Contacts of the helix formed by residues 50 - 75 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER* 1.3 89.8 + - - +
51B ARG* 1.3 64.4 + - - +
52B GLU* 3.4 11.1 + - - +
53B TRP* 3.0 24.8 + - - +
54B SER* 3.1 21.0 + - - -
133B GLY 4.6 0.7 - - - +
135B CYS* 3.6 10.9 - - - -
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASP* 1.3 76.0 - - - +
52B GLU* 1.3 58.2 + - - +
54B SER* 3.2 5.7 + - - -
55B ARG* 2.9 44.7 + - + +
134B HIS 5.2 0.4 - - - +
135B CYS* 3.8 28.6 - - + +
137B ASP* 5.6 7.0 - - + +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 3.3 12.1 + - - +
51B ARG* 1.3 77.0 - - - +
53B TRP* 1.3 62.3 - - - +
55B ARG* 3.3 12.8 + - + +
56B ARG* 3.0 47.3 + - + +
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Residues in contact with TRP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.1 13.2 - - + -
53A TRP* 3.7 31.4 - + - -
56A ARG* 5.6 0.7 - - - -
42B MSE 6.2 0.2 - - - -
43B PHE* 4.1 5.6 - + - -
46B LEU* 4.3 19.7 - - + -
47B GLY 3.0 19.1 + - - -
48B TRP* 3.8 21.9 - - - +
49B SER* 3.3 24.2 - - - +
50B ASP* 3.0 11.7 + - - +
52B GLU* 1.3 73.7 - - - +
54B SER* 1.3 57.1 + - - +
56B ARG* 3.2 47.8 + - + +
57B VAL* 2.8 61.8 + - + +
133B GLY 5.6 0.2 - - - -
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 3.0 27.6 + - - -
43B PHE* 4.0 11.2 - - - -
50B ASP 3.1 11.3 + - - -
51B ARG* 3.4 11.9 - - - -
53B TRP* 1.3 77.3 - - - +
55B ARG* 1.3 55.9 + - - +
57B VAL 3.4 0.3 + - - -
58B GLY* 2.8 24.6 + - - -
133B GLY 3.6 12.8 - - - -
134B HIS* 2.7 30.7 + - - -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 5.3 0.7 - - - +
51B ARG* 2.9 30.4 + - + +
52B GLU* 3.5 13.7 - - - +
53B TRP 3.2 0.2 - - - -
54B SER* 1.3 75.9 - - - +
56B ARG* 1.3 59.9 + - + +
58B GLY* 3.3 1.5 + - - -
59B ALA* 3.0 28.2 + - - +
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY 4.3 7.2 + - - +
46A LEU* 2.8 43.2 + - + +
52B GLU* 3.0 41.3 + - + +
53B TRP* 3.5 37.0 - - + +
55B ARG* 1.3 74.1 - - + +
57B VAL* 1.3 64.0 + - - +
59B ALA* 3.4 6.6 + - - +
60B THR* 2.9 28.1 + - - -
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.1 12.6 - - + -
39B LYS* 3.9 23.3 - - + +
42B MSE 3.7 31.5 - - + +
43B PHE* 3.9 16.8 - - + -
46B LEU* 5.5 0.2 - - + -
53B TRP* 2.8 53.9 + - + +
54B SER 3.8 3.1 - - - +
56B ARG* 1.3 74.6 - - - +
58B GLY* 1.3 53.0 + - - +
60B THR* 3.2 3.8 + - - -
61B ALA* 2.7 32.1 + - - +
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 4.1 5.5 - - - +
39B LYS* 3.7 24.2 - - - -
54B SER 2.8 18.2 + - - -
55B ARG 3.7 2.2 - - - -
57B VAL* 1.3 73.6 - - - +
59B ALA* 1.3 58.5 + - - +
61B ALA* 3.3 1.6 + - - +
62B ILE* 3.0 38.3 + - - +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 5.7 2.7 - - - +
55B ARG 3.0 17.8 + - - +
56B ARG* 3.7 8.5 - - - +
58B GLY* 1.3 74.0 - - - +
60B THR* 1.3 61.4 + - - +
62B ILE* 3.5 13.1 + - - +
63B MSE 3.2 30.3 + - - +
