Contacts of the helix formed by residues 56 - 85 (chain A) in PDB entry 1EFX
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 GLY 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 1.3 77.0 + - - +
57A PRO* 1.3 67.1 - - - -
58A GLU* 3.4 2.2 - - - -
59A TYR* 2.9 34.9 + - - +
60A TRP* 3.2 8.8 + - - -
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY* 1.3 80.2 - - - +
58A GLU* 1.3 59.9 + - + +
60A TRP* 4.0 5.8 - - + +
61A ASP* 2.6 41.6 + - + +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY 3.2 1.3 + - - +
57A PRO* 1.3 79.8 - - + +
59A TYR* 1.3 53.7 + - - +
61A ASP* 3.5 5.9 - - - +
62A ARG* 2.6 40.0 + - - +
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.5 3.5 - - - -
34A VAL* 5.1 2.4 - - + +
52A VAL* 3.2 24.0 - - + +
55A GLU* 3.3 40.2 - - + +
56A GLY 2.9 11.7 + - - +
58A GLU* 1.3 77.2 - - - +
60A TRP* 1.3 82.0 + + - +
62A ARG* 2.8 8.3 + - + +
63A GLU* 2.8 58.1 + - + +
167A TRP* 3.3 39.9 - + - -
171A TYR* 2.3 27.5 + + - -
1C GLY 4.0 1.9 + - - -
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Residues in contact with TRP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.8 24.0 - - + -
45A GLY* 4.0 21.1 - - - +
46A GLU 3.4 24.5 - - - -
47A PRO* 3.3 39.3 - - + -
52A VAL* 3.0 39.0 + - + -
53A GLU* 4.2 5.6 + - - +
55A GLU* 3.9 15.3 + - - +
56A GLY 3.2 14.3 + - - +
57A PRO* 4.0 7.6 - - + +
59A TYR* 1.3 95.2 - + - +
61A ASP* 1.3 56.7 + - - +
63A GLU* 3.7 9.7 + - + +
64A THR* 2.7 31.5 + - - -
67A TYR* 6.0 0.7 - + - -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 2.6 25.2 + - - +
58A GLU* 3.7 5.3 - - - +
60A TRP* 1.3 72.2 - - - +
62A ARG* 1.3 68.1 + - - +
63A GLU 3.1 1.6 - - - -
64A THR* 3.1 6.0 + - - +
65A GLN* 2.9 49.5 + - - +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU 2.6 22.3 + - - +
59A TYR* 2.8 6.2 + - - +
61A ASP* 1.3 78.1 + - - +
63A GLU* 1.3 66.3 + - - +
65A GLN* 3.4 9.1 + - + +
66A LYS* 3.3 44.2 + - + +
163A LEU* 5.0 16.8 - - - +
167A TRP* 4.9 14.5 - - - +
4C ASP* 3.3 29.1 + - - -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.1 4.0 + - - -
34A VAL* 5.5 3.9 - - + +
45A GLY* 5.9 0.2 - - - -
59A TYR* 2.8 48.0 + - + +
60A TRP* 3.7 13.9 - - + +
62A ARG* 1.3 81.8 + - + +
64A THR* 1.3 65.6 + - - +
66A LYS* 2.5 36.7 + - - +
67A TYR* 3.0 40.0 + - + -
167A TRP* 4.9 1.9 - - - -
1C GLY* 3.7 12.8 + - - -
2C ALA* 3.2 27.2 + - - +
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 4.2 1.1 - - + -
44A ARG* 3.7 25.4 - - + +
45A GLY* 2.9 19.0 + - - +
60A TRP 2.7 22.8 + - - -
61A ASP* 3.1 8.6 + - - -
63A GLU* 1.3 74.2 - - - +
65A GLN* 1.3 72.0 + - - +
