Contacts of the helix formed by residues 86 - 114 (chain D) in PDB entry 2ACZ
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 PRO 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D VAL* 3.6 9.3 - - + +
85D LYS* 1.3 91.4 - - + +
87D LEU* 1.3 66.1 + - - +
88D ALA* 3.4 1.8 - - + +
89D LEU* 3.2 20.5 + - + +
90D ARG* 3.2 19.9 + - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LYS 3.1 5.6 + - - +
86D PRO* 1.3 72.2 - - - +
88D ALA* 1.3 64.7 + - - +
90D ARG* 3.4 33.8 + - - +
91D LEU* 3.1 45.8 + - + +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PRO* 3.4 1.9 - - + -
87D LEU* 1.3 80.3 - - - +
89D LEU* 1.3 63.7 + - - +
91D LEU* 3.7 6.2 + - - +
92D MET* 3.4 19.6 + - - +
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D VAL* 3.7 18.4 - - + -
86D PRO* 3.2 24.5 + - + +
88D ALA* 1.3 78.8 - - - +
90D ARG* 1.3 62.9 + - - +
92D MET* 3.3 21.1 + - + +
93D LEU* 3.1 35.5 + - + +
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Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASN* 5.4 2.4 + - - -
6D SER* 4.7 9.1 + - - -
77D TRP* 5.5 0.6 - - - +
80D LEU* 3.2 49.4 - - + -
81D THR* 4.0 10.3 + - - +
84D VAL* 3.3 28.2 + - + +
85D LYS* 3.9 6.9 + - - +
86D PRO 3.2 3.7 + - - +
87D LEU* 3.5 39.7 - - - +
88D ALA 3.3 0.4 - - - -
89D LEU* 1.3 77.0 - - - +
91D LEU* 1.3 74.1 + - - +
93D LEU* 2.8 7.8 + - - +
94D GLN* 2.8 37.0 + - - +
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D SER* 4.5 8.3 - - - -
87D LEU* 3.1 41.7 + - + +
88D ALA* 4.2 5.8 - - - +
90D ARG* 1.3 83.1 - - - +
92D MET* 1.3 57.2 + - - +
94D GLN* 3.4 23.5 + - - +
95D LEU* 2.9 29.7 + - - +
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Residues in contact with MET 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ALA 3.4 10.9 + - - +
89D LEU* 3.3 21.9 + - + +
90D ARG 3.1 0.4 - - - -
91D LEU* 1.3 78.0 - - - +
93D LEU* 1.3 72.2 + - + +
95D LEU* 3.3 11.1 + - + +
96D VAL* 2.9 56.2 + - + +
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 3.6 34.3 - - + -
84D VAL* 4.2 11.9 - - + -
89D LEU* 3.1 35.5 + - + +
90D ARG 2.8 8.5 + - - +
92D MET* 1.3 88.5 - - + +
94D GLN* 1.3 66.2 + - - +
96D VAL* 3.1 8.2 + - + +
97D ILE* 2.8 31.6 + - + +
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Residues in contact with GLN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D SER* 2.8 35.4 - - - +
73D TRP* 6.2 1.6 - - + +
76D MET 5.9 0.2 - - - -
77D TRP* 3.1 32.6 + - + -
80D LEU* 3.6 19.7 - - + +
81D THR* 4.7 0.2 + - - -
90D ARG* 2.8 37.3 + - - +
91D LEU* 3.7 23.1 - - - +
93D LEU* 1.3 72.0 - - - +
95D LEU* 1.3 58.5 + - - +
97D ILE* 3.6 5.6 - - + +
98D VAL* 2.8 44.5 + - + +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU 2.9 14.5 + - - +
92D MET* 3.4 14.8 - - + +
93D LEU 3.1 0.2 - - - -
94D GLN* 1.3 77.4 - - - +
96D VAL* 1.3 61.6 + - + +
98D VAL* 4.7 4.9 - - + -
99D VAL* 2.8 48.9 + - + +
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D MET* 2.9 49.2 + - + +
93D LEU* 3.6 9.0 - - + +
95D LEU* 1.3 77.4 - - + +
97D ILE* 1.3 59.4 + - + +
99D VAL* 3.3 5.8 + - - +
100D ALA* 2.9 31.3 + - + +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 4.0 24.4 - - + -
73D TRP* 5.2 3.1 - - - +
76D MET* 3.7 49.1 - - + -
80D LEU* 3.9 25.1 - - + -
93D LEU* 2.8 17.8 + - + +
94D GLN* 3.6 6.3 - - - +
96D VAL* 1.3 78.8 - - + +
98D VAL* 1.3 60.0 + - + +
100D ALA* 3.0 10.1 - - - +
101D LEU* 2.9 41.4 + - + +
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 5.4 0.2 - - + -
73D TRP* 4.1 54.5 - - + +
94D GLN* 2.8 32.2 + - + +
95D LEU* 4.1 6.1 - - + +
97D ILE* 1.3 72.7 - - + +
99D VAL* 1.3 69.7 + - + +
100D ALA 3.0 1.1 - - - -
101D LEU* 3.2 6.9 + - - +
102D VAL* 2.9 33.9 + - + +
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LEU* 2.8 43.3 + - + +
96D VAL* 3.7 5.2 - - - +
98D VAL* 1.3 78.1 - - + +
100D ALA* 1.3 62.6 + - - +
102D VAL* 3.8 6.6 - - + +
103D VAL* 3.1 35.5 + - + +
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Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C PHE* 4.0 19.1 - - + -
96D VAL* 2.9 16.7 + - + +
97D ILE* 3.0 13.9 - - - +
98D VAL 3.0 0.4 - - - -
