Contacts of the helix formed by residues 60 - 83 (chain A) in PDB entry 3LOC
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.5 5.4 - - - -
55A LEU* 4.3 5.8 - - - -
58A PHE 3.2 6.6 + - - +
59A PRO* 1.3 81.8 - - - +
61A LYS* 1.3 63.8 + - - +
62A GLU* 3.2 12.2 + - - +
63A ALA* 2.9 22.2 + - - +
64A LEU* 3.1 22.2 + - - +
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Residues in contact with LYS 61 (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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30A PHE* 4.0 15.1 - - + -
35A PHE* 3.0 46.6 + - + +
36A HIS* 3.9 12.9 + - - +
38A THR* 2.8 34.4 + - + +
39A ARG* 4.7 1.4 - - - +
40A LEU* 4.1 38.9 - - + +
60A SER* 1.3 75.5 - - - +
62A GLU* 1.3 62.4 + - - +
64A LEU* 3.4 3.5 + - - +
65A TYR* 3.2 24.1 + - - +
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Residues in contact with GLU 62 (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 PHE* 3.8 20.7 - - + -
60A SER* 3.2 9.8 + - - +
61A LYS* 1.3 77.6 - - - +
63A ALA* 1.3 65.8 + - - +
65A TYR* 3.2 3.3 + - - +
66A ILE* 2.9 44.5 + - + +
124A LEU* 4.1 24.1 - - + +
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Residues in contact with ALA 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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58A PHE* 4.6 5.1 - - + -
59A PRO* 3.8 28.7 - - + -
60A SER* 2.9 20.8 + - - +
62A GLU* 1.3 78.6 - - - +
64A LEU* 1.3 56.6 + - - +
66A ILE* 3.3 7.9 + - - +
67A ALA* 2.9 29.7 + - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.9 20.9 - - + -
23A LEU* 4.1 8.3 - - + -
26A ALA* 3.7 22.4 - - + -
30A PHE* 4.4 3.4 - - + -
40A LEU* 4.1 7.4 - - + -
43A ILE* 3.9 25.6 - - + -
54A LEU* 3.9 17.7 - - + -
58A PHE* 3.6 41.5 - - + +
60A SER 3.1 14.1 + - - +
61A LYS* 3.9 5.8 - - - +
63A ALA* 1.3 76.8 - - - +
65A TYR* 1.3 58.9 + - - +
67A ALA* 3.0 5.4 + - - +
68A VAL* 2.9 32.1 + - - +
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Residues in contact with TYR 65 (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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30A PHE* 3.7 50.6 - + + -
35A PHE* 3.7 21.6 + + + +
61A LYS 3.2 16.7 + - - +
62A GLU 3.5 4.5 - - - +
64A LEU* 1.3 75.8 - - - +
66A ILE* 1.3 66.8 + - + +
68A VAL* 3.4 2.9 + - - +
69A LEU* 3.3 45.4 + - + +
113A LEU* 4.4 16.0 + - + +
116A MSE 5.7 0.7 - - - +
117A GLU* 2.5 45.6 + - - +
124A LEU* 3.5 30.5 - - + -
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Residues in contact with ILE 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 GLU* 2.9 40.4 + - + +
63A ALA* 3.8 5.4 - - - +
65A TYR* 1.3 81.7 - - + +
67A ALA* 1.3 58.8 + - - +
69A LEU* 3.3 5.7 + - - +
70A ARG* 2.8 34.1 + - + +
124A LEU* 3.7 27.1 - - + +
125A LEU* 4.6 8.2 - - + +
128A GLU* 4.2 31.4 - - + +
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Residues in contact with ALA 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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23A LEU* 4.1 8.3 - - + -
58A PHE* 3.7 27.6 - - + -
63A ALA 2.9 14.3 + - - +
64A LEU 3.0 9.2 + - - +
66A ILE* 1.3 79.1 - - - +
68A VAL* 1.3 63.7 + - - +
70A ARG* 3.2 7.2 + - - +
71A GLN* 3.1 24.6 + - - +
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Residues in contact with VAL 68 (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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23A LEU* 4.2 16.2 - - + +
26A ALA* 3.7 29.2 - - + -
27A LEU* 4.3 15.7 - - + +
30A PHE* 4.6 2.0 - - + -
64A LEU 2.9 20.1 + - - +
65A TYR* 3.4 7.4 + - - +
67A ALA* 1.3 73.7 - - - +
69A LEU* 1.3 65.9 + - + +
71A GLN* 3.2 33.2 + - - +
72A ILE* 3.6 7.2 + - + +
110A ALA* 5.9 2.5 - - + +