67A TYR* 3.1 8.7 + - - -
68A LYS* 2.8 52.5 + - + +
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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
----------------------------------------------------------
61A ASP* 2.9 47.7 + - - +
62A ARG* 3.6 11.7 - - + +
63A GLU 3.2 0.2 - - - -
64A THR* 1.3 87.1 - - - +
66A LYS* 1.3 59.4 + - + +
68A LYS* 3.6 18.8 + - - +
69A ARG* 2.9 32.5 + - - +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.3 38.2 + - + +
63A GLU* 2.5 44.7 + - - +
64A THR 3.1 0.4 - - - -
65A GLN* 1.3 76.3 - - + +
67A TYR* 1.3 56.3 + - + +
69A ARG* 3.1 6.8 + - - +
70A GLN* 2.6 40.1 + - + +
167A TRP* 5.5 0.4 - - - +
1C GLY* 4.1 3.0 - - - -
2C ALA* 2.9 39.0 + - + +
3C VAL 3.7 7.0 - - - +
4C ASP* 3.6 19.0 - - - +
5C PRO* 3.8 17.1 - - + +
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.2 28.1 + - - -
9A TYR* 4.0 20.9 - + - -
22A PHE* 4.2 6.2 - + - -
24A ALA* 4.0 29.4 - - + -
25A VAL 5.5 0.3 - - - -
34A VAL* 3.4 24.9 - - + +
35A ARG 5.1 0.2 - - - -
36A PHE* 3.3 49.8 - + + -
45A GLY* 4.3 11.0 - - - -
60A TRP* 6.0 0.4 - + - -
63A GLU* 3.0 37.4 + - + -
64A THR 3.7 1.3 - - - +
66A LYS* 1.3 76.1 - - - +
68A LYS* 1.3 63.8 + - - +
70A GLN* 3.0 15.8 + - + +
71A ALA* 3.1 16.1 + - - +
2C ALA* 4.0 11.2 - - + +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.7 13.9 - - + -
43A PRO* 2.5 50.5 + - + +
44A ARG* 5.5 0.2 - - - -
64A THR* 2.8 37.8 + - + +
65A GLN* 3.9 20.0 - - - +
67A TYR* 1.3 74.0 - - - +
69A ARG* 1.3 62.0 + - - +
71A ALA* 3.6 4.5 + - - +
72A GLN* 3.2 20.9 + - - +
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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
----------------------------------------------------------
65A GLN 2.9 19.8 + - - +
66A LYS* 3.4 4.9 - - - +
68A LYS* 1.3 76.2 - - - +
70A GLN* 1.3 67.8 + - - +
72A GLN* 3.3 18.9 + - - +
73A THR* 3.2 25.9 + - - -
5C PRO* 3.2 43.2 + - + +
6C LEU 4.0 9.9 + - - -
20D SER* 4.9 2.4 + - - -
21D GLU* 3.2 30.2 + - - -
70D MET* 3.0 36.2 - - - +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.4 38.4 - - + +
22A PHE* 3.8 11.2 - - + -
66A LYS* 2.6 18.4 + - + +
67A TYR* 3.0 10.9 + - + +
69A ARG* 1.3 70.5 - - - +
71A ALA* 1.3 55.5 + - - +
73A THR* 2.4 33.4 + - - +
74A ASP* 2.9 32.0 + - - +
97A ARG* 3.6 20.6 + - - +
3C VAL* 5.0 2.2 - - - +
4C ASP 4.8 0.4 - - - -
5C PRO* 3.1 42.8 - - + +
6C LEU 4.6 1.6 - - - +
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 5.7 1.1 - - - +
22A PHE* 3.5 44.0 - - + -
36A PHE* 5.1 2.0 - - + -
38A SER* 4.9 7.2 - - - +
67A TYR 3.1 6.7 + - - +
68A LYS* 3.7 9.0 - - - +
70A GLN* 1.3 78.1 - - - +
