Contacts of the helix formed by residues 55 - 78 (chain V) in PDB entry 1V7M
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 MET 55 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53V THR 3.9 10.1 + - - +
54V GLN* 1.3 76.2 - - - +
56V GLU* 1.3 68.6 + - - +
57V GLU* 3.3 3.8 - - + +
58V THR* 3.0 28.1 + - - +
59V LYS* 3.2 11.6 + - - +
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Residues in contact with GLU 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54V GLN 3.8 0.8 + - - -
55V MET* 1.3 75.4 - - - +
57V GLU* 1.3 63.2 + - + +
59V LYS* 3.9 10.5 - - + -
60V ALA* 3.8 4.0 + - - +
142V LEU* 3.4 38.0 - - - +
145V VAL* 3.2 34.9 - - - +
147V GLY* 5.2 2.4 - - - -
148V SER* 4.7 13.5 + - - -
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Residues in contact with GLU 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L SER* 2.9 30.4 + - - -
31L TYR* 3.0 29.9 - - + +
55V MET* 3.3 2.9 - - + +
56V GLU* 1.3 80.5 - - + +
58V THR* 1.3 51.6 + - - +
60V ALA* 2.8 10.4 + - - +
61V GLN* 2.7 34.0 + - - +
107V LEU 5.7 0.2 - - - +
108V LEU* 4.1 22.6 - - + +
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Residues in contact with THR 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L TYR* 3.2 18.4 + - + -
54V GLN* 4.3 18.8 - - + +
55V MET* 3.0 26.3 + - - +
57V GLU* 1.3 75.8 - - - +
59V LYS* 1.3 55.1 + - - +
61V GLN* 2.6 26.5 + - - -
62V ASP* 2.8 35.5 + - - +
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Residues in contact with LYS 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51V TRP* 3.3 40.4 + - + +
52V LYS* 3.1 48.7 + - - +
54V GLN* 3.3 23.6 - - + +
55V MET 3.2 11.2 + - - +
56V GLU* 3.9 16.2 - - + +
58V THR* 1.3 75.8 - - - +
60V ALA* 1.3 59.7 + - - +
62V ASP* 3.5 10.5 + - - +
63V ILE* 3.0 31.5 + - - +
141V PHE 4.4 11.8 + - - -
142V LEU* 3.7 24.9 - - + -
145V VAL* 5.6 0.7 - - - -
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Residues in contact with ALA 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V GLU 3.8 7.9 + - - +
57V GLU* 2.8 13.2 + - - +
59V LYS* 1.3 78.0 - - - +
61V GLN* 1.3 57.8 + - - +
63V ILE* 3.3 5.9 + - - +
64V LEU* 3.0 27.9 + - - +
104V LEU* 4.5 8.6 - - + +
107V LEU* 4.7 11.2 - - + -
108V LEU* 4.2 18.9 - - + +
142V LEU* 3.8 25.3 - - + +
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Residues in contact with GLN 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L TYR* 3.0 47.1 - - + +
33L TYR* 3.4 19.6 + - - -
49L SER* 2.6 31.5 + - - +
57V GLU* 2.7 7.3 + - - +
58V THR* 2.6 19.6 + - - +
60V ALA* 1.3 70.8 - - - +
62V ASP* 1.3 63.2 + - - +
64V LEU* 3.6 2.3 + - - +
65V GLY* 3.1 18.9 + - - -
108V LEU* 3.4 27.0 + - + +
110V THR* 4.8 4.0 - - - +
112V LEU* 4.0 19.9 - - + +
115V GLN* 5.8 0.9 + - - -
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Residues in contact with ASP 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L ASN* 5.6 3.8 + - - -
51V TRP* 3.6 25.3 + - + +
54V GLN* 4.1 11.1 + - - +
58V THR* 2.8 42.5 + - - +
59V LYS* 3.6 8.0 - - - +
61V GLN* 1.3 77.6 - - - +
63V ILE* 1.3 58.5 + - + +
65V GLY* 3.5 3.6 + - - -
66V ALA* 3.0 25.9 + - - +
115V GLN* 5.1 13.4 + - - +
116V GLY* 6.0 0.5 - - - -
138V LYS* 5.3 4.6 - - - +
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Residues in contact with ILE 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51V TRP* 3.6 15.5 - - + -
59V LYS 3.0 21.0 + - - +
60V ALA* 3.6 9.6 - - - +
61V GLN 3.2 0.4 - - - -
62V ASP* 1.3 75.6 - - - +
