Contacts of the helix formed by residues 56 - 85 (chain R) in PDB entry 6NCA
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 GLY 56 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R GLN 4.0 1.2 + - - -
55R GLU* 1.3 79.4 + - - +
57R PRO* 1.3 75.1 - - - +
58R GLU* 3.1 5.4 - - - -
59R TYR* 3.0 15.5 + - - +
60R TRP* 3.4 9.2 - - - -
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Residues in contact with PRO 57 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R GLU 4.6 0.7 - - - +
56R GLY* 1.3 82.7 - - - +
58R GLU* 1.3 61.9 + - - +
59R TYR 3.3 0.2 - - - -
60R TRP* 4.1 9.4 - - + -
61R ASP* 3.1 35.5 + - - +
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Residues in contact with GLU 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R GLY* 3.1 2.6 - - - -
57R PRO* 1.3 76.8 - - - +
59R TYR* 1.3 79.5 + - - +
61R ASP* 3.5 4.9 + - - +
62R GLY* 2.9 26.4 + - - -
167R TRP* 5.8 3.1 - - - -
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Residues in contact with TYR 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16 TYR* 4.5 0.6 + - + -
7R TYR* 4.8 1.2 + - - -
33R PHE* 4.2 5.7 - - - -
34R VAL* 4.2 6.3 - - + +
52R ILE* 3.6 11.8 - - + +
55R GLU* 3.5 36.6 - - + +
56R GLY 3.0 12.4 + - - +
58R GLU* 1.3 90.8 + - - +
60R TRP* 1.3 86.9 + + - +
62R GLY* 3.2 2.0 + - - -
63R GLU* 2.8 71.5 + - + +
167R TRP* 3.8 29.2 - + + -
171R TYR* 2.5 33.1 + + - -
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Residues in contact with TRP 60 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R VAL* 4.2 10.5 - - + -
44R ARG* 3.3 20.2 - - - +
45R MET* 3.5 31.0 - - + -
46R GLU 4.2 2.5 - - - -
47R PRO* 3.4 36.3 - - + -
52R ILE* 3.1 42.8 - - + -
53R GLU* 4.0 9.6 + - - -
55R GLU* 3.4 21.7 + - + +
56R GLY 3.4 22.6 + - - -
57R PRO* 4.3 7.0 - - + +
58R GLU 3.4 0.4 - - - -
59R TYR* 1.3 94.3 - + - +
61R ASP* 1.3 59.0 + - - +
63R GLU* 4.0 1.4 - - + +
64R THR* 2.7 34.9 + - - -
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Residues in contact with ASP 61 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R ARG* 3.1 27.4 + - - +
57R PRO* 3.1 24.3 + - - +
58R GLU* 3.8 5.3 - - - +
60R TRP* 1.3 77.5 - - - +
62R GLY* 1.3 61.5 + - - +
64R THR* 3.6 2.3 + - - -
65R ARG* 3.2 27.6 + - - +
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Residues in contact with GLY 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R GLU* 2.9 16.0 + - - -
59R TYR* 3.6 2.7 - - - -
61R ASP* 1.3 75.8 - - - +
63R GLU* 1.3 64.3 + - - +
65R ARG* 3.2 35.2 + - - +
66R LYS* 3.0 28.9 + - - +
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Residues in contact with GLU 63 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16 TYR* 3.1 32.6 - - - -
26 VAL* 3.0 34.2 + - - +
7R TYR* 4.0 4.7 + - - -
45R MET* 4.0 26.1 - - + +
59R TYR* 2.8 62.7 + - + +
60R TRP* 4.0 4.7 - - - +
62R GLY* 1.3 72.2 - - - +
64R THR* 1.3 63.6 + - - +
66R LYS* 3.5 7.3 + - - +
67R VAL* 3.0 27.2 + - - +
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Residues in contact with THR 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R PHE* 5.0 0.7 - - + -
