Contacts of the helix formed by residues 42 - 73 (chain A) in PDB entry 6M0X
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 ASN 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.3 18.7 + - - +
39A GLN* 3.3 16.4 + - - +
40A ALA 3.0 0.8 - - - -
41A GLU* 1.3 74.0 - - - +
43A ASN* 1.3 57.7 + - - +
44A LEU 3.1 2.9 - - - -
45A VAL* 2.8 38.9 + - + +
46A ARG* 3.1 9.2 + - - +
65B A 4.2 3.2 + - - +
66B A 4.1 16.6 + - - +
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Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 3.0 17.8 + - - +
41A GLU 3.0 0.2 - - - -
42A ASN* 1.3 76.7 - - - +
44A LEU* 1.3 56.5 + - - +
46A ARG* 3.1 10.7 + - - +
47A ARG* 2.8 30.0 + - - +
50A ARG* 5.7 0.2 + - - -
480A PRO* 4.3 4.9 - - + -
13B A 2.8 35.0 + - - +
14B U 3.0 34.7 + - - -
66B A 3.4 39.5 - - - +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU 3.5 12.2 + - - +
42A ASN 3.1 0.2 - - - -
43A ASN* 1.3 78.8 - - - +
45A VAL* 1.3 56.8 + - + +
47A ARG* 3.6 25.0 + - - +
48A THR* 2.5 48.9 + - - +
607A PHE* 4.2 27.4 - - + -
682A ARG* 5.5 4.9 - - - +
12B A 6.0 2.9 - - - +
13B A 4.1 10.1 + - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN* 2.8 36.4 + - + +
44A LEU* 1.3 74.5 - - + +
46A ARG* 1.3 64.0 + - - +
48A THR* 3.4 4.9 + - - -
49A ASN* 2.9 45.8 + - - +
821A LYS* 5.6 1.3 - - + +
65B A 3.5 28.0 - - + +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN 3.1 6.4 + - - +
43A ASN* 3.1 15.8 + - - +
45A VAL* 1.3 78.0 - - - +
47A ARG* 1.3 58.3 + - - +
49A ASN* 3.9 2.0 - - - +
50A ARG* 2.9 49.4 + - - +
238A TYR* 3.4 20.4 + - - -
14B U 4.1 8.3 + - - -
64B G 3.5 9.0 + - - -
65B A 2.7 60.2 + - + +
66B A 3.2 76.4 + - - +
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN* 2.8 16.7 + - - +
44A LEU* 4.0 26.3 - - - +
46A ARG* 1.3 70.8 - - - +
48A THR* 1.3 67.0 + - - +
50A ARG* 3.3 27.6 + - - +
51A GLN* 2.9 57.1 + - - +
13B A 2.3 56.3 + - - -
14B U 2.7 52.6 + - - +
15B C 3.7 0.7 - - - +
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 2.5 38.1 + - - +
45A VAL* 3.7 7.1 - - - -
46A ARG 3.3 0.2 - - - -
47A ARG* 1.3 77.5 + - - +
49A ASN* 1.3 60.7 + - - +
51A GLN* 3.8 9.9 - - - +
52A GLY* 2.9 24.4 + - - -
10C T 5.7 9.6 - - + -
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Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 2.9 32.6 + - - +
46A ARG* 4.0 2.2 - - - +
48A THR* 1.3 78.0 - - - +
50A ARG* 1.3 61.1 + - - +
52A GLY* 3.8 1.7 - - - +
53A ARG* 2.9 51.0 + - + +
65B A 3.2 48.5 + - + +
10C T 5.9 5.1 - - - +
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN* 5.7 0.2 + - - -
46A ARG* 2.9 56.5 + - - +
47A ARG* 3.3 23.7 + - - +
49A ASN* 1.3 77.0 - - - +
51A GLN* 1.3 61.4 + - - +
53A ARG* 3.4 20.9 + - - +
54A ARG* 3.1 43.4 + - + +
238A TYR* 3.7 23.5 + - - -
