Contacts of the helix formed by residues 31 - 60 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C THR* 4.7 10.6 - - - -
77C ILE 2.9 23.8 + - - +
78C ASN* 3.5 18.8 - - - +
79C THR* 4.3 1.7 + - - +
29D LYS 4.3 0.2 - - - -
30D VAL* 1.3 77.7 - - - +
32D GLY* 1.3 65.7 + - - +
33D ASP* 4.1 3.1 + - - +
34D ALA* 3.5 10.9 + - - +
35D LEU* 3.2 20.8 + - - +
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Residues in contact with GLY 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LYS* 4.0 9.1 + - - -
30D VAL 4.0 0.2 + - - -
31D SER* 1.3 75.2 - - - +
33D ASP* 1.3 64.5 + - - +
35D LEU* 3.4 4.6 + - - +
36D GLN* 3.2 22.5 + - - +
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Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C THR* 3.5 26.0 - - + +
103C ILE* 4.7 20.0 - - + +
104C ALA* 5.0 10.6 - - - +
31D SER* 3.5 2.8 + - - +
32D GLY* 1.3 76.0 - - - +
34D ALA* 1.3 58.8 + - - +
36D GLN* 3.4 8.6 - - - +
37D LEU* 3.0 32.3 + - + +
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 4.0 6.1 - - + +
78C ASN* 3.3 35.9 - - - +
79C THR* 4.2 4.7 - - - +
82C VAL* 3.2 25.2 - - + +
30D VAL* 4.1 9.0 - - + -
31D SER* 3.5 15.6 + - - +
32D GLY 3.3 0.6 - - - -
33D ASP* 1.3 77.7 - - - +
35D LEU* 1.3 56.3 + - - +
37D LEU* 3.2 4.0 + - - +
38D MET* 2.8 22.7 + - - +
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LYS* 3.5 36.6 - - + +
15D VAL* 3.6 28.0 - - + -
16D SER* 3.7 20.4 - - - +
19D LEU* 3.7 22.7 - - + -
30D VAL* 3.8 17.2 - - + +
31D SER 3.2 17.0 + - - +
32D GLY* 3.9 4.3 - - - +
33D ASP 3.3 0.2 - - - -
34D ALA* 1.3 71.9 - - - +
36D GLN* 1.3 57.0 + - - +
37D LEU 3.2 1.6 - - - -
38D MET* 3.2 3.4 + - + +
39D VAL* 2.7 38.8 + - - +
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Residues in contact with GLN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ILE* 3.2 50.3 - - + +
12D LYS* 3.1 44.5 - - - +
32D GLY 3.2 10.8 + - - +
33D ASP* 3.4 11.7 - - - +
35D LEU* 1.3 76.0 - - - +
37D LEU* 1.3 58.8 + - - +
39D VAL* 3.2 14.7 - - - +
40D GLU* 3.0 29.5 + - - +
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C THR* 4.3 25.6 - - + +
82C VAL* 3.6 14.7 - - + +
83C LYS* 4.1 20.2 - - + -
96C ILE* 4.5 12.2 - - + +
99C LYS 4.4 0.2 - - - -
100C SER* 3.9 41.1 - - - +
103C ILE* 4.1 20.0 - - + -
33D ASP* 3.0 19.9 + - + +
34D ALA 3.5 5.4 - - - +
36D GLN* 1.3 73.5 - - + +
38D MET* 1.3 61.4 + - - +
40D GLU* 3.3 12.4 - - + +
41D LEU* 2.8 28.4 + - - +
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Residues in contact with MET 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 3.9 32.5 - - + -
65C LEU* 3.9 15.5 - - + -
82C VAL* 2.9 38.4 - - + -
85C LEU* 4.0 20.2 - - + -
15D VAL* 4.0 17.9 - - + -
19D LEU* 4.6 8.7 - - + -
30D VAL* 5.4 0.7 - - + -
34D ALA 2.8 17.9 + - - +
