Contacts of the helix formed by residues 31 - 60 (chain B) in PDB entry 4NE1
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 SER 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE 3.1 20.1 + - - -
78A ASN* 3.9 8.4 - - - +
79A THR* 4.6 2.8 + - - +
29B LYS 4.1 1.0 + - - -
30B VAL* 1.3 78.0 - - - +
32B GLY* 1.3 64.0 + - - +
33B ASP* 4.4 2.9 + - - +
34B ALA* 3.3 16.3 + - - +
35B LEU* 3.2 18.4 + - - +
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 3.4 12.6 + - - -
30B VAL 3.7 1.9 + - - -
31B SER* 1.3 70.5 - - - +
33B ASP* 1.3 63.9 + - - +
35B LEU* 3.5 3.9 + - - +
36B GLN* 3.0 32.5 + - - +
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Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 4.9 12.6 - - + -
103A ILE* 3.6 39.7 - - + +
104A ALA* 4.6 6.4 - - - +
106A ALA* 4.7 16.2 - - - +
31B SER* 3.4 3.4 + - - +
32B GLY* 1.3 78.3 - - - +
34B ALA* 1.3 57.4 + - - +
36B GLN* 3.3 5.2 + - - +
37B LEU* 2.9 32.3 + - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE 4.1 1.1 - - - +
78A ASN 3.8 26.5 - - - +
79A THR* 4.0 2.8 - - - +
82A VAL* 3.8 10.2 - - + +
30B VAL* 3.9 12.8 - - + -
31B SER* 3.3 25.9 + - - +
33B ASP* 1.3 76.7 - - - +
35B LEU* 1.3 55.4 + - - +
37B LEU* 3.1 15.7 - - - +
38B MET* 3.1 28.3 + - - +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 3.7 40.8 - - + +
15B VAL* 3.8 18.6 - - + -
16B SER* 3.7 40.4 - - - +
19B LEU* 5.6 2.0 - - + -
30B VAL* 4.2 16.1 - - + +
31B SER 3.2 12.9 + - - +
32B GLY* 3.8 9.2 - - - +
34B ALA* 1.3 70.8 - - - +
36B GLN* 1.3 60.6 + - - +
37B LEU 3.1 1.6 - - - -
38B MET* 3.0 7.6 + - + +
39B VAL* 2.9 29.3 + - - +
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Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 3.5 31.7 - - + +
12B LYS* 3.5 32.7 - - - +
32B GLY 3.0 20.5 + - - +
33B ASP* 3.4 10.5 - - - +
35B LEU* 1.3 74.1 - - - +
37B LEU* 1.3 59.8 + - - +
39B VAL* 3.3 25.5 - - - +
40B GLU* 3.3 13.2 + - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.8 43.3 - - + +
82A VAL* 3.7 14.5 - - + +
83A LYS* 3.8 23.3 - - + -
96A ILE* 3.9 21.3 - - + +
99A LYS 5.5 0.2 - - - -
100A SER* 3.9 23.8 - - - +
103A ILE* 3.9 10.0 - - + +
33B ASP 2.9 11.6 + - - +
34B ALA* 3.1 21.1 - - - +
36B GLN* 1.3 74.8 - - - +
38B MET* 1.3 56.8 + - - +
40B GLU* 3.2 7.5 + - + +
41B LEU* 2.8 28.1 + - - +
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.8 15.7 - - + -
65A LEU* 5.3 5.6 - - + -
82A VAL* 3.4 31.0 - - + -
85A LEU* 5.1 7.0 - - + -
15B VAL* 3.6 19.3 - - + -
19B LEU* 4.2 24.9 - - + -
34B ALA 3.1 17.4 + - - +
35B LEU* 3.0 14.3 + - + +
37B LEU* 1.3 72.3 - - - +
39B VAL* 1.3 60.3 + - - +
41B LEU* 3.6 25.4 - - + +
42B LEU* 3.0 47.9 + - + +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.2 46.9 - - + +
12B LYS* 4.1 24.2 - - + -
15B VAL* 4.1 16.5 - - + +
35B LEU 2.9 16.5 + - - +
36B GLN* 3.3 18.8 - - - +
38B MET* 1.3 74.5 - - - +
40B GLU* 1.3 60.7 + - + +
43B LYS* 3.0 31.1 + - + +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 4.2 4.9 + - - -
96A ILE* 3.5 17.5 - - + -
99A LYS* 3.4 36.7 - - + +
102A GLU* 4.4 9.2 - - - +
103A ILE* 3.9 18.7 - - + +
36B GLN 3.5 14.1 - - - +
37B LEU* 3.2 10.0 + - + +
39B VAL* 1.3 77.9 - - + +
41B LEU* 1.3 59.7 + - - +
43B LYS* 3.3 24.9 + - - +
44B VAL* 2.8 35.2 + - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 5.6 9.2 - - + -
