Contacts of the helix formed by residues 65 - 95 (chain A) in PDB entry 3BFR
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 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.9 1.1 - - - +
63A GLU* 2.8 19.2 + - - -
64A PRO* 1.3 74.3 - - - +
66A PRO* 1.3 69.5 - - - +
67A ALA* 3.8 8.2 + - - +
68A ASN* 3.2 31.0 + - - +
69A ALA* 3.0 27.0 + - - +
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Residues in contact with PRO 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO 4.4 2.0 - - - +
65A SER* 1.3 89.1 - - - +
67A ALA* 1.3 55.5 + - - +
69A ALA* 3.5 9.3 - - + +
70A ARG* 3.1 27.2 + - - +
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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
----------------------------------------------------------
65A SER* 3.2 8.9 - - - +
66A PRO* 1.3 81.0 - - - +
68A ASN* 1.3 63.9 + - - +
70A ARG* 3.4 18.7 + - - +
71A LYS* 3.6 18.8 + - - +
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.3 32.5 + - + +
60A LEU* 3.3 29.8 - - + +
63A GLU* 2.8 52.1 + - - +
65A SER* 3.2 15.1 + - - +
67A ALA* 1.3 77.5 - - - +
69A ALA* 1.3 64.8 + - - +
71A LYS* 3.1 28.2 + - - +
72A MET* 3.4 6.1 + - - +
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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
----------------------------------------------------------
60A LEU* 4.0 9.6 - - + +
65A SER 3.0 13.6 + - - +
66A PRO* 3.5 13.9 - - + +
68A ASN* 1.3 76.6 - - - +
70A ARG* 1.3 61.0 + - - +
72A MET* 3.1 13.1 + - - +
73A ILE* 3.1 31.3 + - + +
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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
----------------------------------------------------------
66A PRO 3.1 14.3 + - - +
67A ALA* 3.5 12.3 - - - +
68A ASN 3.3 0.4 - - - -
69A ALA* 1.3 75.7 - - - +
71A LYS* 1.3 56.0 + - - +
73A ILE* 3.3 16.9 + - + +
74A ALA* 3.1 24.8 + - - +
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.7 29.4 - - + -
59A LEU* 4.4 6.6 - - + +
67A ALA* 3.6 17.9 + - - +
68A ASN* 3.1 35.7 + - - +
70A ARG* 1.3 75.7 - - - +
72A MET* 1.3 63.8 + - - +
73A ILE 3.3 0.2 - - - -
74A ALA* 3.5 8.7 + - + +
75A ILE* 3.3 28.1 + - + +
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Residues in contact with MET 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 2.9 47.3 - - + +
56A LEU* 3.8 15.3 - - + -
57A SER* 3.9 22.4 - - - +
60A LEU* 3.6 28.9 - - + -
68A ASN 3.4 13.8 + - - +
69A ALA* 3.1 11.8 + - - +
71A LYS* 1.3 76.2 - - - +
73A ILE* 1.3 64.5 + - + +
75A ILE* 3.3 3.1 + - - +
76A GLN* 2.9 34.8 + - - +
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 3.1 21.6 + - + +
70A ARG* 3.5 15.7 - - - +
71A LYS 3.3 0.2 - - - -
72A MET* 1.3 76.6 - - + +
74A ALA* 1.3 63.2 + - - +
76A GLN* 3.2 25.1 + - + +
77A GLN* 4.1 3.1 + - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG 3.1 12.4 + - - +
71A LYS* 3.6 13.7 - - + +
73A ILE* 1.3 79.5 - - - +
75A ILE* 1.3 63.5 + - + +
76A GLN 3.6 0.2 + - - -
77A GLN* 3.9 13.5 + - - +
78A ASN* 4.6 6.4 + - - -
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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
----------------------------------------------------------
49A ALA* 3.6 28.9 - - + +
52A GLN* 3.4 33.9 - - + +
53A PHE* 4.4 5.6 - - + +
56A LEU* 3.7 18.4 - - + -
71A LYS* 3.3 15.0 - - + +
72A MET 3.3 7.4 + - - +
73A ILE 3.2 0.8 - - - -
74A ALA* 1.3 76.0 - - + +
76A GLN* 1.3 66.6 + - - +
