Contacts of the helix formed by residues 87 - 114 (chain A) in PDB entry 4QYD
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASN* 3.5 9.6 - - + +
84A ALA* 2.7 41.9 + - + +
85A LYS 3.3 0.6 - - - -
86A ASP* 1.3 83.7 - - - +
88A ILE* 1.3 64.9 + - - +
89A PHE* 3.6 15.4 + - + -
90A TYR* 3.1 17.0 + - - +
91A ARG* 3.2 26.7 + - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 4.0 11.7 - - + +
87A THR* 1.3 73.1 - - - +
89A PHE* 1.3 93.0 + - + +
91A ARG* 3.6 24.9 - - - +
92A ALA* 3.0 30.7 + - - +
95A ARG* 5.1 1.0 + - - -
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.8 22.9 - - + -
79A CYS* 3.2 16.5 - - - -
83A ASN* 3.6 32.8 - - - +
87A THR* 3.1 13.2 - - + +
88A ILE* 1.3 100.8 - - + +
90A TYR* 1.3 65.2 + - - +
92A ALA* 3.3 7.0 + - - +
93A ALA 3.0 18.2 + - - -
12B ALY 3.5 41.1 - - + -
13B GLY 3.8 26.5 - - - -
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A CYS* 4.5 6.7 - - - -
80A LEU* 3.7 30.4 - - + +
83A ASN* 3.5 21.4 - - + +
84A ALA 3.2 17.3 - - - +
85A LYS* 3.3 38.3 - - + +
87A THR* 3.1 7.5 + - - +
89A PHE* 1.3 78.2 - - - +
91A ARG* 1.3 66.3 - - + +
93A ALA* 3.1 5.4 + - - +
94A VAL* 3.0 43.4 + - + +
8B LYS* 3.8 16.2 - - - -
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS 4.3 9.2 - - - +
86A ASP* 3.0 34.6 + - - +
87A THR 3.2 12.7 + - - +
88A ILE* 3.6 34.7 - - - +
90A TYR* 1.3 82.9 - - + +
92A ALA* 1.3 61.7 + - - +
94A VAL* 3.3 8.1 + - - +
95A ARG* 3.1 39.7 + - - +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 5.5 1.3 - - - +
27A ILE* 3.5 23.8 - - + -
28A PHE* 4.1 14.2 - - + -
88A ILE 3.0 19.3 + - - +
89A PHE 3.5 4.3 - - - +
91A ARG* 1.3 77.9 - - - +
93A ALA* 1.3 57.8 + - - +
95A ARG* 3.3 24.6 + - - +
96A LEU* 2.8 30.1 + - - +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.8 9.3 - - + -
76A VAL* 3.6 15.3 - - + +
79A CYS* 3.8 25.1 - - + -
80A LEU* 3.7 17.0 - - + -
89A PHE 3.0 13.5 + - - +
90A TYR 3.1 8.0 + - - +
92A ALA* 1.3 73.0 - - - +
94A VAL* 1.3 62.3 + - - +
96A LEU* 3.9 3.5 - - - -
97A ARG* 2.9 31.0 + - - +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.7 18.4 - - + -
90A TYR* 3.0 38.1 + - + +
91A ARG* 3.3 9.6 + - - +
93A ALA* 1.3 79.0 - - - +
95A ARG* 1.3 64.9 + - + +
97A ARG* 3.4 7.5 + - - +
98A GLU* 3.4 21.3 + - - +
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Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 5.1 9.3 + - - -
27A ILE* 5.6 1.2 - - - +
88A ILE 5.1 0.8 + - - -
91A ARG* 3.1 31.4 + - - +
92A ALA* 3.6 29.1 - - - +
94A VAL* 1.3 80.3 - - + +
96A LEU* 1.3 57.7 + - - +
98A GLU* 3.1 7.0 + - - +
99A GLN* 2.9 47.0 + - + +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU 3.9 10.8 - - - +
22A LYS* 3.8 29.6 - - + +
23A ASP* 4.5 7.4 - - + +
