR* 3.7 30.7 - - + -
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE 3.1 10.5 + - - +
81B VAL* 3.0 16.4 + - - +
83B ALA* 1.3 74.7 - - - +
85B THR* 1.3 58.2 - - - +
88B ASN* 3.0 6.4 + - - -
89B ILE* 2.6 59.2 + - + +
90B GLN 3.5 24.7 - - - +
91B TYR* 3.7 31.0 - - + +
131B GLY 3.6 17.3 - - - +
132B ILE* 3.8 17.7 - - + +
135B CYS* 3.4 26.4 - - - -
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL 4.3 4.9 + - - -
82B ARG* 3.0 11.0 + - - -
84B MET* 1.3 76.3 - - - +
86B THR* 1.3 69.2 + - + +
88B ASN* 3.0 15.7 + - - +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ARG* 3.2 13.2 + - + +
83B ALA* 3.2 18.2 + - - -
85B THR* 1.3 79.7 - - + +
87B LEU* 1.3 72.7 + - - +
88B ASN* 3.5 1.7 + - - +
142B TYR* 5.6 1.9 - - - +
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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