14B U 3.5 22.2 + - - -
15B C 2.9 36.6 + - - -
64B G 3.5 25.1 + - - +
65B A 5.0 1.1 + - - +
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Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 2.9 45.1 + - - +
48A THR* 3.8 9.6 - - - +
50A ARG* 1.3 72.4 - - + +
52A GLY* 1.3 67.0 + - - +
54A ARG* 3.2 12.5 + - - +
55A LEU* 3.1 28.1 + - + +
15B C 3.3 49.6 + - - +
16B A 4.9 20.0 + - - +
17B G 6.3 1.3 - - - +
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Residues in contact with GLY 52 (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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48A THR 2.9 17.3 + - - -
49A ASN* 3.8 2.7 - - - -
50A ARG 3.4 0.2 - - - -
51A GLN* 1.3 77.0 - - - +
53A ARG* 1.3 60.7 + - - +
55A LEU* 3.2 10.8 + - - +
56A ALA* 3.1 23.6 + - - +
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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 ASN* 2.9 35.6 + - + +
50A ARG* 3.6 21.1 - - - +
51A GLN 3.3 0.2 - - - -
52A GLY* 1.3 74.8 - - - +
54A ARG* 1.3 59.4 + - + +
56A ALA* 3.7 3.2 - - - +
57A ARG* 2.7 38.3 + - - +
51B A 3.6 38.9 - - - +
64B G 3.2 71.6 + - - +
65B A 3.2 48.7 + - - -
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 3.1 36.3 + - + +
51A GLN* 3.2 14.0 + - - +
53A ARG* 1.3 77.1 - - - +
55A LEU* 1.3 61.6 + - + +
57A ARG* 3.6 21.9 - - - +
58A ARG* 3.0 62.7 + - - +
229A PRO* 3.6 10.7 - - - +
238A TYR* 3.2 21.0 - - - +
15B C 2.7 33.5 + - - -
16B A 3.6 22.4 + - - +
63B C 2.9 37.4 + - - -
64B G 4.9 0.2 + - - -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 3.1 18.8 + - + +
52A GLY* 3.2 10.7 + - - +
54A ARG* 1.3 76.1 - - + +
56A ALA* 1.3 58.1 + - - +
58A ARG* 3.4 6.4 + - - +
59A LYS* 2.9 29.0 + - - +
62A ARG* 5.0 0.9 + - - -
17B G 3.6 59.7 - - + +
18B G 3.7 48.5 + - - +
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Residues in contact with ALA 56 (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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52A GLY 3.1 16.5 + - - +
53A ARG* 3.9 4.9 - - - +
55A LEU* 1.3 73.4 - - - +
57A ARG* 1.3 67.1 + - - +
59A LYS* 3.8 8.7 - - - +
60A LYS* 3.0 26.8 + - - +
50B U 5.8 11.0 - - + -
51B A 5.4 5.6 - - - +
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 2.7 24.9 + - - +
54A ARG* 3.6 28.7 - - - +
56A ALA* 1.3 73.9 - - - +
58A ARG* 1.3 60.0 + - + +
60A LYS* 3.5 10.6 + - + +
61A HIS* 2.9 28.7 + - + +
61B G 5.6 1.8 - - + +
62B C 3.0 67.2 + - + +
63B C 2.7 63.0 + - - +
64B G 5.3 4.0 + - - -
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Residues in contact with ARG 58 (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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54A ARG* 3.0 47.9 + - - +
55A LEU* 4.0 4.6 - - - +
57A ARG* 1.3 76.7 - - + +
59A LYS* 1.3 59.9 + - - +
