Contacts of the helix formed by residues 40 - 71 (chain A) in PDB entry 1O86
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 ASP 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 1.3 67.6 + - - +
42A ALA* 3.2 8.2 - - - +
43A GLU* 3.3 21.1 + - - +
44A ALA* 3.1 21.3 + - - +
102A PHE* 4.1 8.0 - - + -
107A LEU* 4.6 7.1 - - + +
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 1.3 77.8 - - - +
42A ALA* 1.3 62.6 + - - +
44A ALA* 3.3 7.2 + - - +
45A SER* 3.2 22.2 + - - -
106A GLN 4.2 3.6 - - - +
107A LEU* 3.7 18.7 - - - +
108A GLN* 2.7 38.7 + - + +
109A ASN* 2.9 32.3 + - + +
112A ILE* 4.7 4.4 - - + +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP 3.2 5.3 - - - +
41A GLU* 1.3 78.2 - - - +
43A GLU* 1.3 63.7 + - - +
45A SER* 3.3 9.4 + - - -
46A LYS* 3.3 23.0 + - - +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 3.3 20.4 + - - +
42A ALA* 1.3 79.5 - - - +
44A ALA* 1.3 58.2 + - - +
46A LYS* 3.5 17.9 + - + +
47A PHE* 2.9 29.1 + - - +
102A PHE* 3.9 18.9 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP 3.1 12.9 + - - +
41A GLU* 3.4 12.1 - - - +
42A ALA 3.1 0.2 - - - -
43A GLU* 1.3 75.9 - - - +
45A SER* 1.3 60.5 + - - +
47A PHE* 3.2 3.8 + - - +
48A VAL* 3.0 30.8 + - - +
102A PHE* 3.7 14.4 - - + -
107A LEU* 4.1 12.3 - - + -
112A ILE* 3.5 22.6 - - + +
116A ILE* 3.9 11.3 - - + +
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU 3.2 9.3 + - - -
42A ALA* 3.3 12.5 + - - -
44A ALA* 1.3 78.0 - - - +
46A LYS* 1.3 59.9 + - - +
48A VAL* 3.5 2.9 + - - +
49A GLU* 3.0 37.9 + - - +
112A ILE* 3.7 25.9 - - - +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 3.3 14.7 + - - +
43A GLU* 3.7 17.5 + - + +
44A ALA 3.2 0.4 - - - -
45A SER* 1.3 79.3 + - - +
47A PHE* 1.3 67.5 + - - +
49A GLU* 3.3 16.5 + - - +
50A GLU* 3.0 59.3 + - + +
98A GLN* 5.9 2.4 - - - +
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU 2.9 18.7 + - - +
44A ALA 3.4 3.8 - - - +
46A LYS* 1.3 80.0 - - - +
48A VAL* 1.3 56.9 + - + +
50A GLU* 3.2 10.1 + - - +
51A TYR* 2.8 39.4 + - + +
95A TYR* 3.3 47.3 - + + -
98A GLN* 3.5 40.8 - - + +
99A ALA* 3.7 21.8 - - + -
102A PHE* 4.0 16.4 - + + -
115A ILE* 6.0 0.4 - - + -
116A ILE* 4.0 25.1 - - + -
119A VAL* 4.2 13.0 - - + -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 3.0 15.7 + - - +
45A SER 3.6 8.3 - - - +
46A LYS 3.3 0.2 - - - -
47A PHE* 1.3 80.7 - - + +
49A GLU* 1.3 60.0 + - + +
51A TYR* 3.3 6.5 + - - +
52A ASP* 2.9 30.2 + - + +
112A ILE* 3.7 25.4 - - + -
115A ILE* 3.8 45.1 - - + -
116A ILE* 4.0 17.5 - - + -
398A PRO* 5.3 6.7 - - + -
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Residues in contact with GLU 49 (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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45A SER* 3.0 24.3 + - - +
46A LYS* 3.6 20.5 - - - +
47A PHE 3.2 0.2 - - - -
48A VAL* 1.3 78.7 - - + +
50A GLU* 1.3 61.7 + - - +
52A ASP* 3.3 6.2 + - - +
53A ARG* 3.1 51.3 + - - +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.0 59.2 + - + +
47A PHE* 3.7 6.9 - - - +
49A GLU* 1.3 74.6 - - - +
51A TYR* 1.3 60.6 + - - +
53A ARG* 3.4 22.8 - - - +
54A THR* 2.8 34.8 + - + +
95A TYR* 4.1 19.0 + - + +
98A GLN* 5.0 8.0 + - - -
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 2.8 26.8 + - + +
48A VAL* 3.6 8.1 - - - +
50A GLU* 1.3 73.2 - - - +
52A ASP* 1.3 59.5 + - + +
54A THR* 3.2 4.0 + - - -
55A SER* 2.6 56.4 + - - -
59A TRP* 3.6 22.5 - - - -
91A HIS* 3.9 10.3 - + - -
92A THR* 6.0 2.9 - - - -
