Contacts of the helix formed by residues 49 - 82 (chain D) in PDB entry 5FN2
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 GLU 49 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASN* 3.8 21.9 - - - +
9D GLU* 4.8 3.6 - - - +
12D LEU* 3.9 38.0 - - + +
47D TYR* 4.3 1.0 - - - +
48D THR* 1.3 80.2 + - - +
50D GLN* 1.3 63.3 + - - +
51D SER 3.3 2.2 - - - -
52D GLN* 2.9 57.8 + - - +
53D ILE* 2.9 22.2 + - + +
56D TYR* 5.3 1.7 + - - -
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLU 3.8 17.9 - - - +
41D ALA* 2.9 21.3 - - - +
42D PHE 5.3 0.3 - - - +
44D VAL* 3.8 19.6 + - + +
45D PRO 4.1 11.9 + - - -
46D ALA* 4.7 0.8 - - - +
47D TYR* 3.3 38.6 + - + +
48D THR 3.2 4.4 + - - -
49D GLU* 1.3 77.2 - - - +
51D SER* 1.3 62.9 + - - +
53D ILE* 3.2 9.7 + - - +
54D LYS* 2.9 40.4 + - - +
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Residues in contact with SER 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D THR 5.1 0.6 + - - -
49D GLU 3.3 0.6 - - - -
50D GLN* 1.3 86.5 - - - +
52D GLN* 1.3 59.7 + - - +
54D LYS* 3.2 8.2 + - - +
55D GLY* 2.9 26.0 + - - -
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Residues in contact with GLN 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 2.9 43.5 + - - +
51D SER* 1.3 80.2 - - - +
53D ILE* 1.3 55.0 + - - +
55D GLY* 3.2 3.1 + - - -
56D TYR* 2.9 59.1 + - + -
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Residues in contact with ILE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASN* 4.9 6.1 - - - +
11D LYS* 4.8 2.7 - - + -
12D LEU* 3.5 44.2 - - + +
15D CYS* 4.4 14.1 - - + -
37D PHE* 4.6 7.0 - - + +
40D GLU* 4.5 12.8 - - + +
41D ALA* 4.3 19.5 - - - +
47D TYR* 6.0 1.8 - - + -
49D GLU* 2.9 26.9 + - + +
50D GLN* 3.3 10.5 - - - +
52D GLN* 1.3 75.3 - - - +
54D LYS* 1.3 58.9 + - - +
56D TYR* 3.2 10.1 + - + +
57D VAL* 2.9 36.1 + - + +
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ALA* 3.4 44.0 - - + -
42D PHE* 4.0 31.7 + - + +
50D GLN* 2.9 23.1 + - - +
51D SER* 3.4 11.7 - - - +
53D ILE* 1.3 77.0 - - - +
55D GLY* 1.3 56.2 + - - +
57D VAL* 3.2 4.7 + - + +
58D TRP* 2.9 33.8 + - + +
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Residues in contact with GLY 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D SER 2.9 13.4 + - - -
52D GLN* 3.2 4.2 + - - -
54D LYS* 1.3 76.0 - - - +
56D TYR* 1.3 58.2 + - - +
58D TRP* 3.1 12.6 - - - +
59D ARG* 2.9 42.8 + - - +
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Residues in contact with TYR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 4.3 24.6 - - + +
15D CYS* 4.0 25.8 - - + -
16D ARG* 4.4 26.0 - - + +
19D TYR* 4.4 15.8 - + + -
49D GLU* 5.3 1.4 + - - -
52D GLN* 2.9 50.7 + - + -
53D ILE* 3.3 11.9 - - + +
55D GLY* 1.3 75.6 - - - +
57D VAL* 1.3 58.3 + - - +
59D ARG* 3.2 22.4 - - - +
60D SER* 2.9 33.4 + - - +
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Residues in contact with VAL 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D CYS* 4.5 7.2 - - - -
33D ASN* 5.0 5.4 - - - +
34D ILE* 3.9 29.4 - - + +
37D PHE* 3.4 39.0 - - + +
38D PHE* 5.0 5.2 - - + -
41D ALA* 4.1 11.4 - - + -
53D ILE* 2.9 19.7 + - + +
54D LYS* 3.2 8.9 + - + +
56D TYR* 1.3 78.2 - - - +
58D TRP* 1.3 56.0 + - - +
60D SER* 3.2 9.4 + - - -
61D ALA* 2.9 28.8 + - + +
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Residues in contact with TRP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS* 2.9 18.1 + - + +
55D GLY* 3.1 15.0 - - - +
57D VAL* 1.3 77.9 - - - +
59D ARG* 1.3 59.9 + - + +
61D ALA* 3.2 9.0 + - + +
62D VAL* 2.9 46.8 + - + +
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Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D TYR* 3.0 40.2 - - + +
30D TRP* 5.7 0.3 - - - -
55D GLY* 2.9 26.0 + - - +
56D TYR* 3.2 24.1 - - - +
58D TRP* 1.3 81.3 - - + +
60D SER* 1.3 56.1 + - - +
62D VAL* 3.2 10.4 + - - +
