Contacts of the helix formed by residues 54 - 79 (chain C) in PDB entry 3PL7
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 ALA 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER* 1.3 65.9 + - - +
56C THR* 3.3 14.8 + - - -
57C LYS* 3.6 27.2 + - + +
58C LYS* 3.4 32.1 + - - +
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 3.1 47.6 + - - +
112A LEU* 4.0 11.8 - - - +
54C ALA* 1.3 76.2 - - - +
56C THR* 1.3 65.7 + - - +
58C LYS* 3.8 7.7 + - - +
59C LEU* 3.4 21.3 + - - +
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.4 25.6 - - + -
122A SER* 3.8 17.0 - - - +
125A GLN* 2.8 40.7 + - - +
126A VAL* 3.7 19.0 - - + +
129A GLU* 5.2 0.8 - - - +
54C ALA 3.9 11.3 + - - +
55C SER* 1.3 80.6 + - - +
57C LYS* 1.3 64.7 + - - +
59C LEU* 3.8 1.8 - - - +
60C SER* 3.2 25.3 + - - -
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Residues in contact with LYS 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 4.6 16.4 - - + -
54C ALA* 3.6 25.8 + - - +
55C SER 3.3 0.4 - - - -
56C THR* 1.3 79.0 + - - +
58C LYS* 1.3 60.8 + - + +
60C SER* 3.4 5.9 + - - -
61C GLU* 2.8 44.2 + - + +
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Residues in contact with LYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 4.8 14.2 + - - +
54C ALA* 3.4 20.5 + - - +
55C SER* 4.1 7.2 - - - +
56C THR 3.4 0.2 - - - -
57C LYS* 1.3 76.6 - - + +
59C LEU* 1.3 57.8 + - - +
61C GLU* 3.6 9.3 - - - +
62C CYS* 2.9 29.8 + - - +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 3.5 51.4 - - + +
109A THR* 4.4 1.1 - - + -
112A LEU* 3.8 33.4 - - + -
126A VAL* 4.5 4.7 - - + -
146A PHE* 4.0 15.9 - - + -
55C SER 3.4 15.8 + - - +
56C THR* 3.8 5.4 - - - +
57C LYS 3.2 0.2 - - - -
58C LYS* 1.3 79.1 - - - +
60C SER* 1.3 52.9 + - - +
62C CYS* 3.1 8.6 + - + +
63C LEU* 2.7 45.6 + - + +
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Residues in contact with SER 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 3.2 31.9 - - - -
129A GLU* 2.9 29.7 + - - +
130A LEU* 3.9 7.9 - - - +
56C THR 3.2 15.4 + - - -
57C LYS 3.4 4.0 + - - -
59C LEU* 1.3 76.4 - - - +
61C GLU* 1.3 58.7 + - - +
63C LEU* 3.5 10.0 - - - +
64C LYS* 2.7 37.9 + - - +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 4.9 10.7 + - - +
193B GLU* 3.6 41.7 - - - +
194B LEU* 3.3 30.6 - - + +
57C LYS* 2.8 35.0 + - + +
58C LYS* 3.6 9.2 - - - +
60C SER* 1.3 78.4 + - - +
62C CYS* 1.3 56.2 + - - +
64C LYS* 3.7 8.4 - - - +
65C ARG* 3.0 26.8 + - - +
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Residues in contact with CYS 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA* 4.1 13.7 - - - -
108A LEU* 4.9 12.1 - - - -
58C LYS 2.9 14.7 + - - +
59C LEU* 3.2 11.9 - - + +
61C GLU* 1.3 76.1 - - - +
63C LEU* 1.3 63.6 + - - +
65C ARG* 3.1 30.6 + - - +
66C ILE* 3.0 48.4 + - - +
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 4.7 12.6 - - + -
105A PHE* 4.8 3.6 - - + -
108A LEU* 4.0 29.8 - - + -
126A VAL* 3.7 29.8 - - + -
130A LEU* 4.1 16.3 - - + +
142A ALA* 3.8 28.8 - - + +
146A PHE* 3.8 24.0 - - + -
59C LEU* 2.7 22.7 + - + +
60C SER* 3.5 6.1 - - - +
62C CYS* 1.3 74.5 - - - +
64C LYS* 1.3 61.1 + - - +
66C ILE* 3.5 4.5 + - + +
67C GLY* 3.0 20.3 + - - -