72A GLN* 1.3 56.6 + - - +
73A THR 2.8 0.3 + - - -
74A ASP* 2.9 3.5 + - - +
75A ARG* 2.7 36.4 + - - +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS 3.2 10.9 + - - +
69A ARG* 3.4 18.7 - - - +
70A GLN 3.1 0.6 - - - -
71A ALA* 1.3 79.2 - - - +
73A THR* 1.3 60.6 + - - +
75A ARG* 3.4 20.3 - - - +
76A VAL* 3.5 13.2 - - - +
70D MET* 3.5 30.9 - - - +
72D ASP* 3.4 32.1 + - - +
73D LEU* 5.4 3.8 - - - +
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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
----------------------------------------------------------
69A ARG* 3.2 20.1 + - - +
70A GLN* 2.4 29.2 + - - +
72A GLN* 1.3 72.0 - - - +
74A ASP* 1.3 68.7 + - - +
75A ARG 2.9 1.8 - - - -
76A VAL* 2.8 10.3 + - - +
77A SER* 2.7 23.1 + - - +
5C PRO* 4.6 4.6 - - + +
6C LEU 4.3 10.5 + - - +
7C LEU 3.9 8.3 - - - +
8C ALA* 3.5 33.4 - - + +
70D MET* 5.6 3.1 - - - -
71D GLN* 5.5 5.6 - - + +
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Residues in contact with ASP 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 4.8 4.0 - - - +
11A ALA* 3.5 25.8 - - + +
20A PRO* 6.3 0.2 - - + -
22A PHE* 2.9 36.0 - - + -
70A GLN* 2.9 23.0 + - - +
71A ALA* 2.9 7.7 + - - +
73A THR* 1.3 77.5 - - - +
75A ARG* 1.3 52.5 + - - +
77A SER* 3.3 13.9 + - - -
78A LEU* 2.6 39.9 + - - +
95A ILE* 5.2 8.8 - - + +
97A ARG* 6.2 0.2 - - - -
116A TYR* 5.3 7.3 - - - -
9C LEU* 5.9 0.7 - - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.1 30.8 + - - -
20A PRO* 3.8 36.3 - - + +
71A ALA 2.7 15.7 + - - +
72A GLN* 3.4 15.0 - - - +
74A ASP* 1.3 78.7 - - - +
76A VAL* 1.3 62.1 + - - +
78A LEU* 3.4 3.7 + - - +
79A ARG* 3.1 17.0 + - - +
41D ARG* 4.9 3.8 - - - +
45D PHE* 2.9 57.8 - - + +
46D LYS 5.2 3.8 + - - -
72D ASP* 3.9 21.5 + - - +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN 3.5 16.6 - - - +
73A THR* 2.8 8.1 + - - +
75A ARG* 1.3 75.2 - - + +
77A SER* 1.3 55.7 + - - +
79A ARG* 3.4 1.4 + - - +
80A ASN* 2.7 43.5 + - - +
8C ALA* 3.9 18.4 - - + -
44D LYS* 4.1 15.0 - - + +
45D PHE* 3.5 30.3 - - + -
71D GLN* 4.0 20.9 - - + +
72D ASP* 3.9 20.0 - - + +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 2.7 17.7 + - - +
74A ASP* 3.3 20.1 + - - -
76A VAL* 1.3 76.3 - - - +
78A LEU* 1.3 66.3 + - - +
80A ASN* 3.1 9.4 + - - +
81A LEU* 3.0 23.7 + - - +
95A ILE* 3.9 10.5 - - - -
8C ALA* 3.5 4.5 - - - -
9C LEU* 2.8 44.1 + - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 3.8 29.4 - - + +
13A SER* 3.7 27.4 - - - +
20A PRO* 3.8 25.4 - - + -
74A ASP 2.6 21.6 + - - +
75A ARG 3.5 3.1 - - - +
77A SER* 1.3 71.1 - - - +
79A ARG* 1.3 55.8 + - - +