63D GLY* 2.9 25.8 + - - -
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D CYS* 5.6 0.2 - - - -
19D TYR* 3.5 20.7 - - - +
30D TRP* 3.9 21.5 - - - +
33D ASN* 3.3 21.9 + - - -
34D ILE* 3.7 18.9 - - - +
56D TYR 2.9 14.9 + - - -
57D VAL 3.3 7.9 - - - -
59D ARG* 1.3 75.9 - - - +
61D ALA* 1.3 58.4 + - - +
63D GLY* 3.2 2.8 + - - +
64D PHE* 2.9 28.2 + - - +
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 3.5 23.3 - - + +
57D VAL* 2.9 13.4 + - + +
58D TRP* 3.3 14.4 - - + +
60D SER* 1.3 75.3 - - - +
62D VAL* 1.3 58.6 + - + +
64D PHE* 3.2 7.4 + - - +
65D LEU* 2.9 30.4 + - - +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D TRP* 2.9 35.9 + - + +
59D ARG* 3.2 10.5 + - - +
61D ALA* 1.3 76.9 - - + +
63D GLY* 1.3 57.5 - - - +
65D LEU* 3.2 11.1 + - + +
66D PHE* 2.9 30.7 + - + +
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Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 6.1 1.1 - - - -
30D TRP* 3.4 28.1 - - - -
59D ARG 2.9 13.9 + - - -
60D SER 3.2 2.4 + - - -
62D VAL* 1.3 78.3 - - - +
64D PHE* 1.3 55.8 + - - +
66D PHE* 3.2 17.5 + - - -
67D TRP* 2.9 25.1 + - - +
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D PRO* 3.4 28.5 - - + -
28D PHE* 5.3 0.9 - + - -
30D TRP* 3.5 15.3 - - + -
31D LEU* 3.3 47.3 - - + -
34D ILE* 4.4 4.0 - - + -
60D SER 2.9 13.1 + - - +
61D ALA* 3.3 13.7 - - - +
63D GLY* 1.3 75.1 - - - +
65D LEU* 1.3 63.3 + - + +
67D TRP* 3.2 7.7 + - - +
68D VAL* 2.9 54.1 + - + +
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ALA 2.9 12.6 + - - +
62D VAL* 3.4 13.2 - - + +
64D PHE* 1.3 84.4 - - + +
66D PHE* 1.3 60.7 + - - +
68D VAL* 3.2 7.3 + - - +
69D ILE* 2.9 48.2 + - + +
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Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 6.0 4.3 - + - -
30D TRP* 4.9 4.9 - + - -
62D VAL* 2.9 15.3 + - + +
63D GLY* 3.2 23.8 - - - +
65D LEU* 1.3 78.6 - - - +
67D TRP* 1.3 86.9 + + - +
69D ILE* 3.2 9.9 + - + +
70D VAL* 2.9 55.6 + - + +
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Residues in contact with TRP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.8 26.9 - - + -
22D GLY 4.8 1.4 + - - -
25D PHE* 3.3 49.1 - + + +
27D PRO* 3.4 43.3 - - + +
30D TRP* 3.9 25.5 - + - -
63D GLY 2.9 8.2 + - - +
64D PHE 3.4 9.0 - - - +
66D PHE* 1.3 96.0 - + - +
68D VAL* 1.3 51.6 - - - +
70D VAL* 3.2 22.3 + - + -
71D LEU* 2.6 49.8 + - + +
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D PRO* 5.8 2.2 - - + -
64D PHE* 2.9 48.0 + - + +
65D LEU* 3.4 10.3 - - + +
67D TRP* 1.3 76.8 - - + +
69D ILE* 1.3 58.8 + - + +
71D LEU* 4.3 9.4 - - + -
72D THR* 2.5 58.6 + - + +
----------------------------------------------------------
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Residues in contact with ILE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU* 2.9 36.1 + - + +
66D PHE* 3.5 13.7 - - + +
68D VAL* 1.3 85.4 - - + +
70D VAL* 1.3 66.8 + - + +
72D THR* 3.0 12.4 + - - +
73D SER* 2.9 27.4 + - - +
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D PHE* 2.9 45.1 + - + +
67D TRP* 3.5 26.0 - - + +
69D ILE* 1.3 81.1 - - + +
71D LEU* 1.3 61.1 + - - +
73D SER* 3.2 7.3 + - - -
74D TRP* 2.9 30.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 4.5 15.0 - - + +
200B LEU* 3.4 44.6 - - + -
27D PRO* 5.6 5.6 - - + -
67D TRP* 2.6 31.0 + - + +
68D VAL* 3.8 9.0 - - + +
70D VAL* 1.3 77.3 - - - +
72D THR* 1.3 59.3 + - + +
74D TRP* 3.2 22.2 + - + +
75D ILE* 2.9 35.2 + - + +
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Residues in contact with THR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D VAL* 2.5 49.7 + - + +
69D ILE* 3.0 17.2 + - - +
71D LEU* 1.3 77.1 - - + +
73D SER* 1.3 56.1 + - - +
75D ILE* 3.2 13.8 + - + +
76D THR* 2.9 33.8 + - - -
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Residues in contact with SER 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ILE* 2.9 21.8 + - - +