93B ARG* 6.4 0.7 - - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.9 9.6 - - + +
42A MSE 3.8 32.5 - - + +
45A GLY* 3.2 23.2 - - - -
46A LEU* 3.4 8.9 - - + +
42B MSE 3.8 20.2 - - - -
56B ARG 2.9 14.7 + - - -
57B VAL 3.5 7.6 - - - -
59B ALA* 1.3 75.4 - - - +
61B ALA* 1.3 59.2 + - - +
63B MSE 3.1 12.6 + - - +
64B MSE 2.9 26.7 + - + +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 3.8 16.4 - - + +
38B PHE* 3.8 14.8 - - + -
39B LYS* 3.6 22.9 - - + -
42B MSE 3.7 12.3 - - + +
57B VAL 2.7 19.9 + - - +
58B GLY 3.3 5.6 + - - +
60B THR* 1.3 73.3 - - - +
62B ILE* 1.3 55.9 + - - +
64B MSE 3.1 7.7 + - - +
65B LEU* 2.8 29.3 + - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 3.5 29.6 - - + +
58B GLY 3.0 22.5 + - - +
59B ALA* 3.7 11.4 - - - +
61B ALA* 1.3 76.8 - - - +
63B MSE 1.3 63.8 + - + +
65B LEU* 3.1 20.6 + - + +
66B TYR* 3.1 34.2 + - + -
83B SER* 4.8 4.5 - - - +
85B PHE* 6.1 2.9 - - + -
90B ASP* 4.1 5.8 - - - +
93B ARG* 3.6 36.3 - - - +
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Residues in contact with MSE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 2.9 44.2 - - + +
44A ASP* 3.6 15.3 - - + +
45A GLY* 3.5 25.4 - - - +
59B ALA* 3.2 16.1 + - - +
60B THR* 3.1 10.2 + - + +
62B ILE* 1.3 80.1 - - + +
64B MSE 1.3 60.5 + - - +
66B TYR* 3.5 6.6 + - - +
67B HIS* 3.0 23.9 + - - +
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Residues in contact with MSE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.3 57.7 - - + +
41A VAL* 4.0 26.2 - - + -
42A MSE 5.0 12.1 - - + -
64A MSE 3.8 20.4 - - + -
38B PHE* 3.5 15.3 - - + -
42B MSE 5.1 5.8 - - + -
60B THR 2.9 15.1 + - - +
61B ALA* 3.4 11.2 - - - +
63B MSE 1.3 72.6 - - - +
65B LEU* 1.3 61.3 + - - +
67B HIS* 3.7 3.9 - - + +
68B THR* 2.9 55.4 + - - +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.8 21.9 - - + +
34B SER 3.8 19.1 - - - -
35B LYS* 3.9 25.6 - - + +
38B PHE* 3.6 33.2 - - + -
61B ALA 2.8 10.5 + - - +
62B ILE* 3.2 16.6 - - + +
64B MSE 1.3 78.0 - - - +
66B TYR* 1.3 57.9 + - + +
69B ALA* 2.9 31.5 + - - +
81B MSE 4.0 25.1 - - + -
82B GLU 4.1 9.0 - - - +
83B SER* 4.5 7.4 - - - -
85B PHE* 4.7 3.8 - - + -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE* 3.1 33.1 + - + +
63B MSE 4.0 6.3 - - - +
65B LEU* 1.3 78.1 - - + +
67B HIS* 1.3 64.6 + - - +
69B ALA* 3.8 3.9 - - - +
70B ALA* 3.1 23.6 + - - +
81B MSE 4.3 10.3 - - + -
85B PHE* 4.0 3.3 - + - -
90B ASP* 2.8 31.7 + - - +
93B ARG* 3.4 56.1 - - + +
94B MSE 3.4 37.1 - - + +
97B LEU* 3.9 21.4 - - + +
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU 5.2 5.9 + - - -
34A SER 5.6 0.6 + - - -
37A ALA* 4.0 24.5 - - + +
38A PHE* 3.6 37.9 - + - -
41A VAL* 4.2 16.7 - - + +
63B MSE 3.0 18.6 + - - +
64B MSE 3.7 11.0 - - + +
65B LEU 3.3 0.2 - - - -
66B TYR* 1.3 78.2 - - - +
68B THR* 1.3 68.2 + - - +