35D LEU* 3.2 10.7 + - + +
37D LEU* 1.3 74.5 - - - +
39D VAL* 1.3 56.6 + - - +
41D LEU* 3.9 18.5 - - + +
42D LEU* 2.8 42.6 + - + +
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Residues in contact with VAL 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLY* 4.7 2.0 - - - -
10D PHE* 3.4 44.7 - - + +
12D LYS* 3.5 23.1 - - + -
15D VAL* 3.9 21.0 - - + +
35D LEU 2.7 20.4 + - - +
36D GLN* 3.2 22.7 - - - +
38D MET* 1.3 72.5 - - - +
40D GLU* 1.3 52.4 + - + +
42D LEU* 3.8 1.3 - - - +
43D LYS* 2.8 41.3 + - + +
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR* 4.7 4.3 - - - -
96C ILE* 3.7 18.8 - - + +
99C LYS* 3.0 35.5 - - + +
102C GLU* 4.9 3.6 - - - +
103C ILE* 3.2 27.0 - - + +
36D GLN* 3.0 20.3 + - - +
37D LEU* 3.3 16.8 - - + +
38D MET 3.2 0.2 - - - -
39D VAL* 1.3 75.8 - - + +
41D LEU* 1.3 53.4 + - - +
43D LYS* 3.1 18.4 + - - +
44D VAL* 2.8 39.8 + - - +
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 4.4 10.4 - - + -
82C VAL* 3.7 24.5 - - + +
85C LEU* 4.0 21.8 - - + +
86C ALA* 4.1 7.2 - - + +
92C LEU* 3.9 29.6 - - + -
96C ILE* 4.3 8.0 - - + +
37D LEU 2.8 19.1 + - - +
38D MET* 3.9 27.1 - - + +
40D GLU* 1.3 71.9 - - - +
42D LEU* 1.3 58.6 + - - +
44D VAL* 3.6 4.4 + - + +
45D PHE* 3.0 26.7 + - - +
81D PHE* 4.1 18.6 - - + -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C THR* 4.3 12.3 - - + +
57C GLN* 5.4 0.2 - - + -
58C CYS* 3.8 30.5 - - - +
61C PHE* 3.8 31.2 - - + -
10D PHE* 4.0 23.3 - - + -
15D VAL* 3.8 33.2 - - + -
18D LEU* 4.9 1.6 - - + -
19D LEU* 6.5 0.2 - - + -
38D MET* 2.8 23.9 + - + +
39D VAL 4.0 2.9 - - - +
41D LEU* 1.3 71.1 - - - +
43D LYS* 1.3 60.5 + - - +
45D PHE* 3.3 11.7 - - + +
46D VAL* 3.1 32.9 + - - +
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Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.8 28.9 - - + +
33C GLU* 4.9 4.0 + - - -
95C TYR* 6.0 1.8 - - - -
8D SER 3.5 18.4 + - - -
9D GLY* 4.2 17.5 - - - -
10D PHE* 4.1 13.9 - - + +
39D VAL* 2.8 27.7 + - + +
40D GLU* 3.4 20.6 - - - +
42D LEU* 1.3 73.8 - - - +
44D VAL* 1.3 56.1 + - + +
46D VAL* 3.5 2.6 + - - +
47D VAL* 3.1 33.9 + - + +
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 4.2 20.2 - - + -
95C TYR* 4.2 28.0 - - + -
96C ILE* 4.2 16.6 - - + -
40D GLU* 2.8 23.9 + - - +
41D LEU* 3.8 6.3 - - + +
43D LYS* 1.3 69.2 - - + +
45D PHE* 1.3 61.8 + - - +
47D VAL* 4.0 7.2 - - + +
48D GLU* 3.0 39.8 + - + +
81D PHE* 4.5 9.6 - - + -
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Residues in contact with PHE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 4.9 2.0 - - + -
53C LEU* 4.0 24.0 - - + -
54C THR* 3.4 40.2 - - - -
57C GLN* 3.9 26.0 - - + -
61C PHE* 5.1 3.4 - + + -
41D LEU 3.0 18.3 + - - +
42D LEU* 3.3 19.1 - - + +
44D VAL* 1.3 78.9 - - - +