80A ASN 2.5 16.1 + - - -
81A LEU* 2.9 11.2 + - - +
82A ARG* 3.0 13.7 + - - +
93A HIS* 4.4 11.2 - - + -
94A ILE* 4.2 11.4 - - - +
95A ILE* 3.6 32.5 - - + +
118A TYR* 4.8 2.2 + - + -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG 3.1 4.3 + - - +
76A VAL 3.8 1.3 - - - +
78A LEU* 1.3 77.5 - - - +
80A ASN* 1.3 63.2 + - - +
82A ARG* 3.2 51.3 + - - +
83A GLY* 3.8 9.5 + - - -
43D GLY 4.2 4.6 + - - -
44D LYS* 3.4 47.4 + - + +
45D PHE* 3.2 42.2 - - + -
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 2.7 24.9 + - - +
77A SER 3.1 10.1 - - - +
78A LEU 2.5 4.9 + - - -
79A ARG* 1.3 69.4 + - - +
81A LEU* 1.3 53.4 + - + +
83A GLY* 2.7 24.4 + - - -
84A TYR* 2.7 38.9 + - + -
146A LYS* 4.6 3.4 - - - +
8C ALA* 3.8 16.2 - - - +
9C LEU 2.8 23.4 + - - +
44D LYS* 3.3 27.4 + - - +
183D ASP* 4.4 2.1 - - - +
184D SER* 3.7 7.4 + - - -
187D GLU* 5.3 2.4 + - - -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER 3.0 9.1 + - - +
78A LEU 2.9 9.1 + - - +
80A ASN* 1.3 70.6 - - - +
82A ARG* 1.3 55.5 + - - +
83A GLY 2.5 17.3 + - - -
84A TYR* 2.7 25.4 + - + +
85A TYR* 2.9 23.9 + - + -
95A ILE* 3.6 16.6 - - + -
118A TYR* 3.3 47.1 - - + -
123A TYR* 3.3 42.0 - - + +
9C LEU* 4.3 22.9 - - + +
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU 3.0 15.6 + - - +
79A ARG* 3.2 58.0 + - - +
81A LEU* 1.3 76.8 - - - +
83A GLY* 1.3 61.0 + - - +
86A ASN 3.5 1.2 + - - -
87A GLN* 2.8 44.9 + - + +
88A SER 3.2 25.7 + - - +
89A GLU* 4.2 33.5 + - - +
91A GLY 5.0 1.3 - - - +
93A HIS* 4.6 11.4 - - + -
118A TYR* 3.9 12.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.8 5.6 + - - -
80A ASN 2.7 9.2 + - - -
81A LEU 2.5 5.3 + - - -
82A ARG* 1.3 81.4 - - - +
84A TYR* 1.3 57.9 + - - +
85A TYR 3.0 1.8 - - - -
86A ASN* 2.5 29.5 + - - +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN* 2.7 53.4 + - + -
81A LEU* 2.7 17.3 + - + +
83A GLY* 1.3 73.0 - - - +
85A TYR* 1.3 62.0 + - + +
86A ASN* 5.0 1.0 - - - +
123A TYR* 3.8 8.3 - - - -
139A ALA* 3.7 33.5 - - + +
142A ILE* 3.2 41.7 - - + +
143A THR* 3.8 15.0 + - - -
146A LYS* 3.0 28.6 + - - +
9C LEU* 3.5 19.4 + - - -
183D ASP* 3.9 16.2 - - + -
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Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 2.9 19.6 + - + +
84A TYR* 1.3 76.2 - - + +
86A ASN* 1.3 74.7 + - - +
87A GLN* 3.5 21.3 - - + +
118A TYR* 3.1 42.0 - + - +
123A TYR* 3.0 31.7 - + - -
137A ASP* 2.9 27.5 + - - -
139A ALA* 3.3 25.6 - - + -
----------------------------------------------------------
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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