28A PHE* 3.5 35.2 - - + -
50A PHE* 4.2 8.3 - - + -
72A PHE* 3.7 30.9 - - + -
75A ILE* 4.5 2.5 - - + -
76A VAL* 4.0 10.5 - - + -
92A ALA 2.8 18.3 + - - +
93A ALA* 3.9 5.6 - - - +
95A ARG* 1.3 73.2 - - - +
97A ARG* 1.3 59.3 + - - +
99A GLN* 4.8 3.1 - - - -
100A GLY* 2.7 36.5 + - - +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 5.2 2.9 - - - -
73A ASN* 5.2 1.4 + - - +
76A VAL* 3.7 24.5 - - + +
77A SER* 4.2 17.2 - - - +
80A LEU* 3.4 32.5 - - + +
93A ALA 2.9 19.0 + - - +
94A VAL* 3.6 7.2 - - - +
96A LEU* 1.3 74.8 - - - +
98A GLU* 1.3 59.5 + - - +
101A GLY* 3.0 25.9 + - - +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 3.4 10.7 + - - +
95A ARG* 3.1 9.9 + - - +
97A ARG* 1.3 83.7 - - + +
99A GLN* 1.3 63.5 + - + +
101A GLY* 3.9 0.5 - - - -
102A ALA* 3.3 19.9 + - - +
105A ARG* 5.4 1.4 + - - -
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Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.9 49.8 - - + +
95A ARG* 2.9 33.3 + - + +
96A LEU* 4.5 1.4 + - - +
98A GLU* 1.3 75.7 - - + +
100A GLY* 1.3 66.0 + - - +
102A ALA* 3.3 8.8 + - - +
103A VAL* 3.3 23.8 + - - +
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 21.3 - - - +
22A LYS* 5.1 1.1 - - - -
72A PHE* 4.0 10.8 - - - -
96A LEU* 2.7 28.5 + - - +
99A GLN* 1.3 71.0 - - - +
101A GLY* 1.3 57.9 + - - +
103A VAL* 3.1 5.5 + - - +
104A LEU* 2.9 32.7 + - - +
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 4.7 1.9 - - - -
97A ARG* 3.0 21.9 + - - +
98A GLU* 3.9 1.8 - - - -
99A GLN 3.2 0.2 - - - -
100A GLY* 1.3 76.3 - - - +
102A ALA* 1.3 55.6 + - - +
104A LEU* 3.4 8.8 + - - +
105A ARG* 3.0 39.1 + - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU 3.3 10.6 + - - +
99A GLN* 3.3 11.3 + - - +
100A GLY 3.3 0.2 - - - -
101A GLY* 1.3 72.4 - - - +
103A VAL* 1.3 66.0 + - + +
105A ARG* 3.4 30.5 + - - +
106A GLN* 3.2 23.1 + - - +
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 3.9 24.9 - - + +
18A GLN* 3.9 30.7 - - + +
19A LEU* 3.8 23.1 - - + -
22A LYS* 4.1 21.5 - - + -
99A GLN 3.3 13.2 + - - +
100A GLY* 3.1 8.7 + - - +
102A ALA* 1.3 78.4 - - + +
104A LEU* 1.3 57.5 + - - +
106A GLN* 3.2 10.0 + - - +
107A ALA* 2.9 26.4 + - + +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 4.1 8.1 - - + -
19A LEU* 4.3 7.2 - - + -
65A PHE* 3.8 23.2 - - + -
68A PHE* 3.9 22.4 - - + -
69A GLU* 3.8 31.3 - - + +
72A PHE* 3.4 36.6 - - + -
73A ASN* 4.4 9.0 - - - +
100A GLY 2.9 15.9 + - - +
101A GLY* 3.9 6.7 - - - +
102A ALA 3.3 0.2 - - - -
103A VAL* 1.3 73.2 - - - +
105A ARG* 1.3 60.0 + - - +
107A ALA* 4.3 1.8 - - - -
108A ARG* 2.8 32.2 + - - +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU 5.4 1.4 + - - -
101A GLY* 3.0 30.7 + - - +
102A ALA* 3.5 30.2 + - - +
104A LEU* 1.3 76.0 - - - +