82A VAL* 3.9 22.9 - - + +
85A LEU* 4.6 10.1 - - + -
86A ALA* 3.8 28.3 - - + +
92A LEU* 4.2 18.2 - - + -
96A ILE* 4.1 11.4 - - + +
37B LEU 2.8 18.8 + - - +
38B MET* 3.6 34.1 - - + +
40B GLU* 1.3 72.4 - - - +
42B LEU* 1.3 58.2 + - - +
44B VAL* 3.4 2.1 + - - -
45B PHE* 2.8 26.3 + - + +
81B PHE* 4.3 13.9 - - + -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.0 19.1 - - + -
58A CYS* 5.2 7.2 - - - -
61A PHE* 3.4 37.9 - - + -
10B PHE* 3.7 34.3 - - + -
15B VAL* 3.8 31.9 - - + -
18B LEU* 5.5 5.6 - - + -
19B LEU* 5.7 1.6 - - + -
38B MET* 3.0 22.4 + - + +
41B LEU* 1.3 72.7 - - - +
43B LYS* 1.3 68.4 + - - +
45B PHE* 3.2 7.7 + - + +
46B VAL* 3.1 26.8 + - + +
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.3 6.1 - - + +
95A TYR* 3.2 29.2 + - - -
8B SER 4.0 29.8 + - - +
9B GLY* 5.1 1.1 - - - -
10B PHE* 3.8 21.9 - - + +
39B VAL* 3.0 21.2 + - + +
40B GLU* 3.3 27.8 - - - +
42B LEU* 1.3 77.2 - - - +
44B VAL* 1.3 61.5 + - + +
46B VAL* 3.4 2.6 + - - +
47B VAL* 3.0 42.7 + - + +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.7 31.2 - - + -
95A TYR* 3.7 34.8 - - + -
96A ILE* 3.8 8.7 - - + -
40B GLU 2.8 24.4 + - - +
41B LEU 4.0 3.4 - - - +
43B LYS* 1.3 78.6 - - - +
45B PHE* 1.3 65.3 + - - +
47B VAL* 3.9 10.1 - - + -
48B GLU* 3.0 36.4 + - + +
81B PHE* 5.2 1.8 - - - -
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 5.3 2.2 - - + -
53A LEU* 4.2 15.3 - - + -
54A THR* 4.1 19.5 - - + -
57A GLN* 3.5 34.5 - - + -
61A PHE* 4.2 12.6 - + + -
41B LEU* 2.8 18.7 + - + +
42B LEU* 3.2 16.6 + - + +
44B VAL* 1.3 73.3 - - - +
46B VAL* 1.3 70.5 + - + +
48B GLU* 4.0 0.7 - - - +
49B ALA* 2.9 33.0 + - + +
77B LEU* 4.0 27.7 - - + +
78B LEU* 5.1 0.9 - - + -
81B PHE* 3.4 53.5 - + + -
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.0 26.5 - - + -
30A LEU* 4.4 20.2 - - + -
31A CYS* 5.0 5.2 - - - -
50A ILE* 4.2 15.3 - - + -
54A THR* 4.4 12.8 - - + +
10B PHE* 3.9 21.5 - - + -
42B LEU* 3.1 15.2 + - + +
43B LYS 4.0 2.7 - - - +
45B PHE* 1.3 84.1 - - + +
47B VAL* 1.3 56.5 + - - +
49B ALA* 3.3 5.2 + - - +
50B ALA* 2.7 36.0 + - + +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 5.0 9.0 - - + -
34A VAL* 5.9 6.0 - - + +
43B LYS* 3.0 38.1 + - + +
44B VAL* 3.6 13.2 - - + +
46B VAL* 1.3 76.6 - - - +
48B GLU* 1.3 62.9 + - + +
50B ALA* 3.2 6.0 + - - +
51B VAL* 2.7 50.4 + - + +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A SER* 5.3 5.5 + - - -
92A LEU* 6.2 1.3 - - + -
44B VAL* 3.0 29.3 + - + +
45B PHE* 4.4 1.1 - - - +
47B VAL* 1.3 81.0 - - + +
49B ALA* 1.3 61.6 + - - +
51B VAL* 4.0 16.1 - - - +
52B ARG* 2.9 63.3 + - - +
55B ARG* 3.5 22.4 + - - -
77B LEU* 4.7 5.2 - - + -
81B PHE* 5.7 4.3 - - + -
----------------------------------------------------------
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 5.2 13.0 - - + -
53A LEU* 5.7 1.1 - - + -
45B PHE* 2.9 24.6 + - + +
46B VAL* 3.3 10.5 - - - +
48B GLU* 1.3 77.0 - - - +
50B ALA* 1.3 56.5 + - - +
52B ARG* 3.9 2.9 - - - +
53B GLY* 3.0 24.8 + - - -
70B LEU* 4.0 16.0 - - + +
73B VAL* 5.0 0.8 - - - +
77B LEU* 3.8 33.6 - - + +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A CYS* 5.7 1.1 - - - -
34A VAL* 4.2 22.2 - - + -
42A PHE* 4.1 25.9 - - + -
50A ILE* 5.5 7.3 - - + +
46B VAL* 2.7 24.2 + - + +
47B VAL* 3.6 4.3 - - - +
