Contacts of the helix formed by residues 31 - 60 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G THR* 6.3 0.2 - - - -
77G ILE 3.5 9.8 + - - -
78G ASN* 4.0 14.7 - - - +
79G THR* 4.2 5.9 + - - +
30H VAL* 1.3 76.0 - - - +
32H GLY* 1.3 60.6 + - - +
33H ASP* 4.6 2.3 - - - +
34H ALA* 3.3 22.7 + - - +
35H LEU* 3.0 25.6 + - - +
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Residues in contact with GLY 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LYS* 3.7 7.2 + - - -
30H VAL 3.9 1.4 + - - -
31H SER* 1.3 70.1 - - - +
33H ASP* 1.3 60.7 + - - +
35H LEU* 3.4 11.4 + - - +
36H GLN* 3.0 31.7 + - - +
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Residues in contact with ASP 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G THR* 4.6 14.1 - - + -
100G SER 6.0 0.4 - - - +
103G ILE* 2.9 40.6 - - + +
104G ALA* 3.3 17.7 - - - +
106G ALA* 4.3 12.2 - - - +
31H SER* 3.4 2.8 + - - +
32H GLY* 1.3 75.0 - - - +
34H ALA* 1.3 59.4 + - - +
36H GLN* 3.3 7.7 + - - +
37H LEU* 2.9 37.0 + - + +
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Residues in contact with ALA 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G ILE 4.8 0.4 - - - +
78G ASN* 3.9 24.2 - - - +
79G THR* 4.1 5.1 - - - +
82G VAL* 3.9 14.6 - - + +
30H VAL* 4.6 9.6 - - + -
31H SER* 3.3 25.0 + - - +
33H ASP* 1.3 77.2 - - - +
35H LEU* 1.3 56.2 + - - +
37H LEU* 3.5 12.4 + - - +
38H MET* 3.1 32.7 + - - +
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Residues in contact with LEU 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LYS* 3.5 51.1 - - + +
13H GLU* 5.6 0.2 - - - -
15H VAL* 4.0 12.1 - - + -
16H SER* 3.7 33.0 - - - +
19H LEU* 5.0 2.7 - - + -
30H VAL* 4.4 15.8 - - + +
31H SER 3.0 14.0 + - - +
32H GLY* 3.4 13.5 - - - +
33H ASP 3.1 0.2 - - - -
34H ALA* 1.3 72.8 - - - +
36H GLN* 1.3 64.0 + - - +
37H LEU 3.1 1.3 - - - -
38H MET* 3.4 4.1 + - + +
39H VAL* 3.2 25.0 + - - +
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Residues in contact with GLN 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ILE* 3.3 53.7 - - + +
12H LYS* 3.3 38.6 + - - +
32H GLY 3.0 12.6 + - - +
33H ASP* 3.3 6.5 - - - +
35H LEU* 1.3 74.8 - - - +
37H LEU* 1.3 57.3 + - - +
39H VAL* 3.4 20.6 - - - +
40H GLU* 3.3 21.6 + - - +
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G THR* 4.6 15.5 - - + -
82G VAL* 4.6 12.8 - - + -
83G LYS* 5.1 12.8 - - + -
96G ILE* 4.1 15.3 - - + +
99G LYS* 3.6 7.4 - - + +
100G SER* 3.6 44.2 - - - +
103G ILE* 3.5 25.6 - - + -
33H ASP* 2.9 24.1 + - + +
34H ALA* 3.6 11.0 - - - +
35H LEU 3.1 0.6 - - - -
36H GLN* 1.3 74.1 - - - +
38H MET* 1.3 58.8 + - - +
39H VAL 3.2 1.6 - - - -
40H GLU* 3.2 8.9 + - + +
41H LEU* 2.9 26.0 + - - +
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Residues in contact with MET 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G CYS* 5.8 2.0 - - - -
61G PHE* 4.5 12.3 - - + -
65G LEU* 5.4 5.4 - - + -
82G VAL* 4.1 22.2 - - + -
85G LEU* 5.3 4.7 - - - -
15H VAL* 3.7 21.5 - - + -
19H LEU* 5.0 22.4 - - + -
30H VAL* 6.2 1.1 - - + -
34H ALA 3.1 19.5 + - - +
35H LEU* 3.4 5.4 + - + +
