Contacts of the helix formed by residues 50 - 75 (chain D) in PDB entry 2RHM
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 ASP 50 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D SER* 1.3 92.7 + - - +
51D ARG* 1.3 60.1 + - - +
52D GLU* 3.4 13.4 + - - +
53D TRP* 3.0 20.4 + - - +
54D SER* 3.0 26.2 + - - -
133D GLY 4.5 0.9 - - - +
135D CYS* 3.7 12.5 - - - -
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ASP* 1.3 74.2 - - - +
52D GLU* 1.3 60.7 + - - +
54D SER* 3.3 5.0 + - - -
55D ARG* 2.9 48.6 + - + +
134D HIS 5.0 0.4 - - - -
135D CYS* 4.0 23.9 - - + +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ASP* 3.3 14.0 + - - +
51D ARG* 1.3 79.0 - - - +
53D TRP* 1.3 65.8 + - - +
55D ARG* 3.2 29.5 + - - +
56D ARG* 2.9 65.0 + - - +
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Residues in contact with TRP 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 4.0 16.6 - - + -
53C TRP* 3.9 25.6 - + - -
42D MSE 5.7 0.2 - - - -
43D PHE* 4.0 11.3 - + - -
46D LEU* 4.1 24.7 - - + -
47D GLY 3.0 19.6 + - - -
48D TRP* 3.5 23.1 - - + +
49D SER* 3.3 24.0 - - - +
50D ASP* 3.0 12.2 + - - +
52D GLU* 1.3 79.6 + - - +
54D SER* 1.3 58.5 + - - +
56D ARG* 3.1 45.8 + - + +
57D VAL* 2.8 49.3 + - + +
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Residues in contact with SER 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 3.0 28.6 + - - -
43D PHE* 4.0 11.4 - - - -
50D ASP 3.0 10.2 + - - -
51D ARG* 3.5 10.1 - - - -
53D TRP* 1.3 77.9 - - - +
55D ARG* 1.3 55.2 + - - +
58D GLY* 2.8 24.8 + - - -
133D GLY 3.6 12.6 - - - -
134D HIS* 2.8 31.1 + - - +
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 5.4 0.2 - - - +
51D ARG* 2.9 37.1 + - + +
52D GLU* 3.2 38.1 + - + +
54D SER* 1.3 73.7 - - - +
56D ARG* 1.3 57.0 + - - +
58D GLY* 3.2 2.1 + - - -
59D ALA* 2.9 30.3 + - - +
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY 3.5 15.9 - - - +
46C LEU* 3.2 43.3 + - + +
53C TRP* 6.1 0.2 - - - -
52D GLU* 2.9 47.8 + - - +
53D TRP* 3.4 31.1 - - + +
55D ARG* 1.3 78.5 - - - +
57D VAL* 1.3 56.2 + - - +
59D ALA* 3.3 7.4 + - + +
60D THR* 2.9 31.9 + - - -
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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
----------------------------------------------------------
46C LEU* 4.0 12.1 - - + -
39D LYS* 3.8 36.3 - - + +
42D MSE 3.7 18.5 - - + +
43D PHE* 3.8 15.5 - - + -
53D TRP* 2.8 59.8 + - + +
54D SER 3.8 3.1 - - - +
56D ARG* 1.3 71.2 - - - +
58D GLY* 1.3 53.1 + - - +
60D THR* 3.2 3.8 + - - -
61D ALA* 2.7 33.3 + - - +
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LYS* 4.1 8.2 - - - +
39D LYS* 3.6 26.3 - - - +
54D SER 2.8 13.8 + - - -
55D ARG* 3.2 3.8 + - - -
57D VAL* 1.3 75.7 - - - +
59D ALA* 1.3 60.7 + - - +
61D ALA* 3.3 2.8 + - - +
62D ILE* 3.0 28.7 + - - +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY* 5.7 2.7 - - - +
55D ARG 2.9 16.5 + - - +
56D ARG* 3.6 7.6 - - - +
58D GLY* 1.3 75.6 - - - +
60D THR* 1.3 61.6 + - - +
62D ILE* 3.4 9.1 + - - +
63D MSE 3.2 29.9 + - - +
93D ARG* 5.9 3.5 + - - +
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL* 4.0 9.9 - - + +