64V LEU* 1.3 58.0 + - - +
65V GLY 3.0 1.3 - - - -
66V ALA* 2.5 25.1 + - - +
67V VAL* 2.7 24.1 + - + +
104V LEU* 3.7 20.2 - - + -
134V LEU* 4.8 9.0 - - + -
138V LYS* 3.4 39.0 - - + +
139V VAL* 3.9 23.8 - - + +
142V LEU* 4.2 11.7 - - + -
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Residues in contact with LEU 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60V ALA 3.0 15.7 + - - +
61V GLN 3.8 5.6 - - - +
62V ASP 3.6 0.2 - - - -
63V ILE* 1.3 75.9 - - - +
65V GLY* 1.3 56.2 + - - +
67V VAL* 3.3 0.9 + - + +
68V THR* 2.5 41.0 + - - +
101V LEU* 4.3 10.3 - - + +
104V LEU* 3.8 29.5 - - + +
105V GLN* 3.8 27.1 - - + +
108V LEU* 3.4 27.6 - - + -
110V THR 3.7 18.6 - - - +
112V LEU* 3.5 24.2 - - + +
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Residues in contact with GLY 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61V GLN 3.1 11.6 + - - -
62V ASP* 3.7 6.5 - - - -
63V ILE 3.0 0.6 - - - -
64V LEU* 1.3 80.3 - - - +
66V ALA* 1.3 59.0 + - - +
68V THR* 3.9 1.1 - - - -
69V LEU 3.5 10.9 + - - -
112V LEU* 4.8 5.1 - - - +
113V PRO 3.7 18.9 - - - +
115V GLN* 3.2 33.2 + - - +
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Residues in contact with ALA 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42V PRO* 2.9 43.4 - - + +
62V ASP 3.0 15.2 + - - +
63V ILE* 2.5 17.6 + - - +
65V GLY* 1.3 73.0 - - - +
67V VAL* 1.3 57.8 + - - +
68V THR 3.3 0.2 - - - -
69V LEU* 3.6 1.6 + - - +
70V LEU 3.2 7.4 + - - -
115V GLN 4.1 9.0 - - - +
116V GLY* 6.0 1.6 - - - -
134V LEU* 4.3 14.6 - - + -
138V LYS* 5.2 7.2 - - + -
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Residues in contact with VAL 67 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63V ILE* 2.7 30.8 + - + +
64V LEU 3.9 3.1 - - - +
66V ALA* 1.3 70.1 - - - +
68V THR* 1.3 60.0 + - - +
70V LEU* 3.6 10.0 - - + +
71V LEU* 2.9 28.2 + - - +
97V VAL* 3.7 25.6 - - + +
100V LEU* 3.5 36.6 - - + -
101V LEU* 4.1 16.7 - - + +
104V LEU* 3.7 16.4 - - + -
131V PHE* 5.6 0.2 - - + -
134V LEU* 5.0 7.0 - - + -
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Residues in contact with THR 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H TRP* 2.9 46.7 - - + +
64V LEU* 2.5 34.6 + - - +
65V GLY* 3.9 5.8 - - - -
67V VAL* 1.3 79.3 - - - +
69V LEU* 1.3 62.0 + - - +
71V LEU* 3.6 5.3 + - + +
72V GLU* 3.1 23.0 + - - +
101V LEU* 3.9 9.6 - - + +
105V GLN* 5.1 0.2 - - - +
112V LEU 3.8 12.0 + - - +
113V PRO 4.3 5.2 - - - -
114V PRO* 4.4 11.3 - - + +
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Residues in contact with LEU 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40V LEU* 4.6 24.3 - - + +
41V LEU 4.7 1.6 - - - -
42V PRO* 4.4 14.1 - - + -
65V GLY 3.5 15.4 + - - +
66V ALA* 3.9 4.9 - - - +
67V VAL 3.3 0.4 - - - -
68V THR* 1.3 75.2 - - - +
70V LEU* 1.3 55.6 + - - +
72V GLU* 3.0 31.5 - - + +
73V GLY* 2.7 31.4 + - - -
114V PRO* 4.2 13.1 - - + +
115V GLN* 4.1 17.9 - - - +
116V GLY 4.8 0.2 - - - +
118V THR* 3.3 34.1 - - + -
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Residues in contact with LEU 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V LEU* 4.6 7.6 - - + -
42V PRO* 3.5 23.0 - - + +
66V ALA 3.2 7.6 + - - +
67V VAL* 3.6 9.9 - - + +
68V THR 3.3 0.4 - - - -
69V LEU* 1.3 74.2 - - - +
71V LEU* 1.3 59.6 + - - +
73V GLY* 2.6 24.6 + - - -
74V VAL* 2.9 21.3 + - + +
93V LEU* 5.5 0.7 - - + -
97V VAL* 3.7 25.8 - - + -
127V ILE 4.2 12.1 - - - +
130V SER* 3.8 22.2 - - - +
131V PHE* 3.5 39.3 - - + +
