Contacts of the helix formed by residues 50 - 75 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER* 1.3 87.9 + - - +
51A ARG* 1.3 53.8 + - - +
52A GLU* 3.1 14.0 - - + +
53A TRP* 2.8 40.2 + - - +
54A SER* 3.7 0.9 + - - -
56A ARG* 5.5 2.8 + - - -
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER 3.8 1.5 + - - -
50A ASP* 1.3 69.8 - - - +
52A GLU* 1.3 63.5 + - - +
53A TRP 3.2 0.2 - - - -
54A SER* 3.5 15.0 + - - +
55A ARG* 3.2 18.9 + - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 3.0 13.7 + - - +
51A ARG* 1.3 75.1 - - - +
53A TRP* 1.3 61.0 + - - +
55A ARG* 3.1 25.6 + - + +
56A ARG* 2.8 61.7 + - - +
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Residues in contact with TRP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 3.9 8.8 - + - -
46A LEU* 3.9 25.8 - - + -
47A GLY 2.9 24.0 + - - -
48A TRP* 3.9 3.4 - - - -
49A SER* 3.8 27.1 - - - -
50A ASP* 2.8 25.4 + - - +
52A GLU* 1.3 75.8 - - - +
54A SER* 1.3 55.6 + - - -
56A ARG* 3.0 50.4 + - - +
57A VAL* 2.7 56.7 + - + +
46B LEU* 3.9 25.4 - - + -
53B TRP* 3.7 26.2 - + - -
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 3.4 24.5 + - - -
43A PHE* 3.5 26.1 - - - -
50A ASP 3.7 1.8 + - - -
51A ARG* 3.5 17.8 + - - -
52A GLU 3.3 0.2 - - - -
53A TRP* 1.3 81.1 - - - +
55A ARG* 1.3 57.1 + - - +
57A VAL* 3.7 1.0 - - - +
58A GLY* 2.8 24.3 + - - -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 5.6 0.2 - - - +
51A ARG 3.2 12.8 + - - +
52A GLU* 3.1 28.8 + - - +
54A SER* 1.3 77.4 - - - +
56A ARG* 1.3 56.7 + - - +
58A GLY* 3.2 3.0 + - - -
59A ALA* 2.9 27.2 + - - +
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 5.5 2.2 + - - -
52A GLU* 2.8 45.3 + - - +
53A TRP* 3.4 41.7 - - + +
55A ARG* 1.3 69.3 - - - +
57A VAL* 1.3 60.5 + - - +
59A ALA* 3.2 8.6 + - - +
60A THR* 2.9 33.3 + - - -
45B GLY 4.4 6.8 - - - +
46B LEU* 2.9 41.0 + - + +
53B TRP* 5.6 1.2 - - - -
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 3.9 23.8 - - + +
42A MSE 3.6 21.8 - - + +
43A PHE* 3.7 25.6 - - + +
53A TRP* 2.7 63.4 + - + +
54A SER 3.7 4.0 - - - +
56A ARG* 1.3 72.2 - - - +
58A GLY* 1.3 57.4 + - - +
60A THR* 3.3 1.5 + - - -
61A ALA* 2.9 27.7 + - - +
46B LEU* 4.0 9.2 - - + -
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 4.0 6.1 - - - +
39A LYS* 3.7 24.2 - - - -
54A SER 2.8 15.8 + - - -
55A ARG* 3.2 4.2 + - - -
57A VAL* 1.3 78.6 - - - +
59A ALA* 1.3 60.7 + - - +
61A ALA* 3.3 3.1 + - - +
62A ILE* 3.1 30.5 + - - +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG 2.9 13.2 + - - +
56A ARG* 3.2 11.6 + - - +
58A GLY* 1.3 75.2 - - - +
60A THR* 1.3 62.2 + - - +
62A ILE* 3.4 13.2 + - - +
63A MSE 3.2 29.5 + - - +
93A ARG* 5.9 3.8 + - - +
45B GLY* 5.6 2.9 - - - +
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Residues in contact with THR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MSE 3.8 17.7 - - - -