46D VAL* 1.3 60.5 + - + +
48D GLU* 3.9 1.6 - - - +
49D ALA* 3.0 32.8 + - + +
77D LEU* 4.3 13.0 - - + -
78D LEU* 5.9 0.2 - - + -
81D PHE* 3.2 55.4 - + + -
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 3.3 54.7 - - + +
30C LEU* 3.9 16.2 - - + -
31C CYS* 4.0 3.8 - - - -
50C ILE* 4.3 2.7 - - + -
54C THR* 3.3 26.5 - - + +
10D PHE* 3.5 11.4 - - + -
42D LEU 3.1 17.9 + - - +
43D LYS 4.0 3.4 - - - +
45D PHE* 1.3 72.7 - - + +
47D VAL* 1.3 55.0 + - - +
49D ALA* 3.5 6.4 + - - +
50D ALA* 2.9 32.4 + - - +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.8 36.3 - - + +
33C GLU* 4.6 4.7 - - - +
34C VAL* 4.2 6.4 - - + +
43D LYS* 3.1 23.7 + - + +
44D VAL* 4.0 7.4 - - + +
46D VAL* 1.3 75.3 - - - +
48D GLU* 1.3 59.4 + - + +
50D ALA* 3.4 6.5 + - - +
51D VAL* 2.7 48.3 + - + +
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D VAL* 3.0 30.2 + - + +
45D PHE 4.0 2.7 - - - +
47D VAL* 1.3 79.8 - - + +
49D ALA* 1.3 65.3 + - - +
51D VAL* 3.7 8.9 - - - +
52D ARG* 3.0 64.9 + - - +
55D ARG* 3.6 27.4 + - - -
81D PHE* 4.7 7.2 - - + -
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 3.8 23.3 - - + -
53C LEU* 5.5 0.7 - - + -
45D PHE* 3.0 23.3 + - + +
46D VAL* 3.6 5.8 - - - +
48D GLU* 1.3 75.4 - - - +
50D ALA* 1.3 61.2 + - - +
52D ARG* 4.0 4.0 - - - +
53D GLY 3.2 16.3 + - - -
70D LEU* 3.9 12.5 - - - +
73D VAL* 4.8 1.4 - - - +
77D LEU* 3.4 35.2 - - + +
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C CYS* 3.1 33.0 - - - -
34C VAL* 3.8 16.7 - - + +
42C PHE* 3.4 24.5 - - + -
50C ILE* 3.8 4.6 - - - +
46D VAL 2.9 12.6 + - - +
47D VAL* 3.5 5.8 - - - +
48D GLU 3.1 0.2 - - - -
49D ALA* 1.3 75.8 - - - +
51D VAL* 1.3 65.5 + - - +
53D GLY* 3.3 9.0 + - - -
54D VAL 3.4 9.4 + - - -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 3.9 17.5 - - + -
38C LYS* 3.7 27.9 - - + +
47D VAL* 2.7 45.9 + - + +
48D GLU* 3.3 14.3 + - - +
50D ALA* 1.3 72.8 - - - +
52D ARG* 1.3 60.8 - - - +
54D VAL* 3.6 4.3 + - - +
55D ARG* 2.8 63.5 + - - +
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Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLU* 3.0 42.7 + - - +
49D ALA* 4.0 3.8 - - - +
51D VAL* 1.3 74.1 - - - +
53D GLY* 1.3 62.8 + - - +
55D ARG* 3.0 31.5 + - - +
56D GLN 3.2 16.6 + - - -
73D VAL* 3.7 30.8 - - + +
76D GLN* 4.1 21.4 + - - +
77D LEU* 4.2 23.9 - - - +
80D ASP* 3.5 32.9 + - - +
81D PHE* 4.4 5.7 - - - -
----------------------------------------------------------
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Residues in contact with GLY 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 4.8 2.7 - - - -
49D ALA 3.2 9.1 + - - -
50D ALA 3.3 4.3 + - - -
52D ARG* 1.3 75.0 - - - +
54D VAL* 1.3 63.5 + - - +
56D GLN* 3.3 4.9 + - - +
57D ALA 3.3 11.8 + - - -