113A LEU* 3.5 32.3 - - + -
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Residues in contact with LEU 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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65A TYR* 3.3 46.4 + - + +
66A ILE* 3.8 3.8 - - + +
68A VAL* 1.3 83.4 - - + +
70A ARG* 1.3 62.2 + - - +
72A ILE* 3.3 11.9 - - + +
73A LEU* 3.1 26.2 + - - +
110A ALA 5.1 0.2 - - - +
113A LEU* 3.8 21.1 - - + +
114A PHE* 3.5 43.4 - - + +
117A GLU* 3.9 8.3 - - + -
124A LEU 6.2 0.2 - - - -
125A LEU* 3.8 32.5 - - + -
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Residues in contact with ARG 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 ILE* 2.8 24.0 + - + +
67A ALA* 3.6 7.6 - - - +
68A VAL 3.2 0.2 - - - -
69A LEU* 1.3 75.7 - - - +
71A GLN* 1.3 63.0 + - - +
73A LEU* 3.4 26.8 + - - +
74A ASP* 3.0 54.1 + - - +
77A LEU* 4.2 19.8 - - - +
81A LYS* 5.5 1.4 - - - +
125A LEU* 5.7 1.1 - - - +
128A GLU* 2.8 46.4 + - - +
132A ASP* 4.6 20.2 + - - +
133A LEU* 5.4 3.8 - - - +
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Residues in contact with GLN 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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23A LEU* 3.5 39.8 + - + +
27A LEU* 6.3 0.6 - - - +
67A ALA 3.1 14.0 + - - +
68A VAL* 3.2 25.3 + - - +
70A ARG* 1.3 77.4 - - - +
72A ILE* 1.3 61.6 + - + +
74A ASP* 3.3 7.8 + - - +
75A ILE* 3.2 33.2 + - + +
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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
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68A VAL 3.6 3.3 + - - +
69A LEU* 3.3 24.2 - - + +
71A GLN* 1.3 75.9 - - - +
73A LEU* 1.3 59.9 + - - +
75A ILE* 4.3 13.9 - - + -
76A TRP* 2.8 63.1 + - + +
103A VAL* 4.7 3.8 - - + -
107A TYR* 3.9 24.9 - - + +
110A ALA* 3.6 44.0 - - + +
111A SER* 4.5 0.7 - - - +
114A PHE* 4.5 16.4 - - + -
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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
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69A LEU 3.1 17.3 + - - +
70A ARG* 3.5 39.7 - - - +
72A ILE* 1.3 78.2 - - - +
74A ASP* 1.3 59.0 + - - +
76A TRP* 3.7 5.0 - - + +
77A LEU* 3.0 46.2 + - + +
114A PHE* 3.9 28.5 - - + -
125A LEU* 4.5 16.4 - - + -
128A GLU* 5.0 3.4 - - + -
129A LEU* 5.1 4.3 - - + -
133A LEU* 4.5 11.9 - - + -
212A URA 3.7 30.3 - - + +
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Residues in contact with ASP 74 (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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70A ARG* 3.0 53.5 + - - +
71A GLN* 3.7 6.5 - - - +
73A LEU* 1.3 73.0 - - - +
75A ILE* 1.3 61.9 + - + +
77A LEU* 4.0 0.8 - - - +
78A ALA* 3.1 29.1 + - - +
81A LYS* 4.0 22.6 + - - +
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Residues in contact with ILE 75 (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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71A GLN* 3.2 25.3 + - + +
72A ILE* 3.8 14.1 - - + +
74A ASP* 1.3 76.6 - - + +
76A TRP* 1.3 66.3 + - - +
77A LEU 3.2 0.7 + - - -
78A ALA* 3.4 14.5 + - - +
79A PRO* 3.7 4.7 - - - +
103A VAL* 4.2 29.3 - - + +
107A TYR* 4.3 38.4 - - + +
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Residues in contact with TRP 76 (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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72A ILE* 2.8 41.3 + - + +
73A LEU* 3.7 10.5 - - + +
75A ILE* 1.3 74.8 - - - +
77A LEU* 1.3 60.5 + - - +
79A PRO* 3.4 10.7 - - - +
96A TYR* 4.2 7.3 + - - -
100A LYS* 3.2 35.0 - - + +
103A VAL* 3.4 32.5 - - + +
104A SER* 5.8 0.8 + - - -
111A SER* 3.7 26.2 + - - -
114A PHE* 3.4 48.2 - + + -
