Contacts of the helix formed by residues 54 - 80 (chain A) in PDB entry 3AXJ
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 GLN 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.8 35.3 - - + +
51A ASP* 2.8 41.8 + - - +
53A SER* 1.3 81.8 - - - +
55A ILE* 1.3 56.3 + - - +
56A SER 3.4 1.6 - - - -
57A ALA* 3.4 13.7 + - + +
58A ALA* 3.0 28.6 + - - +
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Residues in contact with ILE 55 (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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47A ILE* 5.0 0.2 - - - -
48A ILE* 3.8 20.2 - - + -
51A ASP 4.3 2.5 - - - +
52A LEU* 3.4 35.0 - - + +
53A SER 3.4 1.8 - - - -
54A GLN* 1.3 77.0 - - - +
56A SER* 1.3 60.6 + - - +
58A ALA* 3.3 6.2 + - - +
59A CYS* 2.9 31.3 + - - -
109A LEU* 4.1 36.6 - - + +
155A PHE* 4.0 28.3 - - + -
167A ARG* 4.6 10.3 - - - +
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER 4.9 3.0 + - - -
54A GLN 3.4 0.4 - - - -
55A ILE* 1.3 77.9 - - - +
57A ALA* 1.3 68.1 + - - +
59A CYS* 3.3 8.2 + - - +
60A GLY* 3.1 19.9 + - - -
110A GLU* 6.0 2.9 - - - -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER 5.4 1.2 + - - +
54A GLN* 3.4 16.4 + - + +
55A ILE 3.4 0.4 - - - -
56A SER* 1.3 81.0 + - - +
58A ALA* 1.3 62.2 + - - +
60A GLY* 3.3 2.7 + - - -
61A LEU* 3.0 33.4 + - + +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 3.4 31.8 - - + +
45A LEU* 4.2 13.3 - - + +
47A ILE* 3.8 10.8 - - + -
48A ILE* 5.2 1.6 - - + -
54A GLN 3.0 18.0 + - - +
55A ILE* 3.7 5.8 - - - +
56A SER 3.3 0.2 - - - -
57A ALA* 1.3 74.5 - - - +
59A CYS* 1.3 62.6 + - - +
61A LEU* 3.3 12.0 + - - +
62A ALA* 3.0 24.1 + - - +
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Residues in contact with CYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.3 3.6 - - - -
55A ILE* 2.9 22.4 + - - +
56A SER* 3.6 7.2 - - - +
57A ALA 3.3 0.2 - - - -
58A ALA* 1.3 77.2 - - - +
60A GLY* 1.3 56.2 + - - +
62A ALA* 3.4 3.1 + - - +
63A ARG* 3.1 31.7 + - - +
106A VAL* 4.0 24.1 - - + +
109A LEU* 3.8 39.3 - - - -
110A GLU* 3.5 26.5 - - + +
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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
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56A SER 3.1 13.6 + - - -
57A ALA* 3.7 2.9 - - - -
59A CYS* 1.3 72.9 - - - +
61A LEU* 1.3 65.8 + - - +
63A ARG* 3.4 11.5 + - - +
64A LYS* 3.2 28.5 + - - +
110A GLU* 4.6 1.1 + - - -
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Residues in contact with LEU 61 (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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41A ALA* 5.6 0.2 - - - -
44A LYS* 3.9 42.0 - - + +
57A ALA* 3.0 26.6 + - + +
58A ALA* 3.6 7.6 - - - +
60A GLY* 1.3 76.1 - - - +
62A ALA* 1.3 62.3 + - - +
64A LYS* 3.3 13.9 + - + +
65A GLN* 3.2 24.8 + - - +
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Residues in contact with ALA 62 (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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41A ALA* 3.8 29.3 - - + +
44A LYS* 5.3 0.6 - - + +
45A LEU* 4.0 11.7 - - + -
58A ALA 3.0 15.7 + - - +
59A CYS 3.7 4.7 - - - +
61A LEU* 1.3 75.2 - - - +
63A ARG* 1.3 59.8 + - - +
65A GLN* 3.1 4.4 + - - +
66A VAL* 2.9 32.0 + - - +
102A ILE* 4.6 2.2 - - + -
106A VAL* 3.9 20.2 - - + -
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Residues in contact with ARG 63 (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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59A CYS 3.1 19.3 + - - +
60A GLY* 3.8 8.3 - - - +
61A LEU 3.4 0.4 - - - -
62A ALA* 1.3 75.5 - - - +
64A LYS* 1.3 58.5 + - + +
66A VAL* 3.3 9.3 + - - +