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 3.7 30.0 + - - +
130A LEU* 3.7 22.3 - - + +
132A ARG* 5.5 1.8 - - - +
133A ASP* 3.6 26.1 + - - +
139A ARG* 3.4 37.9 - - - +
194B LEU* 4.9 19.7 - - + -
60C SER 2.7 22.5 + - - +
61C GLU* 3.7 9.2 - - - +
63C LEU* 1.3 73.4 - - - +
65C ARG* 1.3 62.3 + - - +
68C ASP* 3.0 34.5 + - - +
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Residues in contact with ARG 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 6.2 0.8 - - - -
104A ALA* 5.5 2.8 - - - +
138B GLY* 6.5 0.2 - - - -
194B LEU* 3.1 37.0 + - + +
195B TYR* 3.5 52.6 + - + +
61C GLU* 3.0 20.2 + - - +
62C CYS* 3.1 41.5 + - - +
64C LYS* 1.3 75.7 - - - +
66C ILE* 1.3 70.4 + - - +
68C ASP* 4.0 3.8 - - - +
69C GLU* 3.2 28.2 + - - +
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 2.9 38.4 - - + -
101A TYR* 3.2 61.3 + - + -
104A ALA* 3.9 10.3 - - + -
105A PHE* 5.3 3.4 - - + -
108A LEU* 5.9 0.4 - - + -
62C CYS* 3.0 40.5 + - - +
63C LEU* 3.9 4.3 - - + +
65C ARG* 1.3 84.4 - - - +
67C GLY* 1.3 59.3 + - - +
69C GLU* 3.0 5.1 + - - +
70C LEU* 2.9 26.5 + - - +
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Residues in contact with GLY 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 3.8 10.5 - - - -
138A GLY* 3.5 30.9 - - - -
139A ARG* 4.3 2.2 - - - -
142A ALA* 4.6 0.7 - - - -
63C LEU 3.0 16.7 + - - -
64C LYS 4.1 0.2 - - - -
66C ILE* 1.3 76.1 - - - +
68C ASP* 1.3 57.8 + - - +
70C LEU* 3.5 2.5 + - - +
71C ASP* 2.8 31.4 + - - +
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASN* 2.8 17.0 + - - +
139A ARG* 2.7 44.8 + - - +
136B ASN* 3.4 33.4 + - - +
137B TRP* 4.9 0.7 + - - +
138B GLY* 4.2 8.9 + - - +
139B ARG* 5.1 0.2 - - - +
194B LEU* 5.7 2.8 - - - +
64C LYS* 3.0 24.7 + - - +
65C ARG* 4.0 4.9 - - - +
67C GLY* 1.3 74.8 - - - +
69C GLU* 1.3 57.9 + - - +
71C ASP* 3.6 6.6 + - - +
72C SER* 2.7 31.9 + - - -
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 2.8 33.0 + - - +
93B ALA* 4.9 3.5 - - - +
96B GLU* 6.0 1.7 - - - +
97B PHE* 4.0 34.0 + - + -
100B ARG* 4.5 6.2 + - - -
101B TYR* 4.1 5.4 + - + -
138B GLY* 4.3 5.2 - - - +
141B VAL* 4.6 3.9 - - + +
195B TYR* 2.8 42.5 + - - +
65C ARG* 3.2 15.4 + - - +
66C ILE* 3.0 6.6 + - - +
68C ASP* 1.3 74.5 - - - +
70C LEU* 1.3 66.8 + - - +
72C SER* 3.0 17.2 + - - -
73C ASN* 3.0 14.2 + - - +
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 4.4 6.5 - - + +
96A GLU* 3.8 31.9 - - + +
97A PHE* 3.8 34.8 - - + -
100A ARG* 4.0 8.1 - - - +
101A TYR* 4.6 3.8 - - + -
138A GLY* 5.2 2.2 - - - -
141A VAL* 4.3 13.5 - - + -
195A TYR* 4.3 17.9 - - + -
101B TYR* 3.6 20.9 + - + +
66C ILE 2.9 15.4 + - - +
67C GLY* 3.7 6.3 - - - +
69C GLU* 1.3 73.8 - - - +
71C ASP* 1.3 61.5 + - - +
73C ASN* 3.2 4.2 + - - +
74C MET* 2.9 38.8 + - + +
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Residues in contact with ASP 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASN* 3.7 25.3 + - - +
137A TRP* 3.8 11.3 + - - +
138A GLY* 3.6 5.9 + - - -
195A TYR* 2.8 28.6 + - - +
136B ASN* 4.9 0.2 + - - -
139B ARG* 2.8 36.1 + - - -
67C GLY 2.8 21.4 + - - +
68C ASP* 3.7 4.9 - - - +
70C LEU* 1.3 70.5 - - - +
72C SER* 1.3 65.3 + - - +
74C MET* 3.5 2.6 + - - +
75C GLU* 3.3 21.1 + - - +
