Contacts of the helix formed by residues 87 - 114 (chain C) in PDB entry 4QYL
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 THR 87 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASN* 3.5 11.3 - - + +
84C ALA* 2.7 40.2 + - + +
86C ASP* 1.3 86.9 - - - +
88C ILE* 1.3 65.8 + - - +
89C PHE* 3.2 9.8 + - + -
90C TYR* 3.2 14.4 + - - +
91C ARG* 3.1 23.9 + - - +
8G GLY* 3.4 16.8 - - - +
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 4.7 10.0 - - + +
86C ASP 3.9 0.4 + - - -
87C THR* 1.3 72.8 - - - +
89C PHE* 1.3 80.1 + - + +
91C ARG* 3.7 8.7 - - - +
92C ALA* 2.8 30.3 + - - +
7G GLY 3.1 23.6 - - - +
8G GLY* 2.9 25.9 + - - +
9G LYS 4.1 10.5 - - - +
10G ALA* 4.1 12.8 - - + -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE* 3.9 24.7 - - + -
28C PHE* 4.3 0.2 - - - -
79C CYS* 3.2 17.2 - - - -
83C ASN* 3.8 25.8 - - - +
87C THR* 3.1 6.8 - - + +
88C ILE* 1.3 86.2 - - + +
90C TYR* 1.4 65.1 + - - +
92C ALA* 3.2 7.0 + - - +
93C ALA 3.0 18.4 + - - -
5G ALY 3.6 44.4 - - + -
6G GLN 3.5 20.6 - - - -
7G GLY* 3.9 11.4 - - - -
8G GLY* 3.5 25.6 - - - -
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C CYS* 4.5 4.5 - - - -
80C LEU* 3.5 45.4 - - + +
83C ASN* 3.3 22.8 - - + +
84C ALA 3.1 19.1 - - - +
85C LYS* 3.6 56.4 + - + +
87C THR* 3.2 7.4 + - - +
89C PHE* 1.4 76.1 - - - +
91C ARG* 1.3 67.4 + - + +
93C ALA* 3.1 4.9 + - - +
94C VAL* 3.0 36.9 + - + +
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Residues in contact with ARG 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LYS 4.1 11.9 - - - +
86C ASP* 4.3 10.9 + - - +
87C THR 3.1 18.8 + - - +
88C ILE* 3.8 7.6 - - - +
90C TYR* 1.3 80.6 - - + +
92C ALA* 1.3 62.4 + - - +
94C VAL* 3.3 7.6 + - - +
95C ARG* 3.1 35.4 + - - +
201C SO4 2.8 45.5 + - - +
10G ALA* 3.9 22.6 - - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASP* 5.7 0.4 - - - +
27C ILE* 3.5 28.3 - - + -
28C PHE* 4.0 13.2 - - + -
88C ILE 2.8 18.6 + - - +
89C PHE 3.2 5.8 + - - +
91C ARG* 1.3 78.1 - - - +
93C ALA* 1.3 56.4 + - - +
95C ARG* 3.4 12.0 + - - +
96C LEU* 2.9 28.4 + - - +
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PHE* 3.8 9.9 - - + -
76C VAL* 3.9 11.4 - - - +
79C CYS* 3.7 24.7 - - + -
80C LEU* 3.7 20.9 - - + -
89C PHE 3.0 13.2 + - - +
90C TYR 3.1 8.0 + - - +
92C ALA* 1.3 73.8 - - - +
94C VAL* 1.3 60.3 + - - +
96C LEU* 3.6 3.7 - - - +
97C ARG* 2.8 31.0 + - - +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 3.8 9.2 - - + -
90C TYR* 3.0 37.8 + - + +
91C ARG* 3.3 10.3 + - - +
93C ALA* 1.3 75.1 - - - +
95C ARG* 1.3 62.6 + - + +
97C ARG* 3.3 29.3 + - - +
98C GLU* 3.1 37.7 + - - +
201C SO4 5.9 2.7 - - - +
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Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS 5.9 1.8 - - - +
24C THR* 5.3 6.9 + - - -
91C ARG* 3.1 22.6 + - - +
92C ALA* 3.6 12.1 - - - +
93C ALA 3.3 0.2 - - - -
94C VAL* 1.3 79.5 - - + +
96C LEU* 1.3 61.4 + - - +