67A GLU* 3.0 39.4 + - + +
106A VAL* 4.0 12.5 - - + +
107A ILE* 3.8 22.8 - - - +
110A GLU* 2.7 40.6 + - - -
123A MSE 3.8 29.0 - - + +
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Residues in contact with LYS 64 (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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60A GLY 3.2 15.6 + - - +
61A LEU* 3.4 15.5 - - + +
62A ALA 3.2 0.4 - - - -
63A ARG* 1.3 79.5 - - + +
65A GLN* 1.3 68.5 + - - +
67A GLU* 3.5 38.3 + - - +
68A LEU* 3.5 18.3 + - + +
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Residues in contact with GLN 65 (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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36A HIS* 5.7 0.3 - - - -
37A LEU* 3.5 43.8 - - - +
40A GLU* 3.5 36.3 + - + +
41A ALA* 3.9 14.1 - - + +
44A LYS* 6.3 0.2 - - + -
61A LEU 3.2 13.0 + - - +
62A ALA 3.1 8.5 + - - +
64A LYS* 1.3 81.3 - - - +
66A VAL* 1.3 63.7 + - - +
68A LEU* 3.2 26.0 + - - +
69A CYS* 3.3 17.0 + - - -
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Residues in contact with VAL 66 (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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41A ALA* 5.3 2.2 - - + -
62A ALA 2.9 18.7 + - - +
63A ARG* 3.7 8.5 - - - +
65A GLN* 1.3 75.7 - - - +
67A GLU* 1.3 66.7 + - + +
69A CYS* 3.0 23.2 + - - +
70A ALA 3.6 3.3 + - - -
99A LEU* 4.6 12.6 - - + -
102A ILE* 4.3 17.9 - - + -
103A ILE* 4.0 36.1 - - + -
106A VAL* 6.3 0.9 - - + -
123A MSE 4.1 33.5 - - + +
124A LEU* 4.5 5.1 - - + +
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Residues in contact with GLU 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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63A ARG* 3.0 24.8 + - + +
64A LYS* 3.6 40.1 + - - +
65A GLN 3.3 0.2 - - - -
66A VAL* 1.3 78.6 - - + +
68A LEU* 1.3 63.6 + - + +
69A CYS 3.4 0.5 + - - -
70A ALA* 3.5 13.2 + - - +
71A GLN* 3.7 14.3 + - - +
123A MSE 5.2 4.3 - - - -
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Residues in contact with LEU 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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37A LEU* 3.7 31.3 - - + +
64A LYS* 3.5 15.9 + - + +
65A GLN* 3.2 22.7 + - - +
67A GLU* 1.3 75.0 - - + +
69A CYS* 1.3 62.2 + - - +
71A GLN* 3.5 39.9 + - - +
72A LYS* 3.6 15.6 + - - +
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Residues in contact with CYS 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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34A ILE* 4.3 8.5 - - + -
37A LEU* 3.8 25.8 - - - -
38A SER 4.7 0.2 - - - -
65A GLN 3.5 13.7 - - - -
66A VAL* 3.0 12.1 + - - +
68A LEU* 1.3 75.1 - - - +
70A ALA* 1.3 59.9 + - - +
72A LYS* 2.9 22.6 + - - +
73A TYR* 3.0 18.9 + - + -
99A LEU* 3.8 42.6 - - + -
124A LEU* 4.0 8.3 - - + -
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Residues in contact with ALA 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 VAL 3.6 1.4 + - - -
67A GLU* 3.5 11.9 + - - +
68A LEU 3.3 0.8 - - - -
69A CYS* 1.3 77.9 - - - +
71A GLN* 1.3 60.2 + - + +
73A TYR* 3.4 3.7 + - - +
74A GLN* 3.2 20.4 + - - +
123A MSE 3.8 11.2 - - - +
124A LEU* 3.4 35.0 - - - +
125A GLY* 4.0 7.8 - - - +
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Residues in contact with GLN 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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67A GLU* 3.7 12.7 + - - +
68A LEU* 3.6 37.0 - - - +
69A CYS 3.2 0.2 - - - -
70A ALA* 1.3 77.2 - - + +
72A LYS* 1.3 67.1 + - + +
74A GLN* 3.3 20.2 + - - +
75A LYS* 3.4 20.3 + - - +