61A HIS* 3.7 6.8 - - - +
62A ARG* 2.9 43.2 + - + +
116A ARG* 6.0 1.1 - - - +
223A ARG* 3.7 13.9 - - - +
229A PRO* 3.7 4.8 - - - +
16B A 2.7 32.7 + - - -
17B G 2.8 41.9 + - - +
61B G 3.3 33.9 + - - +
62B C 2.8 36.1 + - - +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU 2.9 18.3 + - - +
56A ALA* 3.3 9.4 + - - +
58A ARG* 1.3 76.8 - - - +
60A LYS* 1.3 62.3 + - - +
62A ARG* 3.2 43.0 + - - +
63A ARG* 3.7 20.6 + - - +
113A VAL* 4.7 2.1 - - - +
114A LYS* 2.3 52.0 + - + +
115A HIS* 4.2 6.3 + - - -
18B G 5.3 4.3 - - - +
19B A 3.9 14.2 + - - -
20B U 6.0 0.2 + - - -
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Residues in contact with LYS 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 ALA 3.0 17.6 + - - +
57A ARG* 3.8 8.7 - - + +
59A LYS* 1.3 73.6 - - - +
61A HIS* 1.3 67.4 + - - +
63A ARG* 3.2 34.5 - - - +
64A VAL* 3.2 29.1 + - + +
49B A 3.8 26.2 + - - +
50B U 3.0 30.2 + - - -
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Residues in contact with HIS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 2.9 20.9 + - + +
58A ARG* 3.3 5.8 + - - +
60A LYS* 1.3 77.8 - - - +
62A ARG* 1.3 57.2 + - - +
64A VAL* 4.2 19.9 - - + +
65A ARG* 2.8 51.4 + - - +
68A ARG* 4.9 0.2 - - - -
59B A 2.7 58.6 + + - +
61B G 3.1 46.6 + + - +
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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
----------------------------------------------------------
55A LEU 5.0 1.4 + - - -
58A ARG* 2.9 37.4 + - + +
59A LYS* 3.4 41.4 - - - +
60A LYS 3.1 0.6 - - - -
61A HIS* 1.3 79.3 - - - +
63A ARG* 1.3 56.6 + - - +
65A ARG* 3.6 13.4 + - - +
66A LEU* 3.0 22.3 + - - +
113A VAL* 3.0 41.3 + - + +
114A LYS 4.8 1.0 - - - -
116A ARG* 3.3 39.6 - - - +
218A ILE* 3.1 44.9 - - + +
219A LEU 4.5 1.3 - - - -
221A GLY 5.5 0.9 - - - -
18B G 3.1 22.0 + - - -
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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
----------------------------------------------------------
59A LYS* 3.7 15.9 + - - +
60A LYS* 3.2 45.8 + - - +
62A ARG* 1.3 76.9 - - - +
64A VAL* 1.3 63.9 + - + +
66A LEU* 3.6 8.7 - - + +
67A ASN* 3.0 32.7 + - - +
110A LYS* 4.1 29.8 - - + +
113A VAL* 4.0 9.2 - - + +
114A LYS* 3.8 26.7 - - - +
48B G 3.5 30.1 + - - +
49B A 2.7 29.7 + - - -
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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 LYS* 3.2 24.6 + - + +
61A HIS* 3.3 22.0 + - + +
63A ARG* 1.3 79.2 - - + +
65A ARG* 1.3 65.7 + - - +
67A ASN* 3.0 21.2 + - + +
68A ARG* 3.0 38.8 + - - +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A HIS* 2.8 42.4 + - + +
62A ARG* 3.7 29.7 - - - +
64A VAL* 1.3 77.4 - - - +
66A LEU* 1.3 58.2 + - - +
68A ARG* 3.4 8.8 + - + +
69A LEU* 3.0 27.0 + - - +