98C GLU* 3.4 16.3 + - - +
99C GLN* 3.0 48.2 + - - +
201C SO4 2.9 42.3 + - - +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.9 10.8 - - - +
22C LYS* 3.8 28.7 + - + +
23C ASP* 4.2 13.0 - - + +
28C PHE* 3.5 34.5 - - + -
50C PHE* 4.2 8.7 - - + -
72C PHE* 3.6 28.1 - - + -
75C ILE* 4.2 5.6 - - + -
76C VAL* 4.1 11.2 - - + -
92C ALA 2.9 17.2 + - - +
93C ALA* 3.6 5.4 - - - +
95C ARG* 1.3 76.7 - - - +
97C ARG* 1.3 59.1 + - - +
99C GLN* 4.9 1.8 - - - -
100C GLY* 2.8 29.7 + - - +
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Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 4.6 6.5 - - + -
76C VAL* 3.7 24.8 - - + +
80C LEU* 3.4 24.3 - - - +
93C ALA 2.8 18.4 + - - +
94C VAL* 3.3 27.9 + - - +
96C LEU* 1.3 75.3 - - - +
98C GLU* 1.3 64.5 + - - +
100C GLY 4.0 0.2 - - - -
101C GLY* 3.0 21.3 + - - -
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C VAL* 3.1 28.9 + - - +
95C ARG* 3.5 24.7 + - - +
97C ARG* 1.3 81.2 - - - +
99C GLN* 1.3 70.4 + - + +
101C GLY* 3.7 5.4 + - - -
102C ALA* 4.0 8.7 + - - +
201C SO4 5.3 1.9 + - - -
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Residues in contact with GLN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 3.4 54.4 + - + +
24C THR* 5.8 2.5 - - - +
95C ARG* 3.0 39.8 + - - +
98C GLU* 1.3 82.0 + - + +
100C GLY* 1.3 65.5 + - - +
102C ALA* 3.4 14.9 + - - +
103C VAL* 3.5 14.6 + - - +
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.7 21.8 - - - -
22C LYS* 4.6 4.3 - - - +
72C PHE* 3.9 5.8 - - - -
96C LEU* 2.8 19.0 + - - -
99C GLN* 1.3 75.0 - - - +
101C GLY* 1.3 66.7 + - - +
103C VAL* 3.1 5.7 + - - +
104C LEU* 2.9 31.3 + - - +
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Residues in contact with GLY 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 4.8 1.0 - - - -
97C ARG 3.0 17.2 + - - -
98C GLU* 4.1 3.6 - - - -
99C GLN 3.3 0.6 - - - -
100C GLY* 1.3 76.9 - - - +
102C ALA* 1.3 55.0 + - - +
104C LEU* 3.5 8.9 + - - +
105C ARG* 3.0 37.6 + - - +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU 4.0 6.6 + - - +
99C GLN* 3.4 10.4 + - - +
100C GLY 3.2 0.6 - - - -
101C GLY* 1.3 74.8 - - - +
103C VAL* 1.3 66.3 + - + +
105C ARG* 3.4 9.6 + - - +
106C GLN* 3.2 23.4 + - - +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C THR* 4.0 9.0 - - + +
18C GLN* 3.6 43.5 - - + +
19C LEU* 3.7 23.3 - - + -
22C LYS* 3.8 21.8 - - + -
99C GLN 3.5 13.4 + - - +
100C GLY* 3.1 8.2 + - - +
102C ALA* 1.3 78.9 - - + +
104C LEU* 1.3 62.0 + - - +
106C GLN* 3.5 5.7 + - - +
107C ALA* 3.1 22.5 + - - +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C THR* 4.5 2.0 - - + -
19C LEU* 4.2 13.5 - - + -
65C PHE* 3.9 27.1 - - + -
68C PHE* 4.2 19.5 - - + -
69C GLU* 4.0 37.7 - - + +
72C PHE* 3.5 34.3 - - + -
73C ASN* 4.7 2.2 - - - +
100C GLY 2.9 22.2 + - - +
101C GLY* 3.9 6.5 - - - +
103C VAL* 1.3 70.1 - - - +
105C ARG* 1.3 62.0 + - + +
107C ALA* 4.5 2.5 - - - -
108C ARG* 2.9 32.8 + - - +