170A GLN* 3.7 20.4 - - + +
212A URA 3.3 50.3 - + + +
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Residues in contact with LEU 77 (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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70A ARG* 4.2 19.7 - - - +
73A LEU* 3.0 33.5 + - + +
74A ASP* 4.3 0.4 - - - +
75A ILE 3.2 0.2 - - - -
76A TRP* 1.3 75.5 - - - +
78A ALA* 1.3 71.7 + - - +
79A PRO 3.3 0.4 - - - -
80A LEU* 2.8 32.8 + - + +
81A LYS* 2.9 27.8 + - - +
96A TYR* 5.4 0.4 - - - +
133A LEU* 3.9 30.1 - - + -
136A LEU* 3.9 23.6 - - + -
166A TRP* 4.4 1.8 - - + +
212A URA 3.7 23.1 - - + -
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Residues in contact with ALA 78 (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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74A ASP 3.1 17.5 + - - +
75A ILE* 3.6 8.1 - - - +
77A LEU* 1.3 79.7 - - - +
79A PRO* 1.3 69.5 - - + +
80A LEU 3.1 0.2 + - - -
81A LYS* 3.1 20.6 + - - +
82A ALA* 3.2 10.5 + - - +
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Residues in contact with PRO 79 (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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75A ILE 3.7 5.6 - - - +
76A TRP 3.4 15.9 - - - +
77A LEU 3.5 0.4 - - - -
78A ALA* 1.3 97.4 - - + +
80A LEU* 1.3 56.2 + - - +
82A ALA* 3.0 26.4 + - + +
83A PHE* 3.4 15.0 - - + -
96A TYR* 3.7 25.4 - - + -
99A LEU* 3.9 37.9 - - + -
100A LYS* 5.7 0.9 - - + +
103A VAL* 6.5 0.9 - - + -
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Residues in contact with LEU 80 (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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77A LEU* 2.8 30.4 + - + +
79A PRO* 1.3 72.5 - - - +
81A LYS* 1.3 63.7 + - - +
83A PHE* 3.2 41.0 + - + +
96A TYR* 3.5 38.8 - - + +
136A LEU* 5.1 3.4 - - + -
137A ILE* 3.6 30.5 - - + -
140A LYS* 3.5 31.1 - - + -
144A ILE* 5.1 1.8 - - + -
162A ILE* 4.7 12.3 - - + -
166A TRP* 4.5 2.5 - - + -
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Residues in contact with LYS 81 (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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70A ARG* 5.5 1.4 - - - +
74A ASP* 4.0 31.1 + - - +
77A LEU* 2.9 38.7 + - - +
78A ALA* 3.5 13.0 - - - +
80A LEU* 1.3 76.2 - - - +
82A ALA* 1.3 54.9 + - - +
84A ARG* 2.8 31.0 + - - -
136A LEU* 3.8 24.4 - - + +
140A LYS* 3.1 14.9 + - - +
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Residues in contact with ALA 82 (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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78A ALA 3.2 7.7 + - - +
79A PRO* 3.0 21.7 + - + +
80A LEU 3.1 0.4 - - - -
81A LYS* 1.3 75.0 - - - +
83A PHE* 1.3 64.3 + - + +
84A ARG* 3.3 17.5 + - - +
87A PHE* 3.4 20.3 - - + -
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Residues in contact with PHE 83 (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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79A PRO* 3.4 17.3 - - + -
80A LEU* 3.2 32.6 + - + +
82A ALA* 1.3 76.9 - - + +
84A ARG* 1.3 62.3 + - - +
87A PHE* 3.9 10.5 - + + -
92A ALA* 4.0 37.7 - - + -
93A ILE* 4.3 14.8 - - + -
96A TYR* 4.0 30.5 - + + -
140A LYS* 2.9 30.3 + - + -
143A LEU* 3.5 13.7 - - + +
144A ILE* 4.3 25.1 - - + -
147A TRP* 4.8 14.6 - + + -
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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
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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) + - + + + + + -
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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