217A GLU* 4.6 9.1 + - - +
218A ILE* 3.7 44.1 + - + +
221A GLY* 5.8 1.0 + - - -
59B A 4.1 12.8 - - + -
60B U 3.8 41.2 + - - -
61B G 4.4 2.8 + - - -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG 3.0 19.1 + - - +
63A ARG* 3.6 8.7 - - - +
64A VAL 3.1 0.2 - - - -
65A ARG* 1.3 74.8 - - - +
67A ASN* 1.3 64.4 + - - +
69A LEU* 3.4 9.7 + - + +
70A PHE* 3.0 48.4 + - + -
106A PHE* 3.6 27.4 - - + +
109A LEU* 4.2 4.5 - - + +
110A LYS* 3.7 36.6 - - + +
113A VAL* 5.3 3.1 - - + -
215A TYR* 3.8 29.2 - - + -
218A ILE* 4.1 9.4 - - + +
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG 3.0 17.7 + - - +
64A VAL* 3.0 16.6 + - + +
66A LEU* 1.3 77.2 - - - +
68A ARG* 1.3 58.3 + - - +
70A PHE 3.2 1.6 + - - -
71A GLU* 2.8 32.1 + - - +
79A PHE* 3.6 38.4 - - + +
106A PHE* 3.1 28.3 - - - -
110A LYS* 5.0 5.3 + - - +
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A HIS* 4.9 0.2 - - - -
64A VAL* 3.0 37.3 + - - +
65A ARG* 4.0 7.0 - - + +
66A LEU 3.4 0.2 - - - -
67A ASN* 1.3 76.5 - - - +
69A LEU* 1.3 57.2 + - - +
71A GLU* 4.1 16.4 - - + +
72A GLU* 2.9 55.7 + - + +
58B C 2.3 56.1 + - - +
59B A 3.5 30.8 + - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG 3.0 17.4 + - - +
66A LEU* 3.7 13.0 - - + +
67A ASN 3.2 0.4 - - - -
68A ARG* 1.3 74.3 - - - +
70A PHE* 1.3 59.2 + - - +
72A GLU* 3.9 0.8 - - + -
73A SER* 2.9 38.6 + - - +
211A PHE* 3.5 41.5 - - + -
214A ARG* 3.5 46.8 - - + +
215A TYR* 3.9 31.2 - - + +
218A ILE* 4.1 11.7 - - + -
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.0 50.8 + - + +
67A ASN 3.2 3.8 + - - +
69A LEU* 1.3 73.0 - - - +
71A GLU* 1.3 65.4 + - - +
73A SER* 3.7 4.0 + - - -
74A GLY 3.1 2.6 + - - -
75A LEU* 3.1 53.6 + - + -
76A ILE* 3.5 23.2 - - + +
79A PHE* 4.0 14.1 - - + -
102A ASN* 3.9 10.8 - - + -
105A LEU* 4.0 5.6 - - + -
106A PHE* 3.7 40.2 - + + -
109A LEU* 4.0 15.5 - - + -
211A PHE* 3.9 20.0 - + - -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 2.8 21.9 + - - +
68A ARG* 3.7 18.1 - - + +
70A PHE* 1.3 76.3 - - - +
72A GLU* 1.3 59.6 + - + +
74A GLY* 2.9 19.9 + - - -
76A ILE 3.7 8.7 + - - +
77A THR* 4.7 18.0 + - - +
79A PHE* 3.8 21.7 - - + -
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 2.9 38.7 + - + +
69A LEU 4.0 1.8 - - - +
71A GLU* 1.3 75.0 - - + +
73A SER* 1.3 63.3 + - - +
74A GLY* 3.1 1.6 + - - -
214A ARG* 2.4 41.6 + - - +
59B A 5.0 6.2 + - - -
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 2.9 24.8 + - - +
70A PHE* 4.0 3.6 - - - -
72A GLU* 1.3 76.4 - - - +
74A GLY* 1.3 58.4 + - - +
75A LEU* 3.2 30.0 - - - +
206A GLN* 4.4 12.3 - - - +
211A PHE* 3.3 28.9 - - - +
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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).
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