49B ALA* 1.3 71.3 - - - +
51B VAL* 1.3 54.8 + - + +
53B GLY* 3.2 2.7 + - - +
54B VAL* 2.8 40.4 + - - +
70B LEU* 6.0 0.2 - - - -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 2.7 44.3 + - + +
48B GLU* 4.0 14.8 - - - +
50B ALA* 1.3 70.9 - - + +
52B ARG* 1.3 57.4 + - - +
54B VAL* 3.3 10.7 + - + +
55B ARG* 2.9 61.7 + - + +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 4.5 10.3 + - - -
91A SER* 4.9 5.1 + - - -
48B GLU* 2.9 47.4 + - - +
49B ALA* 4.1 2.0 - - - +
51B VAL* 1.3 74.5 - - - +
53B GLY* 1.3 62.6 + - - +
55B ARG* 3.4 33.3 + - - +
56B GLN* 3.2 17.7 + - - +
73B VAL* 3.8 31.7 - - + +
76B GLN* 3.4 41.4 + - - +
77B LEU* 4.6 11.2 - - + +
80B ASP* 2.8 31.6 + - - +
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Residues in contact with GLY 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.0 15.4 + - - -
50B ALA* 3.2 4.7 + - - -
52B ARG* 1.3 74.9 - - - +
54B VAL* 1.3 60.8 + - - +
56B GLN* 3.5 3.2 + - - +
57B ALA* 3.3 17.7 + - - +
65B VAL* 3.4 24.2 - - - +
69B GLN* 4.3 2.4 - - - +
70B LEU* 4.5 14.8 - - - -
73B VAL* 4.2 9.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.5 19.5 - - + -
38A LYS* 4.8 22.2 - - + -
42A PHE* 4.5 4.5 - - + -
50B ALA 2.8 20.6 + - - +
51B VAL* 3.3 13.5 - - + +
53B GLY* 1.3 72.3 - - - +
55B ARG* 1.3 65.1 + - + +
57B ALA* 3.4 3.8 + - - +
58B GLN* 3.2 40.2 + - + +
65B VAL* 3.6 22.7 - - + +
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 3.5 19.2 + - - -
51B VAL* 2.9 49.3 + - + +
52B ARG* 3.4 33.5 + - - +
54B VAL* 1.3 74.1 - - + +
56B GLN* 1.3 58.4 + - - +
58B GLN* 3.6 19.2 - - - +
59B ALA* 3.2 26.0 + - - +
----------------------------------------------------------
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Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG 3.2 8.5 + - - +
53B GLY 4.0 1.1 - - - +
54B VAL 3.3 0.2 - - - -
55B ARG* 1.3 75.1 - - - +
57B ALA* 1.3 64.8 + - - +
59B ALA* 3.0 19.3 + - - +
60B GLU* 2.8 42.5 + - - +
69B GLN* 3.6 30.3 - - + +
72B LYS* 3.5 22.3 - - + +
73B VAL* 3.8 25.0 - - + +
----------------------------------------------------------
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY 3.3 7.9 + - - +
54B VAL 3.7 7.9 - - - +
56B GLN* 1.3 75.5 - - - +
58B GLN* 1.3 58.9 + - - +
61B ASP 3.1 2.8 + - - -
62B ALA* 2.4 38.6 + - + +
64B ARG 3.1 28.0 - - - +
65B VAL* 3.8 21.8 - - + -
69B GLN* 3.5 15.3 - - + +
----------------------------------------------------------
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 5.5 8.1 - - - +
54B VAL* 3.2 25.6 + - + +
55B ARG* 3.6 28.7 - - - +
57B ALA* 1.3 76.6 - - - +
59B ALA* 1.3 59.7 + - - +
61B ASP* 3.0 25.1 + - - +
62B ALA 4.8 1.1 - - - +
----------------------------------------------------------
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG 3.2 15.8 + - - +
56B GLN* 3.0 18.6 + - - +
58B GLN* 1.3 77.1 - - - +
60B GLU* 1.3 59.8 + - - +
61B ASP* 3.0 4.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 2.8 40.7 + - - +
57B ALA 4.4 1.6 - - - +
59B ALA* 1.3 75.8 - - - +
61B ASP* 1.3 70.0 + - - +
62B ALA* 4.8 1.8 - - + +
68B ASP* 5.0 1.9 - - - +
69B GLN* 2.9 35.6 + - + +
72B LYS* 3.6 26.4 + - - +
----------------------------------------------------------
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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