56A ARG 2.9 17.3 + - - -
57A VAL 3.7 3.8 - - - -
59A ALA* 1.3 73.1 - - - +
61A ALA* 1.3 61.6 + - - +
63A MSE 3.2 10.7 + - - +
64A MSE 2.9 27.3 + - + +
41B VAL* 4.1 9.4 - - + +
42B MSE 3.9 31.9 - - + -
45B GLY* 3.2 24.4 + - - -
46B LEU* 3.3 11.1 - - + +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 3.8 8.5 - - + +
38A PHE* 3.7 20.1 - - + -
39A LYS* 3.7 18.6 - - + -
42A MSE 3.6 18.5 - - + +
57A VAL 2.9 16.2 + - - +
58A GLY 3.6 5.2 - - - +
60A THR* 1.3 77.3 - - - +
62A ILE* 1.3 51.8 + - - +
64A MSE 3.1 8.0 + - - +
65A LEU* 2.8 33.8 + - - +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 3.5 35.2 - - + +
58A GLY 3.1 12.6 + - - +
59A ALA* 3.5 11.9 - - - +
61A ALA* 1.3 76.5 - - - +
63A MSE 1.3 64.6 + - + +
65A LEU* 3.0 23.3 + - + +
66A TYR* 3.1 31.3 + - + -
83A SER* 4.7 7.0 - - - +
84A ASN 6.2 0.2 - - - +
85A PHE* 6.2 2.9 - - + -
86A ARG* 6.3 3.4 - - - -
90A ASP* 4.2 7.2 - - - +
93A ARG* 3.6 36.6 - - - +
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Residues in contact with MSE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA* 3.2 19.8 + - - +
60A THR* 3.2 8.3 + - - +
62A ILE* 1.3 77.4 - - + +
64A MSE 1.3 56.4 + - - +
66A TYR* 3.4 7.8 + - - +
67A HIS* 2.9 28.8 + - - +
93A ARG* 6.2 2.0 - - - +
41B VAL* 3.0 40.3 - - + +
44B ASP* 3.9 13.2 - - + +
45B GLY* 3.5 28.3 - - - +
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Residues in contact with MSE 64 (chain A).
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* 3.5 15.3 - - + -
42A MSE 5.2 4.0 - - + -
60A THR* 2.9 21.2 + - + +
61A ALA* 3.1 11.4 + - - +
63A MSE 1.3 73.2 - - - +
65A LEU* 1.3 66.1 + - - +
67A HIS* 3.4 4.4 + - + -
68A THR* 3.0 55.5 + - - +
38B PHE* 3.6 50.9 - - + +
41B VAL* 3.8 28.9 - - + -
42B MSE 5.0 7.4 - - + -
64B MSE 3.8 17.9 - - + -
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.9 26.0 - - + +
34A SER 3.7 19.3 - - - -
35A LYS* 3.9 23.1 - - + +
38A PHE* 3.5 35.2 - - + -
61A ALA 2.8 15.2 + - - +
62A ILE* 3.0 15.2 + - + +
64A MSE 1.3 73.7 - - - +
66A TYR* 1.3 58.6 + - + +
69A ALA* 2.9 30.4 + - - +
81A MSE 3.9 24.8 - - + +
82A GLU 4.1 9.6 - - - +
83A SER* 4.5 7.9 - - - -
85A PHE* 4.6 3.6 - - + -
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Residues in contact with TYR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.1 36.4 + - + -
63A MSE 4.0 7.9 - - - +
65A LEU* 1.3 73.2 - - + +
67A HIS* 1.3 65.6 - - - +
69A ALA* 3.8 3.0 - - - +
70A ALA* 3.1 23.9 + - - +
81A MSE 4.2 11.9 - - + -
85A PHE* 4.1 2.4 - + - -
90A ASP* 2.6 40.5 + - - +
93A ARG* 3.4 49.1 - - + +
94A MSE 3.5 35.6 - - + +
97A LEU* 3.9 22.4 - - + +
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Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A MSE 2.9 18.1 + - - +
64A MSE 3.6 12.1 - - + +
66A TYR* 1.3 79.3 - - - +