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Residues in contact with LYS 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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30A VAL* 3.3 16.2 - - + +
33A GLU* 3.1 42.5 + - + +
34A ILE* 3.4 28.0 - - + -
37A LEU* 4.0 18.4 - - + -
68A LEU* 3.6 13.9 + - - +
69A CYS 2.9 7.6 + - - +
71A GLN* 1.3 77.9 - - + +
73A TYR* 1.3 60.9 + - - +
75A LYS* 3.0 30.6 + - + +
76A LEU 3.0 21.8 + - - -
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Residues in contact with TYR 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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34A ILE* 4.1 14.1 - - + -
69A CYS* 3.0 26.6 + - + -
70A ALA 3.7 7.6 - - - +
71A GLN 3.3 0.2 - - - -
72A LYS* 1.3 74.9 - - - +
74A GLN* 1.3 58.6 + - - +
76A LEU* 3.2 28.6 + - + +
77A ALA* 2.8 29.1 + - - +
92A TRP* 4.8 4.7 - + + -
95A ILE* 4.2 4.2 - - - +
96A THR* 2.7 44.3 + - + +
99A LEU* 3.7 26.8 - - + +
124A LEU* 3.8 31.1 - - + +
125A GLY 5.3 2.5 - - - +
126A LEU* 4.0 27.8 - - + -
134A PHE* 4.0 11.7 - + - -
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Residues in contact with GLN 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 ALA 3.2 12.0 + - - +
71A GLN* 3.5 14.7 - - - +
72A LYS 3.2 0.2 - - - -
73A TYR* 1.3 75.6 - - - +
75A LYS* 1.3 62.4 + - + +
77A ALA* 3.3 9.3 + - + +
78A GLU* 3.1 39.8 + - + +
125A GLY 5.8 0.6 + - - -
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Residues in contact with LYS 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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30A VAL* 4.1 16.6 - - + -
33A GLU* 4.7 6.5 + - - +
71A GLN* 3.4 14.8 + - - +
72A LYS* 3.0 43.5 + - + +
74A GLN* 1.3 74.2 - - + +
76A LEU* 1.3 65.6 + - - +
78A GLU* 3.2 28.4 + - - +
79A LEU* 3.4 18.0 + - - +
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Residues in contact with LEU 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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27A ILE* 3.7 46.0 - - + +
30A VAL* 4.1 11.8 - - + +
31A VAL* 4.4 3.4 - - + -
34A ILE* 4.4 10.8 - - + -
72A LYS 3.0 10.8 + - - +
73A TYR* 3.3 31.4 - - + +
75A LYS* 1.3 74.7 - - - +
77A ALA* 1.3 66.2 + - - +
79A LEU* 3.0 15.7 + - + +
80A VAL* 3.3 18.1 + - - +
92A TRP* 4.0 35.7 - - + -
134A PHE* 3.9 12.1 - - + -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR 2.8 15.9 + - - +
74A GLN* 3.5 14.6 - - + +
76A LEU* 1.3 73.8 - - - +
78A GLU* 1.3 61.0 + - + +
80A VAL 3.4 19.4 + - - +
134A PHE* 3.7 37.7 - - + +
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Residues in contact with GLU 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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74A GLN* 3.1 31.8 + - + +
75A LYS* 3.5 19.5 + - - +
76A LEU 3.1 1.4 - - - -
77A ALA* 1.3 77.2 - - + +
79A LEU* 1.3 62.5 + - + +
80A VAL 3.3 1.3 + - - -
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Residues in contact with LEU 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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23A VAL* 3.5 24.5 - - + +
26A ASN* 3.5 55.6 - - + +
27A ILE* 3.7 20.2 - - + +
30A VAL* 4.0 13.9 - - + -
75A LYS 3.6 13.5 - - - +
76A LEU* 3.0 11.0 + - + +
78A GLU* 1.3 79.4 - - + +
80A VAL* 1.3 60.1 + - - +
81A PRO* 3.5 8.1 - - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.0 15.5 - - + -
76A LEU* 3.3 18.5 + - + +
77A ALA 3.4 12.2 + - - +
78A GLU 3.3 2.5 - - - -
79A LEU* 1.3 80.4 - - - +
81A PRO* 1.3 68.9 - - + +
82A ALA 3.6 1.0 + - - -
84A GLN 3.9 6.7 - - - +
85A TYR* 3.8 34.8 - - + +
88A TYR* 4.4 3.6 - - + -
92A TRP* 3.9 30.1 - - + -
134A PHE* 4.0 16.6 - - + -
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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