Contacts of the helix formed by residues 55 - 80 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X THR 3.8 2.8 + - - +
54X GLN* 1.3 76.6 - - - +
56X GLU* 1.3 83.3 + - + +
57X GLU* 4.7 4.0 - - + +
58X THR* 3.2 16.4 + - - +
59X LYS* 2.9 24.6 + - - +
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Residues in contact with GLU 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X LYS* 5.0 3.3 + - - +
54X GLN 3.6 2.9 + - - +
55X MET* 1.3 86.3 - - + +
57X GLU* 1.3 61.8 + - - +
59X LYS* 2.9 49.9 + - - +
60X ALA* 3.3 9.5 + - - +
142X LEU* 3.7 20.8 - - + +
145X VAL* 3.1 39.1 - - + +
146X GLY* 4.6 1.7 + - - -
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Residues in contact with GLU 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M SER* 2.6 30.2 + - - -
31M TYR* 3.2 25.2 - - + +
55X MET* 3.4 3.9 - - + +
56X GLU* 1.3 78.1 - - - +
58X THR* 1.3 57.5 + - - +
60X ALA* 3.2 8.1 + - - +
61X GLN* 3.1 28.8 + - - +
107X LEU* 6.5 0.7 - - + -
108X LEU* 4.0 24.6 - - + +
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Residues in contact with THR 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M TYR* 2.6 32.8 + - - -
54X GLN* 3.3 39.7 - - + +
55X MET* 3.2 19.6 + - - +
57X GLU* 1.3 73.6 - - - +
59X LYS* 1.3 66.1 + - - +
60X ALA 3.0 1.1 - - - -
61X GLN* 3.5 5.9 + - + +
62X ASP* 2.7 36.3 + - - +
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Residues in contact with LYS 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X TRP* 3.5 56.7 - - + +
52X LYS* 2.7 59.5 + - - +
54X GLN* 3.6 12.8 + - + +
55X MET 2.9 13.8 + - - +
56X GLU* 2.9 45.3 + - - +
58X THR* 1.3 77.5 - - - +
60X ALA* 1.3 62.5 + - - +
62X ASP* 3.4 2.5 + - - +
63X ILE* 3.1 16.3 + - - +
141X PHE 4.9 7.2 - - - -
142X LEU* 3.7 8.7 - - + -
145X VAL* 5.7 0.4 - - - -
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Residues in contact with ALA 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56X GLU 3.3 3.7 + - - +
57X GLU* 3.2 11.3 + - - +
58X THR 3.0 0.6 - - - -
59X LYS* 1.3 78.1 - - - +
61X GLN* 1.3 54.7 + - - +
63X ILE* 2.8 12.0 + - - +
64X LEU* 2.8 32.6 + - - +
104X LEU* 4.4 7.0 - - + +
107X LEU* 4.3 15.9 - - + -
108X LEU* 4.0 20.3 - - + +
142X LEU* 3.8 23.3 - - + -
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Residues in contact with GLN 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M TYR* 3.2 43.6 - - + +
33M TYR* 3.5 15.8 + - - -
49M SER* 2.8 29.8 + - - +
57X GLU* 3.3 13.2 + - - +
58X THR* 3.5 10.3 + - - +
60X ALA* 1.3 73.0 - - - +
62X ASP* 1.3 69.0 - - - +
64X LEU* 3.0 4.0 + - - +
65X GLY* 3.0 19.2 + - - -
108X LEU* 3.8 21.8 - - + +
110X THR* 5.1 3.8 - - - +
112X LEU* 3.8 22.9 - - + +
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Residues in contact with ASP 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X TRP* 3.7 20.6 - - + +
54X GLN* 3.4 18.6 - - - +
58X THR* 2.7 31.5 + - - +
59X LYS 3.6 7.6 - - - +
61X GLN* 1.3 74.8 - - - +
63X ILE* 1.3 65.0 + - - +
65X GLY* 3.0 4.0 + - - +
66X ALA* 3.0 20.9 + - - +
115X GLN* 5.9 6.5 - - - +
117X ARG* 5.7 1.7 + - - -
138X LYS* 5.4 3.4 - - + +
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Residues in contact with ILE 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X TRP* 3.6 14.1 - - + -
59X LYS 3.1 12.1 + - - +
60X ALA* 2.8 9.8 + - - +
62X ASP* 1.3 75.4 - - - +
64X LEU* 1.3 58.1 + - - +
66X ALA* 3.0 7.9 + - - +
67X VAL* 2.8 34.6 + - + +
104X LEU* 3.3 24.2 - - + -
134X LEU* 5.0 4.9 - - + -
138X LYS* 3.2 52.9 - - + +
139X VAL* 3.7 22.4 - - + +
142X LEU* 4.1 17.0 - - + -