43R GLN 3.7 7.6 - - - +
44R ARG* 3.5 48.5 + - + +
45R MET* 3.2 17.4 + - - +
60R TRP 2.7 23.2 + - - -
61R ASP 3.9 4.3 - - - -
63R GLU* 1.3 76.7 - - - +
65R ARG* 1.3 61.9 + - - +
67R VAL* 3.3 9.1 - - + +
68R LYS* 3.2 35.0 + - - +
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Residues in contact with ARG 65 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151N HIS* 6.3 1.3 - - - +
61R ASP* 3.2 15.6 + - - +
62R GLY* 3.2 31.4 + - - +
64R THR* 1.3 77.7 - - - +
66R LYS* 1.3 75.4 + - + +
68R LYS* 3.9 5.2 - - - +
69R ALA* 3.0 28.1 + - + +
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Residues in contact with LYS 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16 TYR* 3.3 33.8 - - + -
26 VAL* 3.5 22.1 - - + +
36 LEU 4.1 7.2 - - - +
46 ASP* 3.9 26.2 - - + +
66 LEU* 6.5 0.4 - - + -
62R GLY* 3.0 34.4 + - - +
63R GLU* 3.5 13.9 + - - +
64R THR 3.4 0.2 - - - -
65R ARG* 1.3 92.8 - - - +
67R VAL* 1.3 56.4 + - - +
69R ALA* 3.1 7.6 + - - +
70R HIS* 2.6 42.4 + - + -
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Residues in contact with VAL 67 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26 VAL* 4.5 7.0 - - + +
9R PHE* 4.8 5.2 - - + -
22R PHE* 4.0 4.9 - - + -
24R ALA* 3.9 16.2 - - + -
36R PHE* 3.7 45.3 - - + -
45R MET* 4.0 19.7 - - + -
63R GLU 3.0 21.6 + - - +
64R THR* 3.3 14.1 - - - +
66R LYS* 1.3 76.3 - - - +
68R LYS* 1.3 55.5 + - - +
70R HIS* 3.2 9.4 + - - +
71R SER* 2.6 33.6 + - - -
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Residues in contact with LYS 68 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R PHE* 4.3 16.6 - - + -
43R GLN* 3.8 33.6 + - - +
44R ARG* 5.6 1.2 - - - +
64R THR* 3.2 25.9 + - - +
65R ARG* 3.9 5.6 - - - +
67R VAL* 1.3 83.6 - - + +
69R ALA* 1.3 56.1 + - - +
71R SER* 3.1 9.8 + - - -
72R GLN* 2.9 27.9 + - - +
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Residues in contact with ALA 69 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66 LEU* 3.9 20.9 - - + +
149N ALA 4.5 2.9 - - - +
151N HIS* 4.2 25.4 - - + +
65R ARG* 3.0 20.3 + - + +
66R LYS* 3.4 9.0 - - - +
68R LYS* 1.3 76.7 - - - +
70R HIS* 1.3 60.7 + - - +
72R GLN* 3.3 9.3 + - - +
73R THR* 3.1 21.8 + - - -
----------------------------------------------------------
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Residues in contact with HIS 70 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26 VAL* 4.0 13.0 - - + -
36 LEU* 2.7 43.2 + - + +
46 ASP 4.9 0.2 - - - -
56 HIS 3.1 24.2 + - - -
66 LEU* 3.9 14.6 - - + +
76 ILE 5.5 1.1 - - - -
9R PHE* 5.3 6.9 - + + -
22R PHE* 4.6 3.8 - - + -
66R LYS* 2.6 32.2 + - + +
67R VAL* 3.4 7.9 - - + +
69R ALA* 1.3 70.6 - - - +
71R SER* 1.3 65.6 + - - +
73R THR* 3.1 11.6 + - - +
74R HIS* 2.8 48.0 + + + +
97R ARG* 4.7 10.7 + - - -
99R TYR* 4.8 5.1 - + - -
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Residues in contact with SER 71 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R PHE* 3.9 40.5 - - - +
36R PHE* 4.7 7.1 - - - -
38R SER* 5.4 2.4 - - - -
