Contacts of the helix formed by residues 53 - 82 (chain A) in PDB entry 6TPN
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 TYR 53 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 2.9 56.0 + - + +
52A GLU* 1.3 75.5 - - - +
54A ALA* 1.3 62.7 + - - +
55A TRP* 3.2 3.6 - - - +
56A VAL* 3.2 28.8 - - + +
57A LEU* 3.2 15.3 + - + +
115A ASP 4.6 2.8 + - - -
116A ILE* 6.3 1.1 - - + -
340A GLU* 3.9 22.8 + - + -
343A TYR* 4.2 5.2 + - - +
344A ALA* 4.1 23.7 + - + -
347A ALA* 4.5 13.8 - - + +
1206A OLA 4.6 20.4 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 4.6 3.9 - - + +
52A GLU* 3.0 15.6 - - - +
53A TYR* 1.3 81.3 - - - +
55A TRP* 1.3 56.9 + - - +
57A LEU* 3.3 3.9 + - - +
58A ILE* 2.8 42.0 + - + +
116A ILE* 4.0 36.6 - - + -
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Residues in contact with TRP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 3.3 40.4 + - + +
53A TYR* 4.9 0.6 - - - +
54A ALA* 1.3 78.1 - - - +
56A VAL* 1.3 74.6 + - + +
58A ILE* 4.1 8.5 - - - +
59A ALA* 2.9 34.5 + - + +
1206A OLA 3.8 28.0 - - - -
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.2 31.3 + - + +
55A TRP* 1.3 100.2 - - + +
57A LEU* 1.3 57.8 + - - +
59A ALA* 4.1 2.2 - - - -
60A GLY 3.3 16.6 + - - -
1206A OLA 3.3 70.7 - - + +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.2 18.5 + - + +
54A ALA* 3.7 7.0 - - - +
55A TRP 3.2 0.4 - - - -
56A VAL* 1.3 81.0 - - + +
58A ILE* 1.3 59.6 + - - +
60A GLY 3.4 0.7 + - - -
61A TYR* 2.8 58.6 + - + -
112A LEU* 4.0 8.7 - - + -
115A ASP* 4.6 15.9 - - + +
116A ILE* 3.7 31.2 - - + -
347A ALA* 4.4 18.4 - - + +
351A TRP* 4.8 0.2 - - + -
1206A OLA 3.5 37.5 - - + -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 2.8 34.4 + - + +
55A TRP* 4.1 5.8 - - - +
57A LEU* 1.3 69.4 - - - +
59A ALA* 1.3 61.6 + - - +
61A TYR* 3.8 0.9 - - - +
62A ILE* 2.9 54.0 + - + +
112A LEU* 3.8 31.0 - - + -
116A ILE* 3.8 12.1 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TRP* 2.9 23.7 + - + +
56A VAL 4.2 2.0 - - - +
58A ILE* 1.3 78.7 - - - +
60A GLY* 1.3 55.5 + - - +
62A ILE* 3.4 7.4 + - - +
63A ILE* 3.1 39.9 + - + +
1206A OLA 3.9 22.7 - - + +
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL 3.3 14.8 + - - -
57A LEU 3.4 2.7 + - - -
58A ILE 3.3 0.4 - - - -
59A ALA* 1.3 80.0 - - - +
61A TYR* 1.3 59.1 + - - +
63A ILE* 4.1 4.9 - - - +
64A VAL* 3.3 17.3 + - - +
351A TRP* 2.8 28.3 + - - -
1206A OLA 4.0 21.5 - - - +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 2.8 50.0 + - + +
58A ILE 3.8 3.8 - - - +
60A GLY* 1.3 77.2 - - - +
62A ILE* 1.3 59.3 + - - +
64A VAL* 3.7 2.3 + - + +
65A PHE* 3.0 28.2 + - - +
108A LEU* 3.8 43.2 - - + +
111A THR* 3.4 23.1 - - + +
112A LEU* 3.9 32.1 - - + -
115A ASP* 4.1 3.7 + - - -
347A ALA 4.5 0.8 + - - -
350A HIS* 3.8 3.3 - - - +
351A TRP* 3.6 48.5 + + + -
354A TYR* 3.8 20.3 - + - -
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 2.9 41.8 + - + +
59A ALA* 3.9 7.2 - - - +
61A TYR* 1.3 76.6 - - + +
63A ILE* 1.3 68.3 + - + +
65A PHE* 3.1 7.1 + - + +
66A VAL* 3.0 35.6 + - + +
112A LEU* 5.6 4.3 - - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA* 3.1 25.9 + - + +
60A GLY* 4.1 4.5 - - - +
62A ILE* 1.3 79.2 - - + +
64A VAL* 1.3 67.3 + - + +
66A VAL* 3.4 4.1 + - - +
67A VAL* 3.1 39.8 + - + +