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Residues in contact with LEU 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X ALA 2.8 11.7 + - - +
61X GLN 3.0 7.8 + - - +
63X ILE* 1.3 77.3 - - - +
65X GLY* 1.3 52.8 + - - +
67X VAL* 4.5 0.9 - - + -
68X THR* 2.6 54.1 + - + +
101X LEU* 4.1 6.5 - - + -
104X LEU* 3.7 23.3 - - + -
105X GLN* 3.6 27.8 - - + +
108X LEU* 3.7 26.0 - - + -
110X THR 3.7 21.5 - - - +
112X LEU* 3.7 26.9 - - + +
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Residues in contact with GLY 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61X GLN 3.0 12.7 + - - -
62X ASP* 3.0 3.8 + - - -
64X LEU* 1.3 77.4 - - - +
66X ALA* 1.3 61.8 + - - +
68X THR* 2.8 19.2 + - - -
69X LEU* 2.9 15.2 + - - +
112X LEU* 4.9 3.3 - - - +
113X PRO 3.7 15.0 - - - -
115X GLN* 3.8 19.3 + - - -
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Residues in contact with ALA 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42X PRO* 3.3 24.4 - - + +
62X ASP 3.0 10.7 + - - +
63X ILE* 3.0 12.1 + - - +
65X GLY* 1.3 75.3 - - - +
67X VAL* 1.3 57.8 + - - +
69X LEU* 3.4 1.4 + - - -
70X LEU* 2.9 25.1 + - - +
115X GLN 4.2 10.2 + - - +
116X GLY* 6.2 0.9 - - - -
134X LEU* 3.9 22.7 - - + -
138X LYS* 5.7 6.7 - - + -
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Residues in contact with VAL 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X ILE* 2.8 25.6 + - + +
64X LEU* 3.8 3.6 - - - +
66X ALA* 1.3 74.2 - - - +
68X THR* 1.3 60.8 + - - +
70X LEU* 3.6 7.6 - - + +
71X LEU* 2.8 28.1 + - - +
97X VAL* 3.8 22.0 - - + -
100X LEU* 3.2 34.3 - - + -
101X LEU* 4.1 25.4 - - + +
104X LEU* 3.7 10.3 - - + -
134X LEU* 4.2 11.2 - - + -
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Residues in contact with THR 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I TRP* 4.0 17.4 - - + -
64X LEU* 2.6 35.1 + - + +
65X GLY* 2.8 15.8 + - - -
67X VAL* 1.3 77.1 - - - +
69X LEU* 1.3 57.3 + - - -
71X LEU* 3.4 7.4 + - - +
72X GLU* 3.3 21.5 + - - +
101X LEU* 3.0 31.9 - - + -
105X GLN* 4.3 2.0 - - - +
112X LEU 3.9 16.1 + - - +
113X PRO 3.7 8.5 + - - -
114X PRO* 3.9 8.2 - - - +
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Residues in contact with LEU 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X LEU* 4.1 19.2 - - + +
41X LEU* 4.1 1.3 - - - -
42X PRO* 3.8 30.7 - - + -
65X GLY 2.9 16.4 + - - +
66X ALA* 3.8 1.3 - - - +
68X THR* 1.3 72.9 + - - +
70X LEU* 1.3 66.0 + - - +
72X GLU* 3.2 21.2 + - - +
73X GLY* 2.9 19.4 + - - -
114X PRO* 3.8 21.5 - - + +
115X GLN 4.0 18.8 - - - +
117X ARG 4.7 1.1 - - - +
118X THR* 3.5 32.8 - - + -
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Residues in contact with LEU 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41X LEU* 4.5 10.5 - - + +
42X PRO* 3.8 16.3 - - + +
66X ALA 2.9 17.9 + - - +
67X VAL* 3.6 7.4 - - + +
69X LEU* 1.3 72.4 - - - +
71X LEU* 1.3 53.1 + - - +
72X GLU 2.6 16.5 + - - -
73X GLY* 2.6 14.7 + - - -
74X VAL* 3.0 28.5 + - + +
93X LEU* 5.2 0.7 - - + -
97X VAL* 3.5 38.1 - - + -
127X ILE* 4.1 19.7 - - + +
130X SER* 4.5 9.6 - - - +
131X PHE* 3.7 31.6 - - + +
134X LEU* 5.2 5.4 - - + -
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Residues in contact with LEU 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I THR* 5.7 1.8 - - + -
31I ASP* 3.2 28.7 - - - +
101I TRP* 4.9 10.8 - - + -
67X VAL 2.8 20.8 + - - +
68X THR* 3.7 7.9 - - - +
69X LEU 3.4 0.4 - - - -
70X LEU* 1.3 73.8 - - - +
72X GLU* 1.3 58.7 + - + +
74X VAL* 3.7 8.9 - - - +
75X MET* 2.9 35.9 + - + +
94X SER* 4.0 3.8 - - - +