67R VAL 2.6 17.4 + - - -
68R LYS* 3.1 17.7 + - - -
70R HIS* 1.3 73.2 - - - +
72R GLN* 1.3 63.1 + - - +
74R HIS* 3.4 2.3 + - - +
75R ARG* 3.2 23.3 + - - +
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Residues in contact with GLN 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149N ALA* 4.2 21.5 - - + +
151N HIS* 6.4 1.3 - - + -
68R LYS 2.9 12.6 + - - +
69R ALA* 3.3 11.2 + - - +
71R SER* 1.3 72.8 + - - +
73R THR* 1.3 65.8 + - - +
75R ARG* 3.1 56.1 + - - +
76R VAL* 3.3 15.6 - - - +
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Residues in contact with THR 73 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66 LEU* 3.6 17.7 - - - +
76 ILE 3.0 30.5 + - - +
86 VAL* 4.7 3.5 - - + +
149N ALA* 4.0 17.4 + - - +
69R ALA 3.1 14.4 + - - -
70R HIS* 3.1 16.8 + - - +
72R GLN* 1.3 75.9 - - - +
74R HIS* 1.3 74.2 + - + +
76R VAL* 3.2 7.4 + - - +
77R ASP* 2.8 36.3 + - - +
97R ARG* 4.9 4.5 - - - +
----------------------------------------------------------
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Residues in contact with HIS 74 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R PHE* 4.3 11.4 - + + -
11R SER* 4.0 23.8 + - - +
22R PHE* 3.1 26.4 - + + -
70R HIS* 2.8 39.9 + - + +
71R SER 4.2 1.1 - - - +
72R GLN 3.4 0.2 - - - -
73R THR* 1.3 78.9 - - + +
75R ARG* 1.3 65.2 + - - +
77R ASP* 3.2 15.0 + - - +
78R LEU* 3.2 16.8 + - - +
95R VAL* 4.3 7.1 - - + +
96R GLN 6.3 0.2 - - - -
97R ARG* 3.2 38.4 + - + +
116R TYR* 3.0 29.6 - + - -
----------------------------------------------------------
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Residues in contact with ARG 75 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R SER* 4.5 1.9 + - - -
19R GLU* 2.4 41.2 + - - +
20R PRO* 3.5 34.1 - - + +
71R SER 3.2 12.4 + - - +
72R GLN* 3.1 54.2 + - - +
74R HIS* 1.3 77.7 - - - +
76R VAL* 1.3 68.8 + - + +
78R LEU* 3.6 11.7 + - - +
79R GLY* 3.6 7.6 + - - -
----------------------------------------------------------
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Residues in contact with VAL 76 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86 VAL* 4.5 7.0 - - + -
145N HIS* 4.5 14.1 - - + +
146N LYS* 4.2 29.2 - - + +
149N ALA* 3.8 18.8 - - + -
72R GLN* 3.3 18.6 - - + +
73R THR 3.2 7.3 + - - +
75R ARG* 1.3 80.4 - - + +
77R ASP* 1.3 61.5 + - - +
79R GLY* 3.1 4.0 + - - +
80R THR* 2.7 41.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP 77 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76 ILE 4.9 0.2 - - - +
86 VAL* 3.7 12.1 - - - +
96 VAL* 3.0 36.6 + - + +
73R THR* 2.8 22.0 + - - +
74R HIS* 3.2 14.0 + - - +
76R VAL* 1.3 76.4 - - - +
78R LEU* 1.3 56.9 + - - +
80R THR* 4.1 6.3 - - - -
81R LEU* 2.7 42.2 + - + +
95R VAL* 5.1 4.3 - - + -
116R TYR* 2.1 35.4 + - + +
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Residues in contact with LEU 78 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R SER* 3.8 24.5 - - - +
12R VAL 4.1 0.7 - - - -
13R SER* 3.6 37.2 - - - +
20R PRO* 4.3 7.2 - - + -
74R HIS 3.2 7.4 + - - +
75R ARG 3.9 7.4 - - - +