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C GLY 3.0 23.2 + - - +
102C ALA* 3.7 8.3 - - - +
103C VAL 3.3 0.2 - - - -
104C LEU* 1.3 77.7 - - + +
106C GLN* 1.3 62.0 + - - +
108C ARG* 3.5 4.7 + - - +
109C ARG* 3.3 27.8 + - - +
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 5.7 1.2 - - - +
18C GLN* 4.8 10.0 + - - +
102C ALA 3.2 14.0 + - - +
103C VAL* 3.8 5.4 - - - +
105C ARG* 1.3 77.3 - - - +
107C ALA* 1.3 72.3 + - - +
109C ARG* 3.3 26.2 + - - +
110C GLN* 3.0 52.8 + - - +
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.7 8.8 - - + +
15C THR* 3.3 35.9 - - + +
18C GLN* 5.2 2.2 - - - +
65C PHE* 3.7 13.0 - - + -
103C VAL 3.1 17.3 + - - +
106C GLN* 1.3 82.4 + - - +
108C ARG* 1.3 67.0 + - - +
110C GLN* 3.1 9.2 + - - +
111C ALA* 2.9 21.8 + - - +
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE* 3.7 34.7 - - + +
66C ASP* 2.8 36.3 + - - +
69C GLU* 2.8 31.1 + - - +
104C LEU 2.9 19.7 + - - +
105C ARG* 3.9 5.6 - - - +
107C ALA* 1.3 77.0 - - - +
109C ARG* 1.3 58.5 + - - +
111C ALA* 3.0 5.0 + - + +
112C GLU* 2.9 49.0 + - + +
117C ASP* 4.8 11.5 + - - -
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 3.3 18.8 + - - +
106C GLN* 3.5 32.2 - - - +
107C ALA 3.2 0.2 - - - -
108C ARG* 1.3 79.8 - - - +
110C GLN* 1.3 75.4 + - - +
112C GLU* 3.4 16.8 + - - +
113C LYS* 3.0 37.1 + - + +
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Residues in contact with GLN 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.2 17.5 - - + -
106C GLN* 3.0 48.2 + - - +
107C ALA* 3.1 8.2 + - - +
109C ARG* 1.3 97.6 - - - +
111C ALA* 1.3 62.5 + - - +
113C LYS* 3.3 30.2 + - - +
114C MET* 3.1 27.3 + - + +
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE* 5.1 2.5 - - + -
11C LEU* 3.6 21.9 - - + +
65C PHE* 4.0 21.1 - - + -
107C ALA 2.9 10.1 + - - +
108C ARG* 3.0 9.8 + - + +
110C GLN* 1.3 74.6 - - - +
112C GLU* 1.3 62.3 + - - +
114C MET* 3.2 21.9 - - - +
115C GLY 3.2 3.8 + - - -
116C ILE 4.4 3.1 - - - +
117C ASP* 3.0 28.4 + - - +
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ARG* 2.9 37.9 + - + +
109C ARG* 3.6 20.4 + - - +
111C ALA* 1.3 79.2 - - - +
113C LYS* 1.3 61.3 + - + +
115C GLY* 3.1 13.2 + - - +
117C ASP* 3.6 29.8 - - - +
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Residues in contact with LYS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG* 3.0 36.4 + - + +
110C GLN* 3.3 30.4 + - - +
112C GLU* 1.3 76.5 - - + +
114C MET* 1.3 59.0 + - - +
115C GLY 3.8 0.2 + - - -
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Residues in contact with MET 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PRO* 3.6 32.1 - - + +
8C PHE* 3.9 32.3 - - - -
11C LEU* 4.0 22.4 - - + -
110C GLN* 3.1 12.7 + - + +
111C ALA* 3.2 20.9 - - - +
112C GLU 3.1 0.2 - - - -
113C LYS* 1.3 78.1 - - - +
115C GLY* 1.3 67.9 + - - +
116C ILE 4.4 0.4 - - - +
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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