106A GLN* 1.3 62.4 + - - +
108A ARG* 3.6 5.2 + - - +
109A ARG* 3.2 32.9 + - + +
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN* 4.8 11.2 + - - +
102A ALA 3.2 10.9 + - - +
103A VAL* 3.6 10.7 - - - +
105A ARG* 1.3 79.8 - - - +
107A ALA* 1.3 63.3 + - - +
109A ARG* 3.2 12.2 + - + +
110A GLN* 3.1 28.1 + - + +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.8 7.7 - - + +
15A THR* 3.3 31.9 - - + +
65A PHE* 3.6 20.4 - - + -
103A VAL* 2.9 17.2 + - + +
104A LEU* 3.9 0.9 - - - +
105A ARG 3.3 0.2 - - - -
106A GLN* 1.3 74.9 - - - +
108A ARG* 1.3 59.4 + - - +
110A GLN* 3.0 10.6 + - - +
111A ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PHE* 3.6 27.3 - - + +
66A ASP* 3.0 32.5 + - - -
69A GLU* 2.8 37.5 + - - +
104A LEU 2.8 18.3 + - - +
105A ARG* 3.8 7.0 - - - +
106A GLN 3.3 0.2 - - - -
107A ALA* 1.3 76.3 - - - +
109A ARG* 1.3 57.1 + - + +
111A ALA* 3.2 3.8 + - - +
112A GLU* 2.9 47.4 + - + +
116A ILE* 4.6 13.8 - - + +
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Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 3.2 19.0 + - + +
106A GLN* 3.5 13.2 - - + +
107A ALA 3.2 0.4 - - - -
108A ARG* 1.3 78.7 - - + +
110A GLN* 1.3 63.8 + - - +
112A GLU* 3.5 20.2 + - - +
113A LYS* 3.4 25.2 + - - +
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Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.9 24.2 - - + +
106A GLN* 3.1 22.9 + - + +
107A ALA* 3.0 11.0 + - - +
109A ARG* 1.3 76.3 - - - +
111A ALA* 1.3 60.9 + - - +
113A LYS* 3.0 30.6 + - - +
114A MET* 3.3 23.4 + - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.3 2.7 - - + -
11A LEU* 3.6 17.6 - - + +
65A PHE* 4.1 16.6 - - + -
107A ALA 2.9 12.1 + - - +
108A ARG 3.2 8.5 + - - +
110A GLN* 1.3 76.0 - - - +
112A GLU* 1.3 63.0 + - - +
114A MET* 3.1 20.3 + - - +
116A ILE* 3.3 41.2 + - + +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 2.9 39.8 + - + +
109A ARG* 3.6 21.9 - - - +
110A GLN 3.2 0.2 - - - -
111A ALA* 1.3 79.0 - - - +
113A LYS* 1.3 63.6 + - + +
114A MET 3.3 6.8 + - - +
116A ILE* 3.9 23.3 - - + +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ARG* 3.4 13.9 + - - +
110A GLN* 3.0 22.4 + - - +
112A GLU* 1.3 80.6 - - + +
114A MET* 1.3 62.9 + - + +
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Residues in contact with MET 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLN 5.2 7.2 - - - +
7A PRO* 3.6 39.7 - - + +
8A PHE* 3.9 19.5 - - + -
11A LEU* 3.7 33.4 - - + -
110A GLN* 3.5 20.2 - - + +
111A ALA* 3.1 8.7 + - - +
112A GLU 3.1 6.4 - - - +
113A LYS* 1.3 84.0 - - + +
115A GLY* 1.3 62.0 + - - +
116A ILE* 3.8 2.5 - - + +
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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