76R VAL 3.3 0.4 - - - -
77R ASP* 1.3 76.5 - - - +
79R GLY* 1.3 57.8 + - - +
81R LEU* 4.0 2.7 - - - +
82R ARG* 2.9 30.3 + - - +
93R HIS* 3.5 35.9 - - + +
95R VAL* 3.6 28.7 - - + -
118R TYR* 4.0 6.0 + - + -
----------------------------------------------------------
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Residues in contact with GLY 79 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R ARG 3.6 6.0 + - - -
76R VAL* 3.1 7.2 + - - -
78R LEU* 1.3 75.8 - - - +
80R THR* 1.3 65.1 + - - +
82R ARG* 3.3 13.6 + - - +
83R GLY* 3.2 17.0 + - - -
----------------------------------------------------------
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Residues in contact with THR 80 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86 VAL* 4.7 0.5 - - - +
96 VAL* 3.3 27.5 + - - +
146N LYS* 3.8 26.4 - - - +
76R VAL* 2.7 30.1 + - - +
77R ASP* 3.7 5.5 - - - -
79R GLY* 1.3 75.6 - - - +
81R LEU* 1.3 61.7 + - - +
83R GLY* 3.2 10.9 + - - -
84R TYR* 3.2 33.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 VAL* 3.8 19.1 - - + -
77R ASP* 2.7 29.0 + - + +
78R LEU 4.0 0.9 - - - +
80R THR* 1.3 69.4 - - - +
82R ARG* 1.3 64.6 + - - +
84R TYR* 3.1 28.9 + - + +
85R TYR* 3.4 19.8 + - + -
95R VAL* 3.6 15.5 - - + -
116R TYR* 5.3 4.0 - - + -
118R TYR* 3.5 43.3 - - + -
123R TYR* 3.3 44.0 - - + +
----------------------------------------------------------
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Residues in contact with ARG 82 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R LEU 2.9 19.8 + - - +
79R GLY* 3.5 11.2 - - - +
80R THR 3.3 0.2 - - - -
81R LEU* 1.3 75.7 - - - +
83R GLY* 1.3 67.8 + - - +
85R TYR 3.8 0.3 + - - -
86R ASN* 3.4 4.0 + - - +
87R GLN* 3.2 60.4 + - + +
88R SER* 4.1 4.7 - - - +
89R GLU* 3.2 58.9 + - - +
93R HIS* 6.0 3.6 - - + +
118R TYR* 4.4 3.5 + - - +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R GLY 3.2 6.5 + - - -
80R THR 3.2 7.7 + - - -
81R LEU 3.2 0.4 - - - -
82R ARG* 1.3 86.6 - - - +
84R TYR* 1.3 66.5 + - - +
86R ASN* 3.3 17.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 VAL 3.0 21.5 + - - -
146N LYS* 5.9 0.2 - - - -
80R THR* 3.2 25.6 + - + +
81R LEU* 3.1 24.9 + - + +
83R GLY* 1.3 79.4 - - - +
85R TYR* 1.3 64.6 + - + +
86R ASN* 3.6 4.0 + - - +
123R TYR* 3.4 16.6 - - - -
139R ALA* 4.1 23.6 - - + +
142R THR* 4.0 23.4 - - + +
143R THR* 3.4 22.1 + - - -
146R LYS* 3.5 21.7 + - - -
----------------------------------------------------------
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Residues in contact with TYR 85 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R LEU* 3.4 19.0 + - + +
82R ARG 3.8 0.2 + - - -
83R GLY 3.3 0.4 - - - -
84R TYR* 1.3 77.5 - - + +
86R ASN* 1.3 69.3 - - - +
87R GLN* 3.1 26.1 + - + +
118R TYR* 3.5 35.0 - + - -
121R LYS* 6.5 0.9 - - - -
123R TYR* 3.5 29.2 - + - -
137R ASP* 3.4 23.9 + - - -
139R ALA* 3.5 24.2 - - + +
----------------------------------------------------------
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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