37H LEU* 1.3 72.6 - - - +
39H VAL* 1.3 58.2 + - - +
41H LEU* 3.1 34.5 - - + +
42H LEU* 2.9 64.7 + - + +
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Residues in contact with VAL 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 3.6 39.5 - - + +
11H ARG 4.2 4.7 - - - +
12H LYS* 4.4 13.7 - - + -
15H VAL* 3.8 22.0 - - + -
35H LEU 3.2 14.7 + - - +
36H GLN* 3.4 17.9 - - - +
38H MET* 1.3 75.0 - - - +
40H GLU* 1.3 56.5 + - + +
43H LYS* 2.8 46.2 + - + +
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Residues in contact with GLU 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G TYR* 4.2 8.2 - - + -
96G ILE* 4.3 11.9 - - + -
99G LYS* 3.0 50.9 + - + +
102G GLU* 4.8 4.3 - - - +
103G ILE* 3.7 14.3 - - + +
36H GLN* 3.3 16.7 + - - +
37H LEU* 3.2 13.6 + - + +
39H VAL* 1.3 78.3 - - - +
41H LEU* 1.3 55.3 + - - +
43H LYS* 3.4 19.6 - - - +
44H VAL* 2.9 36.6 + - - +
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Residues in contact with LEU 41 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G PHE* 4.3 20.6 - - + -
82G VAL* 5.4 4.9 - - + +
85G LEU* 4.8 10.1 - - + +
86G ALA* 4.8 14.8 - - + -
92G LEU* 4.3 13.0 - - + -
96G ILE* 4.1 15.0 - - + +
37H LEU 2.9 15.9 + - - +
38H MET* 3.1 41.7 + - + +
40H GLU* 1.3 73.6 - - - +
42H LEU* 1.3 62.8 + - + +
44H VAL* 3.2 6.4 + - - +
45H PHE* 2.7 25.8 + - + +
81H PHE* 4.2 25.1 - - + -
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G THR* 4.2 21.8 - - + -
57G GLN* 5.6 1.6 - - + -
58G CYS* 4.3 12.8 - - - -
61G PHE* 3.9 33.0 - - + -
10H PHE* 3.8 33.9 - - + -
15H VAL* 4.1 22.4 - - + -
18H LEU* 5.2 2.9 - - + -
38H MET* 2.9 27.4 + - + +
41H LEU* 1.3 72.6 - - + +
43H LYS* 1.3 66.6 + - - +
45H PHE* 3.2 16.6 - - + +
46H VAL* 3.0 29.3 + - + +
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Residues in contact with LYS 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G LEU* 3.5 30.6 - - + +
33G GLU* 5.8 0.2 + - - -
95G TYR* 4.4 15.7 - - - +
99G LYS* 6.0 1.1 - - - +
8H SER* 3.0 38.0 + - - +
10H PHE* 4.2 7.9 - - + +
39H VAL* 2.8 29.5 + - + +
40H GLU* 3.4 27.6 - - - +
42H LEU* 1.3 77.1 - - - +
44H VAL* 1.3 62.6 + - - +
47H VAL* 3.1 28.5 + - + +
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Residues in contact with VAL 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G SER 6.5 0.2 - - - -
92G LEU* 4.9 17.7 - - + -
95G TYR* 3.3 58.6 - - + +
96G ILE* 5.8 0.9 - - + -
40H GLU 2.9 19.9 + - - +
41H LEU* 3.8 5.2 - - - +
43H LYS* 1.3 71.7 - - + +
45H PHE* 1.3 58.0 + - - +
46H VAL 3.5 0.2 - - - -
47H VAL* 3.8 9.9 - - + -
48H GLU* 2.9 45.2 + - + +
81H PHE* 4.0 4.5 - - + -
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Residues in contact with PHE 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ILE* 4.2 5.6 - - + -
53G LEU* 3.3 37.5 - - + -
54G THR* 3.6 27.6 - - + -
57G GLN* 3.9 34.1 - - + -
61G PHE* 4.7 6.7 - + - -
41H LEU* 2.7 19.5 + - + +
42H LEU* 3.2 22.9 + - + +
44H VAL* 1.3 71.2 - - - +
46H VAL* 1.3 66.6 + - + +
49H ALA* 3.0 30.4 + - + +
77H LEU* 5.4 1.1 - - + -
78H LEU* 4.9 2.9 - - + -
81H PHE* 3.5 49.3 - + + -