95A TYR* 3.7 34.7 - + + -
115A ILE* 4.7 8.7 - - + -
119A VAL* 3.5 44.7 - - + +
399A VAL* 4.0 15.0 - - + -
400A ALA* 4.1 11.3 - - + +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 2.9 19.8 + - + +
49A GLU* 3.7 6.7 - - - +
50A GLU 3.3 0.2 - - - -
51A TYR* 1.3 83.4 - - + +
53A ARG* 1.3 63.2 + - - +
55A SER* 3.8 1.0 - - - -
56A GLN* 3.0 50.1 + - - +
397A LEU 4.6 0.2 - - - +
398A PRO* 3.5 15.0 - - + +
399A VAL* 2.7 41.5 + - + +
402A ARG* 4.8 2.1 + - - -
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 3.1 41.5 + - - +
50A GLU* 3.4 36.9 - - - +
52A ASP* 1.3 78.2 - - - +
54A THR* 1.3 69.1 + - + +
56A GLN* 3.7 17.0 + - - +
57A VAL* 3.6 19.6 + - - +
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Residues in contact with THR 54 (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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50A GLU* 2.8 23.6 + - + +
51A TYR 3.2 2.6 + - - -
53A ARG* 1.3 81.3 - - + +
55A SER* 1.3 65.2 + - - +
57A VAL* 3.4 7.5 + - - +
58A VAL* 3.2 23.2 + - - +
91A HIS* 3.0 25.4 + - - -
95A TYR* 3.5 22.9 - - + +
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Residues in contact with SER 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 2.6 40.9 + - - -
52A ASP 3.8 3.6 - - - -
54A THR* 1.3 74.5 + - - +
56A GLN* 1.3 57.1 + - - +
58A VAL* 3.1 9.9 - - - +
59A TRP* 2.7 50.4 + - - +
91A HIS* 3.0 17.9 - - - -
399A VAL* 3.8 19.7 - - - -
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Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.0 43.9 + - - +
53A ARG* 3.8 12.2 - - - +
55A SER* 1.3 78.3 - - - +
57A VAL* 1.3 59.0 + - + +
59A TRP* 4.3 0.3 - - - +
60A ASN* 3.0 31.7 + - - +
360A TYR* 3.8 27.9 - - - +
361A ASN* 5.1 4.7 - - - -
399A VAL* 4.9 7.6 - - + -
402A ARG* 4.2 20.9 + - - +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG 3.6 15.3 - - - +
54A THR* 3.4 8.2 + - - +
55A SER 3.2 0.6 - - - -
56A GLN* 1.3 76.8 - - + +
58A VAL* 1.3 66.3 + - - +
60A ASN* 3.3 5.6 + - - +
61A GLU* 3.1 40.0 + - - +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR 3.2 13.6 + - - +
55A SER* 3.1 19.7 - - - +
57A VAL* 1.3 79.3 - - - +
59A TRP* 1.3 68.9 + - + +
61A GLU* 3.3 8.8 + - - +
62A TYR* 3.0 26.2 + - - +
84A LYS* 4.8 7.2 + - + +
87A GLN* 4.5 3.6 - - + +
88A ILE* 3.6 37.5 - - + +
91A HIS* 3.8 24.9 - - + +
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Residues in contact with TRP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 3.6 25.1 - - - -
55A SER* 2.7 36.5 + - - +
56A GLN 4.3 0.4 - - - +
58A VAL* 1.3 84.8 - - + +
60A ASN* 1.3 60.1 + - - +
62A TYR* 3.7 2.0 - - - +
63A ALA* 2.9 30.3 + - - +
88A ILE* 3.5 28.8 - - + +
91A HIS* 4.4 6.3 + - - -
92A THR* 5.2 3.9 + - - -
118A LYS* 5.6 6.1 - - - -
360A TYR* 3.3 53.4 - + + -
399A VAL* 3.2 38.4 - - + -
400A ALA* 5.2 3.4 - - - -
403A GLU* 5.9 3.1 - - - -
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN 3.0 21.0 + - - +
57A VAL* 3.6 6.2 - - - +
58A VAL 3.3 0.2 - - - -
59A TRP* 1.3 78.6 - - - +
61A GLU* 1.3 67.1 + - - +
63A ALA* 3.4 4.2 + - - +
64A GLU* 3.2 21.7 + - - +
359A PHE* 2.9 38.9 + - - +
360A TYR 4.9 1.1 - - - +
361A ASN* 3.7 26.5 - - + +
364A ASP* 5.5 0.8 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.1 36.8 + - - +
58A VAL* 3.7 4.0 - - - +
59A TRP 3.3 0.2 - - - -
60A ASN* 1.3 80.7 - - - +
62A TYR* 1.3 63.9 + - - +
64A GLU* 3.2 15.2 + - - +
65A ALA* 3.3 11.4 + - - +
84A LYS* 2.5 45.6 + - - +
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Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL 3.0 16.5 + - - +