1206A OLA 4.3 20.4 - - + +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY 3.3 10.5 + - - +
61A TYR* 4.1 2.9 - - + +
62A ILE 3.3 0.4 - - - -
63A ILE* 1.3 80.7 - - + +
65A PHE* 1.3 57.5 + - - +
67A VAL* 4.7 0.4 - - - -
68A ALA* 2.8 32.5 + - + +
108A LEU* 4.0 7.6 - - + -
351A TRP* 3.3 38.8 - - + +
354A TYR* 3.3 41.7 - - + +
355A ALA* 4.1 12.8 - - + -
358A ALA* 4.3 11.9 - - + -
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR 3.0 20.3 + - - +
62A ILE* 3.1 8.7 + - + +
64A VAL* 1.3 76.5 - - - +
66A VAL* 1.3 73.6 + - + +
69A LEU* 3.1 46.6 + - + +
104A THR* 3.1 43.4 - - + +
105A ILE* 4.5 7.9 - - + -
108A LEU* 3.6 20.4 - - + -
109A PRO* 4.6 10.1 - - + -
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.0 28.1 + - + +
63A ILE* 4.0 4.7 - - - +
65A PHE* 1.3 86.0 - - + +
67A VAL* 1.3 62.3 + - + +
69A LEU* 3.9 2.0 - - - -
70A ILE* 2.9 50.3 + - + +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.1 28.9 + - + +
64A VAL* 4.1 1.8 - - - +
66A VAL* 1.3 80.3 - - + +
68A ALA* 1.3 58.8 + - - +
70A ILE* 4.8 2.0 - - - -
71A GLY* 2.9 29.2 + - - +
358A ALA* 3.7 30.5 - - + +
361A PRO* 5.1 0.6 - - + +
362A ILE* 4.1 17.9 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 2.8 20.0 + - + +
67A VAL* 1.3 79.5 - - - +
69A LEU* 1.3 61.4 + - - +
72A ASN* 2.5 42.6 + - - +
101A VAL* 4.7 1.0 - - - +
104A THR* 3.7 25.7 + - + +
108A LEU* 5.8 0.2 - - + -
354A TYR* 4.5 3.8 - - + +
357A SER* 4.1 3.8 - - - -
358A ALA* 3.9 21.1 - - + +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.1 39.5 + - + +
66A VAL* 4.0 2.9 - - - +
68A ALA* 1.3 74.8 - - - +
70A ILE* 1.3 71.7 + - + +
72A ASN* 4.6 0.8 - - - +
73A VAL* 3.3 37.2 + - + +
101A VAL* 4.3 15.0 - - + -
104A THR* 4.2 11.6 - - + +
105A ILE* 3.8 33.7 - - + -
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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 VAL* 2.9 35.9 + - + +
67A VAL* 4.4 2.9 - - - +
69A LEU* 1.3 83.2 - - + +
71A GLY* 1.3 64.0 + - - +
73A VAL* 4.0 2.5 - - - +
74A LEU* 3.1 45.4 + - + +
379A PHE* 4.2 16.8 - - + -
382A TRP* 3.6 32.1 - - + -
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Residues in contact with GLY 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 20.1 + - - -
70A ILE* 1.3 80.5 - - - +
72A ASN* 1.3 60.0 + - - +
74A LEU* 3.3 11.3 + - - +
75A VAL* 3.1 24.3 + - - +
361A PRO* 3.6 21.2 - - - +
375A PHE* 4.6 1.4 - - - -
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Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 2.5 33.5 + - - +
71A GLY* 1.3 74.8 - - - +
73A VAL* 1.3 61.8 + - - +
75A VAL* 3.2 16.7 + - - +
76A CYS* 3.3 8.3 + - - -
97A SER* 3.1 36.1 + - - -
100A ALA* 3.6 19.6 - - - +
101A VAL* 3.6 19.3 - - + -
357A SER* 3.0 28.3 + - - +
360A ASN* 5.4 2.1 - - - +
361A PRO* 3.8 12.0 - - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.3 27.5 + - + +
70A ILE* 4.1 2.5 - - - +
72A ASN* 1.3 74.8 - - - +
74A LEU* 1.3 62.5 + - + +
76A CYS* 3.2 9.6 + - + +
77A VAL* 2.9 39.7 + - + +
101A VAL* 4.1 21.1 - - + -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.1 32.8 + - + +
71A GLY* 3.5 10.8 - - - +
73A VAL* 1.3 77.6 - - + +
75A VAL* 1.3 57.6 + - - +
77A VAL* 3.9 7.1 - - + +
78A ALA* 2.9 32.9 + - - +
375A PHE* 3.7 24.9 - - + +
378A ALA* 3.7 33.9 - - + +
379A PHE* 3.6 32.3 - - + +
382A TRP* 5.5 7.6 - - + -