97X VAL* 3.8 25.6 - - + -
98X ARG* 3.2 43.5 - - + +
101X LEU* 4.7 14.8 - - + -
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Residues in contact with GLU 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I TYR* 5.4 3.3 + - - -
40X LEU* 6.1 0.3 - - - +
68X THR 3.3 11.9 + - - +
69X LEU* 3.2 23.8 + - - +
70X LEU 2.6 5.9 + - - -
71X LEU* 1.3 75.8 - - + +
73X GLY* 1.3 62.8 + - - +
75X MET* 4.1 5.4 - - - +
76X ALA* 2.9 27.0 + - + +
114X PRO* 3.9 24.8 - - - +
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Residues in contact with GLY 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39X VAL* 3.3 24.1 - - - +
40X LEU 3.4 23.8 + - - -
41X LEU* 4.1 4.0 - - - -
69X LEU 2.9 8.7 + - - -
70X LEU 2.6 12.0 + - - -
72X GLU* 1.3 71.4 - - - +
74X VAL* 1.3 63.4 + - - +
76X ALA* 3.2 11.9 + - - +
77X ALA* 3.2 8.8 + - - +
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Residues in contact with VAL 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41X LEU* 4.6 1.8 - - - +
70X LEU* 3.0 39.0 + - + +
71X LEU* 3.7 9.2 - - - +
73X GLY* 1.3 72.4 - - - +
75X MET* 1.3 60.3 + - + +
77X ALA* 2.9 23.9 + - - +
78X ARG* 3.2 13.0 + - - +
90X LEU* 3.6 29.4 - - + +
93X LEU* 4.1 21.3 - - + -
94X SER* 4.0 13.9 - - - -
97X VAL* 4.9 5.2 - - + -
127X ILE* 4.5 14.8 - - + -
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Residues in contact with MET 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I THR* 3.8 31.0 - - + -
71X LEU* 2.9 25.0 + - + +
72X GLU* 4.1 6.1 - - - +
74X VAL* 1.3 76.4 - - + +
76X ALA* 1.3 62.8 + - - +
78X ARG* 3.5 25.2 + - + +
79X GLY* 3.1 19.9 + - - -
94X SER* 4.6 6.1 - - - -
98X ARG* 3.6 28.3 - - - +
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Residues in contact with ALA 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39X VAL* 3.8 13.9 - - + -
72X GLU* 2.9 21.8 + - + +
73X GLY* 3.2 8.7 + - - +
75X MET* 1.3 76.1 - - - +
77X ALA* 1.3 60.3 + - - +
79X GLY* 3.7 5.5 + - - -
80X GLN* 3.2 26.4 + - - +
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Residues in contact with ALA 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X LEU* 4.5 18.5 - - + +
39X VAL* 4.0 10.0 - - + +
73X GLY 3.2 8.6 + - - +
74X VAL* 2.9 12.6 + - - +
76X ALA* 1.3 73.0 - - - +
78X ARG* 1.3 67.9 + - - +
79X GLY 2.9 1.3 - - - -
80X GLN* 2.8 28.6 + - - +
81X LEU* 3.6 12.0 - - + +
90X LEU* 3.7 19.1 - - + -
127X ILE* 5.2 5.6 - - + -
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Residues in contact with ARG 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X VAL* 3.2 7.0 + - - +
75X MET* 3.7 33.8 - - + +
77X ALA* 1.3 78.3 - - - +
79X GLY* 1.3 60.2 + - - +
81X LEU* 3.1 28.3 + - - +
87X SER* 2.6 56.6 + - - +
88X SER* 4.7 2.2 + - - +
90X LEU* 4.0 20.7 - - + +
91X GLY* 3.3 28.5 - - - +
94X SER* 4.7 2.1 + - - -
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Residues in contact with GLY 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75X MET 3.1 14.1 + - - -
76X ALA* 4.1 4.5 - - - -
77X ALA 2.9 2.2 + - - -
78X ARG* 1.3 77.1 - - - +
80X GLN* 1.3 58.2 + - - +
81X LEU 3.1 6.7 + - - +
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Residues in contact with GLN 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X LEU* 3.5 7.6 - - + +
36X PRO* 3.4 29.7 - - + +
37X THR* 2.7 61.1 + - - +
38X PRO 4.8 0.4 + - - -
39X VAL* 3.6 18.2 - - - +
76X ALA* 3.2 21.2 + - - +
77X ALA* 2.8 10.0 + - - +
79X GLY* 1.3 77.1 - - - +
81X LEU* 1.3 63.6 + - + +
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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