59A TRP 3.7 4.7 - - - +
60A ASN 3.3 0.2 - - - -
61A GLU* 1.3 73.0 - - - +
63A ALA* 1.3 69.9 + - - +
64A GLU 3.2 0.2 + - - -
65A ALA* 3.2 2.1 + - - -
66A ASN* 2.9 44.1 + - + +
81A LEU* 3.6 26.1 - - + +
84A LYS* 3.9 31.1 - - + +
85A ASN* 3.5 32.3 + - - -
88A ILE* 3.9 29.8 - - + -
124A ARG* 5.0 5.5 + - - -
360A TYR* 6.4 1.1 - + - -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP 2.9 17.4 + - - +
60A ASN 3.6 3.4 - - - +
62A TYR* 1.3 79.3 - - - +
64A GLU* 1.3 56.9 + - - +
66A ASN* 3.5 7.2 + - - +
67A TRP* 2.9 30.8 + - - +
357A TRP* 3.9 7.8 - - + -
358A ASP 4.3 6.7 - - - +
359A PHE* 3.5 38.2 - - + -
360A TYR* 4.5 5.4 - - + -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASN* 3.2 11.1 + - - +
61A GLU* 3.3 13.2 - - - +
62A TYR 3.1 0.4 - - - -
63A ALA* 1.3 76.8 - - - +
65A ALA* 1.3 60.4 + - - +
67A TRP* 3.2 3.1 + - - +
68A ASN* 2.9 41.1 + - - +
359A PHE* 4.0 11.2 - - + -
366A ARG* 5.9 2.0 - - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU 3.3 2.5 + - - +
62A TYR 3.2 5.4 + - - +
64A GLU* 1.3 79.6 - - - +
66A ASN* 1.3 63.3 + - - +
68A ASN* 3.5 9.7 + - - +
69A TYR* 3.1 22.3 + - - +
77A THR* 4.8 2.1 - - - +
80A ILE* 4.4 13.5 - - + -
81A LEU* 4.0 18.5 - - + +
84A LYS* 3.7 34.5 - - + -
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Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 2.9 41.2 + - + +
63A ALA* 3.7 5.5 - - - +
65A ALA* 1.3 77.0 - - - +
67A TRP* 1.3 63.9 + - - +
69A TYR* 3.3 1.6 + - - +
70A ASN* 3.0 42.1 + - - +
81A LEU* 3.6 25.2 - - + +
357A TRP* 3.4 22.0 - - + -
702A LPR 6.4 0.2 - - - -
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Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA 2.9 19.2 + - - +
64A GLU* 3.5 3.8 - - - +
66A ASN* 1.3 74.1 - - - +
68A ASN* 1.3 78.5 + - - +
70A ASN* 3.1 2.3 + - - -
71A THR* 2.9 53.1 + - + +
338A LYS 3.3 21.6 + - - -
340A MET* 4.1 9.0 - - + -
357A TRP* 3.5 50.6 - + + -
359A PHE* 3.8 13.9 - + + -
366A ARG* 3.2 52.7 - - + +
367A ILE 3.7 17.0 - - - -
368A LYS* 3.9 14.6 - - + -
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 2.9 29.1 + - - +
65A ALA* 3.8 8.1 - - - +
67A TRP* 1.3 86.5 - - - +
69A TYR* 1.3 57.9 + - - +
71A THR* 3.6 6.1 + - - -
72A ASN* 3.1 33.6 + - - +
77A THR* 3.9 15.0 - - + +
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Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 3.1 17.2 + - - +
66A ASN 3.7 3.8 - - - +
67A TRP 3.1 0.6 - - - -
68A ASN* 1.3 76.5 - - - +
70A ASN* 1.3 73.4 + - - +
72A ASN 3.2 9.5 + - - -
73A ILE* 3.2 54.6 + - + +
74A THR 3.8 1.3 - - - -
77A THR* 3.1 26.7 - - - +
78A SER* 2.6 36.4 + - - -
81A LEU* 3.9 24.5 - - + -
140A LEU* 3.4 17.4 - - + +
143A GLU* 5.3 10.5 - - + -
144A THR* 2.4 29.6 + - - +
351A VAL* 5.6 1.6 - - + -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 3.0 42.3 + - - +
67A TRP 3.6 3.8 - - - +
69A TYR* 1.3 85.2 - - - +
71A THR* 1.3 58.2 + - - +
143A GLU* 5.5 4.2 - - - +
350A VAL* 3.3 4.7 - - - +
351A VAL* 2.8 62.5 + - - +
357A TRP* 3.6 19.8 - - + -
368A LYS* 3.7 22.8 - - + +
702A LPR 5.8 3.3 - - - -
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 2.9 60.6 + - + +
68A ASN* 3.6 6.9 + - - -
70A ASN* 1.3 78.8 - - - +
72A ASN* 1.3 59.7 + - - +
340A MET* 4.0 14.1 - - + -
348A ARG* 2.6 38.9 + - - -
350A VAL* 3.2 15.4 - - - +
368A LYS* 3.9 17.0 - - + -
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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