70D VAL* 3.2 6.7 + - - -
72D THR* 1.3 80.8 + - - +
74D TRP* 1.3 56.5 + - - +
76D THR* 3.2 8.9 + - - -
77D ILE* 2.9 40.4 + - - +
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Residues in contact with TRP 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ASP* 3.2 26.7 + - - -
196B ILE* 3.9 27.3 - - + +
197B THR* 2.7 33.8 + - - +
200B LEU* 6.1 0.4 - - + -
70D VAL* 2.9 16.6 + - + +
71D LEU* 3.3 20.9 - - + +
73D SER* 1.3 76.7 - - - +
75D ILE* 1.3 57.3 + - - +
77D ILE* 3.2 26.0 + - + +
78D PHE* 2.9 31.6 + + + +
92D LEU* 4.0 23.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 6.3 1.6 - - + -
194B ASP* 5.1 1.6 - - - +
197B THR* 3.9 33.7 - - + +
71D LEU* 2.9 21.8 + - + +
72D THR* 3.4 16.6 - - + +
74D TRP* 1.3 78.9 - - - +
76D THR* 1.3 63.1 + - - +
78D PHE* 3.2 9.2 + - + +
79D GLN* 2.9 40.0 + - + +
----------------------------------------------------------
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D THR* 2.9 16.6 + - - -
73D SER* 3.5 10.9 - - - -
75D ILE* 1.3 81.9 - - - +
77D ILE* 1.3 59.3 + - + +
79D GLN* 3.2 9.0 + - + +
80D ILE* 2.9 43.8 + - + +
----------------------------------------------------------
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Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D SER* 2.9 27.8 + - - +
74D TRP* 3.4 27.4 - - + +
76D THR* 1.3 77.2 - - + +
78D PHE* 1.3 56.3 + - - +
80D ILE* 3.2 2.5 + - - -
81D TYR* 2.6 60.8 + - + +
85D TRP* 5.3 6.1 - - + +
----------------------------------------------------------
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Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ALA* 3.4 35.2 - - + -
193B VAL* 3.8 1.8 - - - -
194B ASP* 3.3 44.2 - - + +
74D TRP* 2.9 19.9 + + + +
75D ILE* 3.4 10.3 - - + +
77D ILE* 1.3 77.2 - - - +
79D GLN* 1.3 66.2 + - - +
81D TYR 5.1 0.7 - - - -
82D ARG* 3.0 53.2 + - + +
89D GLY 4.4 0.9 - - - -
92D LEU* 3.4 35.2 - - + -
93D SER* 3.5 30.1 - - - -
----------------------------------------------------------
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Residues in contact with GLN 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.0 20.2 - - - +
192B ALA* 2.7 41.0 + - - +
193B VAL* 5.2 1.8 - - - +
75D ILE* 2.9 25.3 + - + +
76D THR* 3.2 11.2 + - + +
78D PHE* 1.3 79.7 - - - +
80D ILE* 1.3 66.3 + - + +
82D ARG* 4.8 5.9 + - - -
83D PRO* 3.9 10.7 - - - +
----------------------------------------------------------
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Residues in contact with ILE 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D THR* 2.9 31.0 + - + +
77D ILE* 4.0 2.9 - - - +
79D GLN* 1.3 79.4 - - + +
81D TYR* 1.3 89.0 + - + +
82D ARG 3.3 1.3 - - - -
83D PRO* 3.1 28.1 - - - +
84D ARG* 4.0 12.4 + - - +
----------------------------------------------------------
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Residues in contact with TYR 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ILE* 2.6 40.8 + - + +
78D PHE* 4.0 2.2 - - - -
80D ILE* 1.3 91.2 - - + +
82D ARG* 1.3 57.9 + - - -
83D PRO 4.2 0.4 - - - -
84D ARG* 4.0 34.5 - - + +
85D TRP* 3.1 56.0 + + + +
----------------------------------------------------------
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Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 4.3 12.7 - - - +
192B ALA* 3.2 33.8 - - - +
78D PHE* 3.0 45.0 + - + +
79D GLN* 4.8 6.5 + - - -
81D TYR* 1.3 73.9 - - - +
83D PRO* 1.3 78.9 - - + +
85D TRP 2.8 22.4 - - - +
86D GLY 4.8 0.3 - - - +
89D GLY* 4.7 12.5 - - - +
90D ASP* 5.0 8.0 - - - +
93D SER* 4.1 14.8 - - - -
97D PRO* 3.9 23.4 - - - +
100D THR* 4.6 7.9 + - - +
101D PRO 2.9 32.3 + - - -
----------------------------------------------------------
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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