77A GLN 3.2 2.7 - - - -
78A ASN* 3.2 23.5 + - + +
79A ILE* 3.2 18.7 + - + +
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.6 32.3 - - - -
72A MET* 2.9 27.8 + - - +
73A ILE* 3.2 17.8 + - + +
75A ILE* 1.3 76.9 - - - +
77A GLN* 1.3 57.8 + - - +
79A ILE* 3.2 20.4 + - - +
80A LYS* 3.0 29.3 + - - +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE 4.1 2.7 + - - +
74A ALA 3.9 10.4 + - - +
75A ILE 3.2 0.8 - - - -
76A GLN* 1.3 77.7 - - - +
78A ASN* 1.3 64.5 + - - +
80A LYS* 3.3 37.3 + - - +
81A PHE* 2.9 41.8 + - + +
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Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 4.0 14.3 - - + +
52A GLN* 5.0 4.0 + - - -
74A ALA 4.9 8.3 + - - -
75A ILE* 3.2 22.0 + - + +
77A GLN* 1.3 82.1 - - - +
79A ILE* 1.3 58.8 + - - +
81A PHE* 4.5 4.0 - - - +
82A HIS* 3.0 53.8 + - + +
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.8 21.2 - - + -
49A ALA* 3.6 24.0 - - + +
50A VAL* 4.5 6.7 - - + +
53A PHE* 4.0 24.5 - - + -
75A ILE* 3.2 17.4 + - + +
76A GLN* 3.2 35.6 + - - +
78A ASN* 1.3 74.5 - - - +
80A LYS* 1.3 60.1 + - - +
83A GLY* 2.8 30.0 + - - -
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN 3.0 15.9 + - - +
77A GLN* 3.3 37.8 + - - +
79A ILE* 1.3 77.4 - - - +
81A PHE* 1.3 64.6 + - - +
84A GLY* 2.8 28.4 + - - -
161A ASN* 5.9 1.6 + - - +
162A GLN 4.2 2.4 - - - +
163A ASP* 3.0 35.7 + - - +
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 3.6 26.6 - + - -
77A GLN* 2.9 36.1 + - + +
78A ASN* 4.3 4.7 - - - +
80A LYS* 1.3 79.9 - - - +
82A HIS* 1.3 83.5 + + - +
85A GLY* 2.8 23.9 + - - -
161A ASN* 4.5 8.1 - - + -
162A GLN* 3.2 41.1 - - + +
178A TRP* 4.0 23.8 - + - -
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Residues in contact with HIS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.2 13.7 - - + -
42A TYR* 3.6 27.7 - + - +
45A GLY* 3.5 28.3 - - - -
46A PHE* 3.3 22.4 - - - +
78A ASN* 3.0 42.1 + - + +
81A PHE* 1.3 96.5 - + - +
83A GLY* 1.3 61.4 + - - +
85A GLY* 3.3 0.7 + - - +
86A PHE* 2.8 30.5 + - - +
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.4 28.3 - - - -
79A ILE 2.8 20.1 + - - -
80A LYS 4.0 0.2 - - - -
82A HIS* 1.3 77.0 - - - +
84A GLY* 1.3 55.2 + - - +
86A PHE* 3.3 4.7 + - - +
87A THR* 2.9 33.7 + - - +
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS 2.8 15.3 + - - -
83A GLY* 1.3 72.4 - - - +
85A GLY* 1.3 57.8 + - - +
87A THR* 3.5 9.4 - - - -
88A ASN* 2.8 37.1 + - - +
162A GLN* 3.2 26.0 - - - -
164A THR* 4.9 6.3 - - - -
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 3.9 0.5 - - - -
42A TYR* 3.6 27.5 - - - -
81A PHE 2.8 17.6 + - - -
82A HIS 3.3 0.6 + - - -
84A GLY* 1.3 72.4 - - - +
86A PHE* 1.3 63.3 + - - +
89A HIS* 2.7 28.9 + - - +
162A GLN* 3.5 19.4 - - - +
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.5 40.8 - - + -
11A THR 3.3 26.7 - - - -
39A HIS* 3.1 27.9 - + - -
42A TYR* 3.6 11.0 - - + +
43A VAL* 3.8 12.6 - - + -
46A PHE* 4.3 14.1 - + + -
82A HIS 2.8 16.5 + - - +
83A GLY* 3.6 7.0 - - - +
85A GLY* 1.3 75.6 - - - +
87A THR* 1.3 69.4 + - - +
90A CYS* 3.2 35.3 + - - -
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY 2.9 23.8 + - - +
84A GLY* 3.3 13.7 - - - +
86A PHE* 1.3 82.6 - - - +
88A ASN* 1.3 75.2 + - - +
90A CYS* 3.2 8.0 + - - +
91A LEU* 3.0 36.4 + - - +
164A THR* 4.4 14.5 + - + +
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Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 2.8 23.9 + - - +