134V LEU* 4.5 7.9 - - + -
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Residues in contact with LEU 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H THR* 6.0 1.1 - - - -
31H ASP* 3.8 17.9 - - + +
101H TRP* 5.0 14.1 - - + -
67V VAL 2.9 16.1 + - - +
68V THR* 4.0 6.7 - - + +
70V LEU* 1.3 74.4 - - - +
72V GLU* 1.3 66.0 + - + +
74V VAL* 3.5 7.9 + - - +
75V MET* 3.1 42.3 + - + +
94V SER* 4.7 3.6 - - - +
97V VAL* 3.6 27.4 - - + -
98V ARG* 3.5 43.3 - - + +
101V LEU* 4.9 10.8 - - + -
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Residues in contact with GLU 72 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H TYR* 5.6 1.7 + - - -
68V THR 3.1 15.3 + - - +
69V LEU* 3.0 32.2 - - + +
71V LEU* 1.3 83.3 - - + +
73V GLY* 1.3 61.7 + - - +
75V MET* 3.6 5.4 + - - +
76V ALA* 3.3 23.5 + - + +
114V PRO* 3.5 26.8 - - + +
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Residues in contact with GLY 73 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39V VAL* 3.7 26.1 - - - +
40V LEU 4.0 9.0 - - - -
41V LEU* 4.5 5.8 - - - -
69V LEU 2.7 11.0 + - - -
70V LEU 2.6 13.9 + - - -
72V GLU* 1.3 69.6 - - - +
74V VAL* 1.3 63.7 + - - +
76V ALA* 3.2 3.5 + - - -
77V ALA* 3.2 21.1 + - - +
127V ILE* 4.9 0.7 - - - -
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Residues in contact with VAL 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V LEU* 5.1 0.4 - - - +
70V LEU* 2.9 25.5 + - + +
71V LEU* 3.7 12.1 - - - +
73V GLY* 1.3 70.1 - - - +
75V MET* 1.3 60.9 + - + +
77V ALA* 4.0 0.9 - - - +
78V ARG* 2.9 33.0 + - + +
90V LEU* 3.9 21.4 - - + +
93V LEU* 4.0 18.8 - - + -
94V SER* 3.1 30.3 - - - +
97V VAL* 4.5 6.7 - - + -
127V ILE* 3.8 27.2 - - + +
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Residues in contact with MET 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H THR* 3.6 24.7 - - - +
71V LEU* 3.1 31.1 + - + +
72V GLU* 3.9 6.7 - - - +
73V GLY 3.2 0.6 - - - -
74V VAL* 1.3 77.9 - - + +
76V ALA* 1.3 52.2 + - - +
78V ARG* 3.4 24.5 - - + +
79V GLY* 2.8 29.6 + - - -
94V SER* 4.2 15.3 - - - -
98V ARG* 3.9 20.2 - - - +
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Residues in contact with ALA 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39V VAL* 4.3 11.2 - - + -
72V GLU* 3.3 15.5 + - + +
73V GLY* 3.2 6.3 + - - +
75V MET* 1.3 76.9 - - - +
77V ALA* 1.3 58.7 + - - +
79V GLY* 3.4 4.1 - - - -
80V GLN* 3.2 30.4 + - - +
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Residues in contact with ALA 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35V LEU* 3.7 34.7 - - + +
39V VAL* 3.9 8.2 - - + +
73V GLY 3.2 15.5 + - - +
74V VAL* 4.1 3.1 - - - +
76V ALA* 1.3 71.9 - - - +
78V ARG* 1.3 57.6 + - - +
79V GLY 3.0 4.3 - - - -
80V GLN* 3.0 26.8 + - - +
81V LEU* 3.4 21.2 - - - +
90V LEU* 4.7 8.1 - - + -
127V ILE* 5.2 6.3 - - + -
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Residues in contact with ARG 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74V VAL 2.9 16.6 + - - +
75V MET* 3.4 32.6 - - + +
77V ALA* 1.3 75.7 - - - +
79V GLY* 1.3 55.1 + - - +
80V GLN 3.6 0.2 - - - -
81V LEU* 3.0 23.3 - - - +
87V SER* 3.2 41.0 + - - +
88V SER* 4.3 5.9 + - - +
90V LEU* 3.4 27.9 + - + +
91V GLY* 3.1 31.9 + - - -
94V SER* 5.1 0.6 + - - -
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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
------------------------------------------------------------
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