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Residues in contact with VAL 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G VAL* 3.9 27.4 - - + -
30G LEU* 3.4 37.9 - - + -
31G CYS* 3.7 24.7 - - - +
50G ILE* 3.7 20.1 - - + +
54G THR* 4.3 2.0 - - - +
10H PHE* 4.0 5.4 - - + -
42H LEU 3.0 17.7 + - - +
45H PHE* 1.3 82.1 - - + +
47H VAL* 1.3 53.3 + - - +
49H ALA* 3.4 2.1 + - - +
50H ALA* 2.8 33.8 + - + +
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Residues in contact with VAL 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G LEU* 4.6 14.6 - - + +
34G VAL* 4.1 20.3 - - + +
95G TYR* 6.5 0.4 - - + -
43H LYS* 3.1 25.7 + - + +
44H VAL* 4.1 10.5 - - + +
45H PHE 3.4 0.2 - - - -
46H VAL* 1.3 75.4 - - - +
48H GLU* 1.3 65.6 + - + +
50H ALA* 3.7 5.1 - - - +
51H VAL* 2.8 46.7 + - + +
----------------------------------------------------------
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Residues in contact with GLU 48 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G SER* 5.6 7.0 - - - +
44H VAL* 2.9 34.6 + - + +
47H VAL* 1.3 77.8 - - + +
49H ALA* 1.3 66.1 + - - +
51H VAL* 4.0 18.9 - - - +
52H ARG* 3.2 64.8 + - - +
55H ARG* 4.0 5.8 + - - -
77H LEU* 4.0 9.1 - - + +
81H PHE* 4.4 15.3 - - + -
----------------------------------------------------------
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Residues in contact with ALA 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ILE* 3.4 31.4 - - + -
53G LEU* 4.8 4.9 - - + -
45H PHE* 3.0 20.9 + - + +
46H VAL* 3.5 2.2 - - - +
48H GLU* 1.3 75.5 - - - +
50H ALA* 1.3 60.7 + - - +
53H GLY* 3.3 18.2 + - - -
70H LEU* 4.0 13.3 - - + +
73H VAL* 4.6 2.8 - - - +
77H LEU* 3.7 28.8 - - + +
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Residues in contact with ALA 50 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G CYS* 4.7 2.9 - - - -
34G VAL* 4.4 10.8 - - + -
42G PHE* 3.1 37.9 - - + -
46G THR* 5.7 2.7 - - - -
50G ILE* 3.7 7.0 - - + +
46H VAL* 2.8 21.1 + - + +
47H VAL 3.7 4.3 - - - +
49H ALA* 1.3 71.2 - - - +
51H VAL* 1.3 53.6 + - - +
53H GLY* 3.1 2.8 + - - -
54H VAL* 2.6 40.7 + - - +
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Residues in contact with VAL 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G VAL* 4.9 12.3 - - + +
47H VAL* 2.8 39.9 + - + +
48H GLU* 3.6 17.2 + - - +
49H ALA 3.6 0.2 - - - -
50H ALA* 1.3 72.2 - - - +
52H ARG* 1.3 54.0 + - + +
54H VAL* 3.5 7.8 - - - +
55H ARG* 2.6 69.2 + - + +
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Residues in contact with ARG 52 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G SER* 5.4 1.8 - - - -
91G SER* 5.5 5.3 + - - -
48H GLU* 3.2 39.8 + - - +
51H VAL* 1.3 73.7 - - - +
53H GLY* 1.3 60.2 + - - +
55H ARG* 3.4 37.5 - - - +
56H GLN 2.9 22.3 + - - -
73H VAL* 3.1 36.9 - - + +
76H GLN* 3.9 31.3 + - - +
77H LEU* 4.9 9.4 - - + +
80H ASP* 3.0 32.4 + - - +
----------------------------------------------------------
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Residues in contact with GLY 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G THR* 6.4 1.1 - - - -