42C MSE 3.8 30.1 - - + +
45C GLY* 3.2 22.9 - - - -
46C LEU* 3.3 10.4 - - + +
42D MSE 3.8 20.9 - - - -
56D ARG 2.9 17.8 + - - -
57D VAL 3.6 4.5 - - - -
59D ALA* 1.3 74.7 - - - +
61D ALA* 1.3 58.5 + - - +
63D MSE 2.9 13.8 + - - +
64D MSE 2.9 25.7 + - + +
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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
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35D LYS* 3.7 27.8 - - + +
38D PHE* 3.8 12.0 - - + -
39D LYS* 3.7 11.2 - - + -
42D MSE 3.7 12.5 - - + +
57D VAL 2.7 20.7 + - - +
58D GLY 3.6 4.9 - - - +
60D THR* 1.3 71.6 - - - +
62D ILE* 1.3 57.3 + - - +
64D MSE 3.1 8.0 + - - +
65D LEU* 2.9 31.9 + - - +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LYS* 3.6 27.6 - - + +
58D GLY 3.0 16.5 + - - +
59D ALA* 3.5 12.3 - - - +
61D ALA* 1.3 75.6 - - - +
63D MSE 1.3 64.8 + - + +
65D LEU* 3.2 16.2 + - + +
66D TYR* 3.1 45.8 + - + -
83D SER* 3.8 14.1 - - - +
85D PHE* 4.7 6.1 - - + -
90D ASP* 4.5 11.7 - - - +
93D ARG* 3.4 34.1 - - - +
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Residues in contact with MSE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C VAL* 2.9 43.4 - - + +
44C ASP* 3.7 15.0 - - + +
45C GLY* 3.6 26.5 - - - +
59D ALA* 3.2 18.0 + - - +
60D THR* 2.9 11.9 + - - +
62D ILE* 1.3 78.9 - - + +
64D MSE 1.3 55.5 + - - +
66D TYR* 3.6 4.9 + - - +
67D HIS* 3.1 28.2 + - - +
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Residues in contact with MSE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C PHE* 3.4 52.7 - - + +
41C VAL* 3.8 28.5 - - + -
42C MSE 5.1 5.4 - - + -
64C MSE 4.2 17.7 - - + -
38D PHE* 3.4 21.3 - - + -
42D MSE 5.1 5.2 - - + -
60D THR* 2.9 20.2 + - + +
61D ALA* 3.1 6.0 + - - +
63D MSE 1.3 72.5 - - - +
65D LEU* 1.3 66.4 + - - +
67D HIS* 3.6 4.0 - - + +
68D THR* 2.9 54.4 + - - +
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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
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33D LEU* 3.7 27.9 - - + +
34D SER 3.7 20.0 - - - -
35D LYS* 3.8 24.7 - - + +
38D PHE* 3.5 34.3 - - + -
61D ALA 2.9 11.7 + - - +
62D ILE* 3.2 21.3 + - + +
64D MSE 1.3 75.9 - - - +
66D TYR* 1.3 59.2 + - + +
69D ALA* 2.8 32.2 + - - +
81D MSE 3.9 26.2 - - + +
82D GLU 4.1 6.3 - - - +
83D SER* 4.6 3.4 - - - -
85D PHE* 4.7 1.3 - - + -
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Residues in contact with TYR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ILE* 3.1 37.1 + - + +
63D MSE 4.2 4.7 - - - +
65D LEU* 1.3 80.8 - - + +
67D HIS* 1.3 61.8 + - - +
69D ALA* 3.8 4.0 - - - +
70D ALA* 3.1 23.9 + - - +
81D MSE 4.2 10.5 - - + -
85D PHE* 4.1 2.0 - + - -
90D ASP* 2.9 31.4 + - - +
93D ARG* 3.5 54.3 - - + +
94D MSE 3.4 38.0 - - + +
97D LEU* 3.8 22.1 - - + +
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Residues in contact with HIS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 5.3 5.3 + - - -
34C SER 5.8 0.2 + - - -
37C ALA* 4.0 22.0 - - + +
38C PHE* 3.7 37.6 - + - -
41C VAL* 4.0 21.6 - - + +
63D MSE 3.1 18.9 + - - +
64D MSE 3.6 9.2 - - + +
66D TYR* 1.3 79.3 - - - +