70B ALA* 3.4 10.9 + - - +
71B THR* 3.6 13.9 + - + +
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.6 6.7 - - + -
38A PHE* 4.0 7.3 - - - -
68A THR* 3.3 33.4 + - + +
33B LEU* 3.8 21.8 - - + -
38B PHE* 4.3 4.7 - - + -
64B MSE 2.9 37.6 + - - +
65B LEU 4.0 1.8 - - - -
67B HIS* 1.3 75.1 - - - +
69B ALA* 1.3 65.6 + - - +
70B ALA 3.3 0.2 + - - -
71B THR* 3.3 10.3 - - - +
72B ILE* 3.2 25.9 + - + +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.7 12.7 - - + +
65B LEU 2.9 19.0 + - - +
66B TYR* 3.8 5.6 - - - +
67B HIS 3.3 0.2 - - - -
68B THR* 1.3 78.8 - - - +
70B ALA* 1.3 57.6 + - - +
72B ILE 3.3 0.5 + - - -
73B LEU* 2.9 35.5 + - + +
79B LEU* 3.7 12.6 - - + +
81B MSE 3.9 24.7 - - - -
97B LEU* 4.2 12.8 - - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR 3.1 15.7 + - - +
67B HIS* 3.7 7.0 - - - +
68B THR 3.2 0.6 - - - -
69B ALA* 1.3 78.4 - - - +
71B THR* 1.3 60.4 + - - +
74B GLN* 2.9 39.4 + - - +
97B LEU* 3.7 18.4 - - + +
100B ILE* 3.8 23.1 - - + -
101B ALA* 3.8 6.3 - - + +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 5.7 0.3 - - - +
30A LEU 4.5 2.4 + - - +
31A PRO* 3.4 17.1 - - + +
32A LEU* 2.9 48.0 + - - +
33A LEU* 4.4 8.7 - - + -
67B HIS* 3.6 10.3 + - - +
68B THR* 3.3 20.6 + - - +
70B ALA* 1.3 80.2 - - - +
72B ILE* 1.3 63.3 + - + +
74B GLN* 3.6 13.6 + - - +
75B SER 3.4 14.0 + - - -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 4.3 6.3 - - + -
72A ILE* 3.8 38.4 - - + -
31B PRO* 4.5 10.1 - - + -
33B LEU* 4.3 18.6 - - + -
68B THR* 3.2 28.0 + - + +
69B ALA 3.8 1.3 - - - +
71B THR* 1.3 77.7 - - + +
73B LEU* 1.3 64.1 + - - +
75B SER* 2.7 25.7 + - - +
77B GLN* 3.3 34.2 + - + +
79B LEU* 3.6 26.9 - - + -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 5.2 0.5 + - - -
4B PRO* 3.5 29.3 - - + +
5B ALA 4.0 13.2 - - - +
6B LEU* 4.5 6.3 - - + -
69B ALA* 2.9 22.2 + - + +
72B ILE* 1.3 77.8 - - - +
74B GLN* 1.3 56.0 + - - +
76B GLY* 3.0 20.8 + - - -
77B GLN 3.6 16.4 - - - +
79B LEU* 3.6 17.7 - - + -
97B LEU* 4.0 18.8 - - + -
101B ALA* 3.8 31.1 - - + +
102B PRO 4.8 1.1 - - - +
103B PHE* 3.9 24.0 - - + -
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.8 17.5 + - - +
70B ALA* 2.9 28.1 + - - +
71B THR* 3.8 16.1 + - - +
72B ILE 3.3 0.2 - - - -
73B LEU* 1.3 76.3 - - - +
75B SER* 1.3 59.9 + - - +
76B GLY 3.2 0.6 + - - -
100B ILE* 3.0 49.4 + - - +
101B ALA* 3.8 4.9 - - + +
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Residues in contact with SER 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.5 46.4 + - - +
30A LEU 3.8 1.8 - - - -
31A PRO* 3.6 36.9 - - - +
77A GLN* 3.9 7.6 + - - +
71B THR 3.4 3.3 + - - -
72B ILE 2.7 18.6 + - - -
74B GLN* 1.3 77.0 - - - +
76B GLY* 1.3 57.2 + - - +
77B GLN* 3.6 11.3 + - - +
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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