49H ALA 3.3 14.0 + - - -
50H ALA* 3.1 6.3 + - - -
52H ARG* 1.3 76.6 - - - +
54H VAL* 1.3 60.6 + - - +
56H GLN* 3.4 3.1 + - - +
57H ALA* 3.2 19.8 + - - +
65H VAL* 4.0 9.8 - - - +
69H GLN* 3.8 7.1 - - - +
70H LEU* 3.9 28.0 - - - -
73H VAL* 3.7 1.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G VAL* 4.7 6.1 - - + -
38G LYS* 5.5 6.7 - - + -
40G MET* 3.9 15.3 - - + -
42G PHE* 3.2 34.8 - - + -
50H ALA 2.6 23.9 + - - +
51H VAL* 3.5 7.4 - - - +
53H GLY* 1.3 68.6 - - - +
55H ARG* 1.3 66.1 + - + +
56H GLN 3.2 0.3 + - - -
57H ALA* 3.2 3.8 + - - +
58H GLN* 3.2 51.1 + - - +
65H VAL* 3.8 19.9 - - + +
----------------------------------------------------------
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Residues in contact with ARG 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H GLU* 4.0 6.7 + - - -
51H VAL* 2.6 52.0 + - + +
52H ARG* 3.4 40.8 - - - +
54H VAL* 1.3 73.3 - - + +
56H GLN* 1.3 56.9 + - - +
58H GLN* 3.8 13.3 + - - +
59H ALA* 3.0 30.0 + - - +
----------------------------------------------------------
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Residues in contact with GLN 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H ARG 2.9 17.8 + - - +
53H GLY 3.7 2.5 - - - +
54H VAL 3.2 0.2 - - - -
55H ARG* 1.3 75.8 - - - +
57H ALA* 1.3 64.4 + - - +
59H ALA* 3.2 16.8 + - - +
60H GLU* 2.8 49.8 + - - +
69H GLN* 3.3 32.1 - - + +
72H LYS* 4.1 17.8 - - + +
73H VAL* 3.6 12.2 - - + +
----------------------------------------------------------
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Residues in contact with ALA 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H GLY 3.2 12.3 + - - +
54H VAL 3.2 8.5 + - - +
56H GLN* 1.3 74.0 - - - +
58H GLN* 1.3 59.6 + - + +
60H GLU* 4.0 0.7 - - - +
61H ASP 3.3 3.5 + - - -
62H ALA* 2.7 34.6 + - + +
64H ARG 3.7 24.5 - - - +
65H VAL* 3.9 17.3 - - + -
69H GLN* 3.3 22.1 - - + +
----------------------------------------------------------
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Residues in contact with GLN 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LYS* 5.2 8.3 - - - +
40G MET* 3.1 46.7 - - + +
54H VAL* 3.2 26.3 + - - +
55H ARG* 4.0 14.3 - - - +
57H ALA* 1.3 80.4 - - + +
59H ALA* 1.3 60.6 + - - +
61H ASP* 3.3 15.8 + - - +
62H ALA 4.9 2.0 - - - +
----------------------------------------------------------
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Residues in contact with ALA 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ARG 3.0 21.2 + - - +
56H GLN* 3.2 13.8 + - - +
58H GLN* 1.3 74.0 - - - +
60H GLU* 1.3 57.0 + - - +
61H ASP* 3.4 1.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 4.7 7.6 - - - +
56H GLN* 2.8 46.2 + - - +
57H ALA 4.2 0.9 - - - +
59H ALA* 1.3 74.6 - - - +
61H ASP* 1.3 68.9 + - - +
62H ALA* 4.7 0.3 - - - -
68H ASP* 5.3 0.3 - - - +
69H GLN* 2.6 36.0 + - - +
72H LYS* 3.7 24.5 + - - +
----------------------------------------------------------
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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