68D THR* 1.3 66.7 + - - +
70D ALA* 3.4 15.1 + - - +
71D THR* 3.6 10.1 + - + +
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.6 7.6 - - + -
38C PHE* 4.0 7.1 - - - -
68C THR* 3.3 32.0 + - + +
33D LEU* 3.9 13.5 - - + -
38D PHE* 4.3 4.3 - - - -
64D MSE 2.9 37.0 + - - +
65D LEU 4.0 2.0 - - - -
67D HIS* 1.3 76.3 - - - +
69D ALA* 1.3 66.8 + - - +
70D ALA 3.3 0.2 + - - -
71D THR* 3.3 8.8 + - - +
72D ILE* 3.2 34.7 + - + +
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.7 3.5 - - + +
65D LEU 2.8 19.8 + - - +
66D TYR* 3.8 5.4 - - - +
67D HIS 3.4 0.2 - - - -
68D THR* 1.3 76.7 - - - +
70D ALA* 1.3 57.1 + - - +
72D ILE 3.3 0.7 + - - -
73D LEU* 2.9 38.0 + - + +
79D LEU* 3.7 20.7 - - + +
81D MSE 3.9 24.2 - - - -
97D LEU* 4.1 12.8 - - + -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D TYR 3.1 14.3 + - - +
67D HIS* 3.5 11.4 - - - +
68D THR 3.2 0.4 - - - -
69D ALA* 1.3 75.4 - - - +
71D THR* 1.3 57.4 + - - +
73D LEU 3.4 0.2 + - - -
74D GLN* 2.9 43.9 + - - +
97D LEU* 3.7 17.7 - - + +
100D ILE* 4.1 19.7 - - + -
101D ALA* 3.9 5.0 - - + +
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Residues in contact with THR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 5.8 0.2 - - - +
30C LEU 4.4 2.1 + - - +
31C PRO* 3.4 10.4 - - + +
32C LEU* 2.9 48.5 + - - +
33C LEU* 4.4 9.0 - - + -
67D HIS* 3.6 7.0 + - + +
68D THR* 3.3 20.1 + - - +
70D ALA* 1.3 78.9 - - - +
72D ILE* 1.3 67.2 + - + +
74D GLN* 3.6 13.6 + - - +
75D SER* 3.3 21.3 + - - -
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Residues in contact with ILE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PRO* 4.3 10.3 - - + -
72C ILE* 4.0 32.1 - - + -
31D PRO* 4.3 9.9 - - + -
33D LEU* 4.3 12.1 - - + -
68D THR* 3.2 31.9 + - + +
71D THR* 1.3 77.8 - - + +
73D LEU* 1.3 64.4 + - - +
75D SER* 2.7 24.4 + - - +
77D GLN* 3.3 39.0 + - + +
79D LEU* 3.7 31.6 - - + -
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ARG* 4.7 1.6 + - - -
4D PRO* 3.5 29.8 - - + +
5D ALA 3.8 15.5 - - - +
6D LEU* 4.5 6.7 - - + -
69D ALA* 2.9 25.0 + - + +
72D ILE* 1.3 75.7 - - - +
74D GLN* 1.3 58.3 + - - +
76D GLY* 2.9 20.3 + - - -
77D GLN 3.5 18.2 - - - +
79D LEU* 4.0 13.7 - - + -
97D LEU* 4.0 18.6 - - + -
101D ALA* 3.9 18.2 - - + +
102D PRO 4.6 1.1 - - - +
103D PHE* 4.0 33.4 - - + -
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Residues in contact with GLN 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ARG* 3.4 20.4 + - - +
70D ALA* 2.9 31.7 + - - +
71D THR* 3.9 14.4 + - - +
72D ILE 3.2 0.4 - - - -
73D LEU* 1.3 76.5 - - - +
75D SER* 1.3 59.2 + - - +
76D GLY 3.1 0.8 + - - -
100D ILE* 2.9 43.2 + - - +
101D ALA* 3.8 6.5 - - + +
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Residues in contact with SER 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ARG* 3.4 45.3 + - - +
30C LEU 3.8 2.2 - - - -
31C PRO* 3.7 26.6 - - - +
77C GLN* 4.4 5.5 + - - +
71D THR 3.3 12.6 + - - -
72D ILE 2.7 19.1 + - - -
73D LEU 3.1 0.8 - - - -
74D GLN* 1.3 75.4 - - - +
76D GLY* 1.3 57.8 + - - +
77D GLN* 3.6 13.9 + - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il