65D VAL* 3.0 26.3 - - - +
69D GLN* 4.3 0.2 - - - +
70D LEU* 3.9 31.4 - - - -
73D VAL* 4.4 0.6 - - - +
----------------------------------------------------------
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 4.2 4.5 - - + -
38C LYS* 3.4 34.1 - - + -
40C MET* 3.1 38.3 - - + +
41C GLN 4.0 5.2 - - - +
42C PHE* 3.3 33.6 - - + -
50D ALA 3.4 3.7 + - - +
51D VAL 3.8 7.4 - - - +
53D GLY* 1.3 71.7 - - - +
55D ARG* 1.3 63.8 + - - +
56D GLN 3.3 0.9 + - - -
57D ALA* 3.4 2.9 + - - +
58D GLN* 3.4 27.5 + - - +
65D VAL* 3.6 8.3 - - + +
----------------------------------------------------------
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LYS* 5.0 11.0 - - + +
48D GLU* 3.6 17.6 + - - -
51D VAL* 2.8 55.9 + - + +
52D ARG* 3.0 37.5 - - - +
53D GLY 3.4 0.2 - - - -
54D VAL* 1.3 77.2 - - + +
56D GLN* 1.3 59.0 + - - +
58D GLN* 4.7 4.3 - - - +
59D ALA* 3.5 21.1 + - - +
----------------------------------------------------------
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Residues in contact with GLN 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ARG 3.2 5.1 + - - -
53D GLY 3.7 4.3 - - - +
54D VAL 3.2 0.6 - - - -
55D ARG* 1.3 74.4 - - - +
57D ALA* 1.3 64.7 + - - +
59D ALA* 3.2 16.3 + - - +
60D GLU* 2.9 32.8 + - - +
69D GLN* 3.0 33.7 - - + +
72D LYS* 3.4 31.2 - - - +
73D VAL* 3.4 28.1 - - + +
----------------------------------------------------------
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 5.4 2.7 - - + -
53D GLY 3.3 4.0 + - - -
54D VAL 3.4 1.5 + - - +
56D GLN* 1.3 77.8 - - - +
58D GLN* 1.3 54.7 + - - +
60D GLU* 3.6 2.1 + - - +
61D ASP 3.2 7.3 + - - -
62D ALA* 2.7 34.4 + - + +
64D ARG 3.7 9.4 - - - +
65D VAL* 3.3 46.7 - - + +
69D GLN* 3.1 18.8 - - + +
----------------------------------------------------------
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Residues in contact with GLN 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LYS* 3.9 16.1 + - - +
39C ALA* 4.9 4.4 + - - +
40C MET* 3.7 44.7 - - + +
54D VAL* 3.4 17.3 + - - +
55D ARG* 4.7 4.2 - - - +
56D GLN 3.4 0.8 - - - -
57D ALA* 1.3 74.3 - - - +
59D ALA* 1.3 61.3 + - - +
61D ASP* 3.1 31.1 + - - +
62D ALA 4.5 1.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ARG 3.5 18.3 + - - +
56D GLN* 3.2 12.4 + - - +
58D GLN* 1.3 75.1 - - - +
60D GLU* 1.3 57.5 + - - +
61D ASP* 3.1 7.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN* 2.9 40.4 + - - +
57D ALA 3.7 4.3 - - - +
59D ALA* 1.3 75.4 - - - +
61D ASP* 1.3 66.1 + - - +
62D ALA* 3.3 2.5 + - + +
68D ASP* 4.4 2.3 - - - +
69D GLN* 2.4 41.0 + - - +
72D LYS* 4.2 17.6 + - - +
----------------------------------------------------------
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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