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Residues in contact with SER 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 4.1 5.2 - - - -
130B LEU* 4.3 2.4 - - - +
138B GLY 3.1 24.8 - - - -
139B ARG* 3.2 15.5 + - - +
142B ALA* 3.9 21.3 - - - -
68C ASP 2.7 22.9 + - - -
69C GLU* 3.1 10.8 - - - -
71C ASP* 1.3 74.7 + - - +
73C ASN* 1.3 63.9 + - - +
75C GLU* 3.1 16.7 + - - +
76C LEU* 3.1 17.6 + - - +
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Residues in contact with ASN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 4.1 6.5 - - - +
97B PHE* 4.8 0.7 - - + -
101B TYR* 3.1 50.6 - - + +
103B ARG* 4.6 1.4 + - - +
104B ALA* 3.5 22.5 - - - +
69C GLU 3.0 7.8 + - - +
70C LEU 3.2 6.3 + - - +
72C SER* 1.3 76.3 - - - +
74C MET* 1.3 72.8 + - - +
75C GLU 3.0 0.2 - - - -
76C LEU* 3.0 28.0 + - - +
77C GLN* 2.9 38.7 + - - +
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Residues in contact with MET 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 6.4 0.2 - - - -
96A GLU* 3.4 30.7 - - - +
194A LEU* 4.4 17.8 - - + +
195A TYR* 3.4 62.8 - - + +
70C LEU* 2.9 21.9 + - + +
71C ASP 3.9 3.4 - - - +
72C SER 3.3 0.2 - - - -
73C ASN* 1.3 101.6 - - - +
75C GLU* 1.3 58.9 + - - +
77C GLN* 3.9 22.5 + - - +
78C ARG* 3.5 18.5 + - - +
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU 4.0 7.2 - - - +
130B LEU* 4.0 23.6 - - + +
133B ASP* 3.8 18.9 - - - +
139B ARG* 4.4 13.9 + - - +
71C ASP* 3.3 12.1 + - - +
72C SER* 3.2 12.3 - - - +
73C ASN 3.0 0.4 - - - -
74C MET* 1.3 76.9 - - - +
76C LEU* 1.3 63.6 + - - +
77C GLN 3.2 1.6 - - - -
78C ARG* 2.7 56.2 + - - +
79C MET* 3.2 31.0 - - + +
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 4.1 25.1 - - + -
101B TYR* 5.4 0.2 - - + -
104B ALA* 4.0 20.0 - - + -
105B PHE* 4.1 24.5 - - + -
108B LEU* 3.5 40.4 - - + +
130B LEU* 4.5 22.9 - - + -
142B ALA* 4.8 4.7 - - + +
146B PHE* 5.2 6.3 - - + -
72C SER 3.1 12.4 + - - +
73C ASN* 3.0 22.6 + - - +
75C GLU* 1.3 76.4 - - - +
77C GLN* 1.3 62.0 + - - +
79C MET* 3.4 20.8 + - + +
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Residues in contact with GLN 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 5.6 0.2 + - - -
100A ARG* 4.9 1.4 - - - +
194A LEU 5.1 3.1 - - - +
103B ARG* 2.7 46.2 - - - +
104B ALA* 4.4 4.9 - - + -
108B LEU* 5.6 0.4 - - - -
73C ASN* 2.9 42.5 + - - +
74C MET* 3.9 27.4 - - - +
76C LEU* 1.3 78.7 - - - +
78C ARG* 1.3 61.2 + - - +
79C MET 3.0 9.9 + - - +
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Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 4.1 27.0 - - + +
129B GLU* 3.4 37.2 + - - +
132B ARG* 5.6 5.0 - - - +
133B ASP* 6.0 1.3 - - - -
74C MET 3.5 14.0 + - - +
75C GLU* 2.7 44.9 + - - +
77C GLN* 1.3 78.0 - - - +
79C MET* 1.3 65.0 - - - +
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Residues in contact with MET 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.7 31.9 - - + +
111B GLN* 3.9 18.2 - - - +
112B LEU* 6.5 0.7 - - + -
126B VAL* 4.5 15.7 - - - +
129B GLU* 3.9 18.6 - - + -
130B LEU* 3.6 41.7 - - + +
75C GLU* 3.2 31.6 - - + +
76C LEU* 3.6 18.6 - - + +
77C GLN 3.0 10.8 + - - +
78C ARG* 1.3 85.9 - - - +
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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