68A THR* 1.3 65.1 + - - +
70A ALA* 3.5 10.4 + - - +
71A THR* 3.6 14.4 + - + +
32B LEU 5.1 7.0 + - - -
34B SER 5.6 0.2 + - - -
37B ALA* 3.9 22.5 - - + +
38B PHE* 3.6 39.0 - + - -
41B VAL* 4.0 22.8 - - + +
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.8 16.2 - - + -
38A PHE* 4.2 4.6 - - - -
64A MSE 3.0 36.2 + - - +
67A HIS* 1.3 75.7 - - - +
69A ALA* 1.3 67.7 + - - +
71A THR* 3.2 9.7 - - - +
72A ILE* 3.1 36.8 + - + +
33B LEU* 4.5 7.0 - - + -
38B PHE* 4.1 7.3 - - - -
68B THR* 3.3 30.9 - - + +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.7 7.1 - - + +
65A LEU 2.9 20.1 + - - +
66A TYR* 3.8 4.9 - - - +
68A THR* 1.3 76.4 - - - +
70A ALA* 1.3 57.3 + - - +
72A ILE* 3.2 1.2 + - - +
73A LEU* 2.8 37.6 + - + +
79A LEU* 3.9 16.2 - - + -
81A MSE 3.9 25.1 - - - -
97A LEU* 4.1 12.8 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A TYR 3.1 15.5 + - - +
67A HIS* 3.7 7.4 - - - +
68A THR 3.2 0.2 - - - -
69A ALA* 1.3 79.2 - - - +
71A THR* 1.3 57.9 + - - +
73A LEU 3.8 0.3 - - - -
74A GLN* 2.8 42.7 + - - +
97A LEU* 3.7 19.5 - - + +
100A ILE* 3.9 21.3 - - + -
101A ALA* 3.8 4.8 - - + +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A HIS* 3.6 10.6 + - - +
68A THR* 3.2 21.5 + - - +
70A ALA* 1.3 79.0 - - - +
72A ILE* 1.3 63.4 + - + +
74A GLN* 3.5 14.2 + - - +
75A SER* 3.3 15.4 + - - -
25B ALA* 5.8 0.2 - - - +
30B LEU 4.4 2.1 + - - +
31B PRO* 3.3 15.5 - - + +
32B LEU* 2.8 47.7 + - - +
33B LEU* 4.4 9.0 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 4.4 12.6 - - + -
33A LEU* 4.2 14.8 - - + -
68A THR* 3.1 34.8 + - + +
71A THR* 1.3 78.8 - - + +
73A LEU* 1.3 62.9 + - - +
75A SER* 2.5 25.3 + - - +
77A GLN* 3.3 35.7 + - + +
79A LEU* 3.6 22.9 - - + -
31B PRO* 4.2 9.4 - - + -
72B ILE* 3.8 35.0 - - + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 3.6 28.2 - - + +
5A ALA 3.9 13.7 - - - +
6A LEU* 4.5 6.3 - - + -
69A ALA* 2.8 25.9 + - + +
72A ILE* 1.3 71.9 - - - +
74A GLN* 1.3 58.8 + - - +
76A GLY* 2.8 21.7 + - - -
77A GLN 3.6 16.8 - - - +
79A LEU* 3.6 16.8 - - + -
97A LEU* 4.0 18.6 - - + -
101A ALA* 3.9 28.3 - - + +
102A PRO 4.6 1.8 - - - +
103A PHE* 4.0 24.0 - - + -
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 2.8 27.6 + - - +
71A THR* 3.8 14.8 + - - +
73A LEU* 1.3 75.4 - - - +
75A SER* 1.3 58.2 + - - +
76A GLY 3.2 1.0 + - - -
100A ILE* 3.0 47.1 + - - +
101A ALA* 3.8 7.2 - - + +
102A PRO* 6.4 0.2 - - - -
29B ARG* 4.2 17.3 + - - +
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLY 5.7 0.5 - - - +
71A THR 3.3 5.4 + - - -
72A ILE 2.5 21.6 + - - -
74A GLN* 1.3 77.3 - - - +
76A GLY* 1.3 58.0 + - - +
77A GLN* 3.6 2.6 + - - +
29B ARG* 3.3 38.8 + - - +
30B LEU 3.9 1.6 - - - -
31B PRO* 3.6 28.4 - - - +
77B GLN* 3.2 21.8 + - - -
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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