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY 3.1 14.4 + - - +
72A ASN 3.3 8.5 - - - +
73A VAL 3.1 1.0 - - - -
74A LEU* 1.3 74.8 - - - +
76A CYS* 1.3 65.3 + - - +
78A ALA* 4.0 1.4 - - - +
79A VAL* 3.3 24.9 + - - +
93A ILE* 4.0 25.1 - - + +
94A VAL* 4.4 7.2 - - + -
97A SER* 3.3 23.8 - - - +
361A PRO* 4.2 8.1 - - + -
364A TYR* 3.9 19.3 - - + -
371A PHE* 4.2 8.7 - - + -
375A PHE* 3.8 21.5 - - + -
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Residues in contact with CYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN 3.6 14.6 - - - -
73A VAL* 3.2 10.4 + - + +
75A VAL* 1.3 76.0 - - - +
77A VAL* 1.3 64.4 - - + +
79A VAL* 3.3 2.1 + - - +
80A TRP* 3.0 37.1 + - + -
94A VAL* 3.9 31.2 - - + -
97A SER* 4.2 13.0 - - - -
98A LEU* 4.2 20.6 - - + -
101A VAL* 5.7 2.7 - - - -
----------------------------------------------------------
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 2.9 33.7 + - + +
74A LEU* 3.9 9.2 - - + +
76A CYS* 1.3 79.2 - - + +
78A ALA* 1.3 57.7 + - - +
80A TRP* 3.4 4.1 + - - +
81A LYS* 2.9 64.8 + - + +
378A ALA* 4.8 11.9 - - + -
----------------------------------------------------------
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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 LEU 2.9 19.8 + - - +
75A VAL 4.0 3.1 - - - +
76A CYS 3.3 0.2 - - - -
77A VAL* 1.3 78.2 - - - +
79A VAL* 1.3 61.4 + - - +
81A LYS* 4.7 1.1 - - - -
82A ASN* 3.6 23.4 + - - +
85A MET* 3.8 17.1 - - + +
371A PHE* 4.5 8.5 - - + -
374A GLU* 3.7 37.7 - - + +
375A PHE* 4.6 4.5 - - + -
378A ALA* 6.1 2.0 - - + -
----------------------------------------------------------
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL 3.3 15.0 + - - +
76A CYS 3.3 2.3 + - - +
77A VAL 3.1 0.6 - - - -
78A ALA* 1.3 77.3 - - - +
80A TRP* 1.3 66.8 + - + +
81A LYS 3.2 1.6 - - - -
82A ASN 2.9 22.3 - - - +
85A MET* 4.1 23.1 - - + +
86A ARG* 3.7 19.2 - - + +
90A ASN* 4.4 13.0 - - + +
91A LEU* 4.7 11.7 - - + -
94A VAL* 3.6 29.4 - - + -
371A PHE* 4.2 22.4 - - + -
----------------------------------------------------------
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A CYS* 3.0 35.1 + - + +
77A VAL* 3.8 3.1 - - - +
79A VAL* 1.3 81.3 - - + +
81A LYS* 1.3 61.3 + - - +
83A HIS* 5.2 1.0 + - - -
86A ARG* 3.3 60.9 + - + +
91A LEU* 4.2 22.4 - - + -
94A VAL* 4.1 21.5 - - + +
98A LEU* 6.3 0.2 - - - +
170A LEU* 5.1 17.5 - - + -
----------------------------------------------------------
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 2.9 40.6 + - + +
78A ALA* 4.5 2.2 - - - +
80A TRP* 1.3 81.1 - - - +
82A ASN* 1.3 61.6 + - - +
83A HIS* 3.7 14.7 + - - -
374A GLU* 4.6 11.2 - - - +
377A ALA 5.4 0.8 + - - -
378A ALA* 4.8 15.5 - - + +
381A TRP* 4.6 26.3 - - - +
388A HIS* 5.0 10.7 - - - -
----------------------------------------------------------
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA 3.6 8.1 + - - +
79A VAL 2.9 20.5 - - - +
81A LYS* 1.3 77.1 - - - +
83A HIS* 1.3 63.3 + - - +
84A HIS* 3.0 40.6 + - - +
85A MET* 3.3 38.8 + - + +
86A ARG* 3.8 1.4 - - - +
370A LYS* 5.3 4.8 - - - +
374A GLU* 4.0 23.8 + - - +
----------------------------------------------------------
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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