85A GLY 4.4 0.9 - - - +
87A THR* 1.3 74.1 - - - +
89A HIS* 1.3 56.8 + - - +
91A LEU* 3.4 9.5 + - - +
92A PHE* 2.9 26.7 + - - +
141A TRP* 3.4 33.6 - - + +
143A PHE* 3.3 17.4 - - - -
162A GLN* 3.4 21.6 + - - +
163A ASP 3.2 22.8 + - - -
164A THR* 2.8 25.3 + - - -
174A ALA* 4.4 0.3 - - - +
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Residues in contact with HIS 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS* 3.1 22.9 + + - -
38A HIS* 5.1 0.8 - - - +
39A HIS* 3.4 29.6 - + + +
42A TYR* 3.4 28.2 - + - -
85A GLY 2.7 20.3 + - - -
87A THR 3.3 0.4 - - - -
88A ASN* 1.3 74.1 - - - +
90A CYS* 1.3 64.8 + - - +
92A PHE* 3.4 6.0 - + - +
93A TRP* 3.0 42.4 + + - +
141A TRP* 3.7 13.1 - + - -
162A GLN* 3.5 12.8 - - - -
176A ASP* 3.4 2.2 + - - -
180A HIS* 3.9 0.2 + - - -
216A MN3 2.1 37.2 + - - -
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Residues in contact with CYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 4.0 19.2 - - + +
39A HIS* 3.6 11.2 + - - -
86A PHE* 3.2 50.2 + - - +
87A THR* 3.2 11.1 + - - +
89A HIS* 1.3 76.5 - - - +
91A LEU* 1.3 62.2 + - + +
93A TRP* 3.6 6.0 + - - +
94A GLU* 3.3 29.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 3.0 29.1 + - - +
88A ASN* 3.5 13.0 - - - +
90A CYS* 1.3 75.4 - - + +
92A PHE* 1.3 63.1 + - - +
94A GLU* 3.3 1.3 + - - -
95A ASN* 2.8 30.7 + - - +
143A PHE* 4.3 15.7 - - + -
164A THR* 4.7 3.8 - - - +
171A PRO* 3.8 37.5 - - + -
174A ALA* 4.1 9.6 - - + -
209A ARG* 3.6 32.5 + - - +
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.9 4.7 - - + -
31A ASN* 5.7 0.7 - - - -
34A HIS* 3.7 28.5 - + - -
88A ASN 2.9 15.0 + - - +
89A HIS* 3.2 13.4 + + - +
91A LEU* 1.3 75.4 - - - +
93A TRP* 1.3 87.8 + + - +
95A ASN* 3.2 16.7 + - - +
96A LEU* 3.3 40.1 - - + +
141A TRP* 3.9 8.7 - + + -
174A ALA* 3.2 21.5 - - - -
175A ILE* 4.0 0.2 - - - -
176A ASP* 3.5 25.8 - - + -
193A TYR* 3.7 19.5 - - - -
197A ILE* 3.8 19.3 - - + -
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Residues in contact with TRP 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 3.8 18.8 - - + -
16A LYS* 6.1 0.9 - - - +
17A TRP* 3.9 31.8 + + + -
31A ASN* 3.8 21.5 - - + -
34A HIS* 3.5 41.3 - + + -
35A TYR* 3.9 38.1 - + + -
39A HIS* 3.0 27.0 - + - -
89A HIS* 3.0 29.6 + + + -
90A CYS* 4.2 2.5 - - - +
92A PHE* 1.3 93.9 - + - +
94A GLU* 1.3 63.0 + - + +
96A LEU* 3.1 29.2 + - + +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 6.0 4.0 - - + +
14A ASP 5.5 2.3 - - - +
16A LYS* 3.3 37.8 + - - +
90A CYS 3.3 17.9 + - - +
91A LEU* 3.8 4.0 - - - +
92A PHE 3.2 0.6 - - - -
93A TRP* 1.3 82.4 - - + +
95A ASN* 1.3 57.1 + - - +
96A LEU 3.3 3.8 + - - +
202A ASN* 3.9 9.0 + - - -
205A GLU* 3.2 34.3 - - + +
209A ARG* 4.0 11.7 - - - +
----------------------------------------------------------
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Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU 2.8 26.7 + - - -
92A PHE* 3.2 6.5 + - - +
94A GLU* 1.3 74.8 - - - +
96A LEU* 1.3 62.0 + - - +
172A LEU 4.3 5.2 - - - +
173A VAL* 3.9 11.4 - - + +
174A ALA* 2.9 40.8 + - - +
175A ILE* 4.8 1.0 - - - +
201A VAL* 3.5 8.5 - - - +
202A ASN* 2.8 34.9 + - - +
205A GLU* 4.4 1.3 - - + -
209A ARG* 2.7 32.9 - - - +
----------------------------------------------------------
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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