99D VAL* 1.3 77.8 - - - +
101D LEU* 1.3 54.6 + - - +
103D VAL* 3.2 7.8 + - - +
104D TYR* 2.9 43.3 + - + +
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 3.5 28.9 - - + -
65D LEU 5.2 0.2 - - - +
68D ILE* 4.4 6.1 - - + -
69D LEU* 3.5 34.0 + - + +
72D ALA* 3.8 13.0 - - + -
73D TRP* 3.4 38.4 - - + +
97D ILE* 2.9 25.1 + - + +
98D VAL* 3.7 9.2 - - - +
100D ALA* 1.3 73.1 - - - +
102D VAL* 1.3 68.4 + - - +
104D TYR* 3.2 27.7 + - + +
105D VAL* 3.3 15.9 + - - +
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Residues in contact with VAL 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 4.8 17.7 - - + -
73D TRP* 6.0 0.9 - - + -
98D VAL* 2.9 31.6 + - + +
99D VAL* 3.8 7.4 - - + +
101D LEU* 1.3 74.9 - - - +
103D VAL* 1.3 68.8 + - + +
105D VAL* 2.9 19.9 + - + +
106D ILE* 3.0 37.8 + - + -
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL* 3.1 30.0 + - + +
100D ALA* 3.2 7.2 + - - +
102D VAL* 1.3 83.3 - - + +
104D TYR* 1.3 67.0 + - + +
106D ILE* 4.4 9.4 - - + +
107D TYR* 2.8 33.9 + - + +
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Residues in contact with TYR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C PHE* 3.1 39.0 + + - -
39C VAL* 4.0 5.4 + - - -
41C VAL* 3.7 18.2 - - + -
42C GLY* 3.4 28.2 + - - -
45C LEU* 3.4 32.2 - - + +
65D LEU* 3.9 9.9 - - + +
68D ILE* 5.2 5.4 - - + -
100D ALA* 2.9 24.0 + - + +
101D LEU* 3.4 35.0 - - + +
102D VAL 3.1 0.4 + - - -
103D VAL* 1.3 79.7 - - + +
105D VAL* 1.3 59.4 + - + +
107D TYR* 3.8 1.2 - - - -
108D GLY* 2.9 24.6 + - - -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU* 4.3 2.6 - - + +
65D LEU* 3.4 44.2 - - + +
66D PHE* 3.8 17.5 - - + +
69D LEU* 4.4 13.2 - - + -
101D LEU 3.7 11.9 - - - +
102D VAL* 2.9 8.3 + - + +
104D TYR* 1.3 80.6 - - + +
106D ILE* 1.3 61.0 + - + +
108D GLY* 2.9 14.9 + - - -
109D PHE* 3.0 37.9 + - + -
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D VAL* 3.0 41.7 + - + +
103D VAL* 4.0 9.0 - - + +
105D VAL* 1.3 77.0 - - + +
107D TYR* 1.3 67.3 + - - +
109D PHE* 3.1 13.8 + - + +
110D VAL* 3.0 28.9 + - + +
113D TRP* 5.2 0.8 - - + -
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 3.3 42.6 + - + -
46C TRP* 4.3 8.9 + + - -
49C GLY* 3.2 24.8 - - - -
103D VAL* 2.8 30.6 + - + +
104D TYR* 3.9 1.3 - - - +
106D ILE* 1.3 76.1 - - - +
108D GLY* 1.3 58.1 + - - +
110D VAL* 3.2 16.6 + - + -
111D VAL* 2.8 49.1 + - + +
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Residues in contact with GLY 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 4.9 7.2 - - - -
61D THR* 6.1 0.4 - - - -
62D LEU* 3.5 7.2 - - - -
65D LEU* 3.6 17.5 - - - -
104D TYR 2.9 16.4 + - - -
105D VAL 2.9 6.6 + - - -
107D TYR* 1.3 79.0 - - - +
109D PHE* 1.3 62.5 + - - +
111D VAL* 3.2 4.5 + - - +
112D VAL* 3.0 27.0 + - - +
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LEU* 3.5 35.9 - - + +
105D VAL* 3.0 52.7 + - + -
106D ILE* 3.1 12.1 + - + +
108D GLY* 1.3 73.9 - - - +
110D VAL* 1.3 64.7 + - - +
112D VAL* 3.1 1.8 + - - +
113D TRP* 2.9 56.3 + + + -
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ILE* 3.0 21.6 + - + +
107D TYR* 3.6 22.2 - - + +
109D PHE* 1.3 80.3 - - - +
111D VAL* 1.3 62.3 + - - +
113D TRP* 3.4 41.5 + - + +
114D GLY* 3.5 9.0 + - - -
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 4.9 3.4 - - + +
48C LEU* 4.4 20.4 - - + +
49C GLY* 4.0 8.5 - - - +
52C LEU* 3.9 26.7 - - + -
107D TYR* 2.8 61.9 + - + +
108D GLY* 3.6 6.3 - - - +
110D VAL* 1.3 73.5 - - + +
112D VAL* 1.3 66.9 + - + +
114D GLY* 3.4 6.1 + - - -
115D VAL* 3.2 19.6 - - - +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 6.4 0.9 - - + -
52C LEU* 6.0 0.7 - - - -
52D PHE* 5.4 10.3 - - + -
58D LYS* 3.4 53.7 + - + -
61D THR* 4.7 13.0 - - + -
62D LEU* 4.3 24.2 - - + -
108D GLY 3.0 18.7 + - - +
109D PHE* 3.7 4.9 - - - +
111D VAL* 1.3 79.5 - - + +
113D TRP* 1.3 66.1 + - + +
114D GLY 3.0 4.5 - - - -
115D VAL* 3.0 21.0 + - - +
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Residues in contact with TRP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D LYS* 4.5 7.5 + - - +
106D ILE* 6.3 0.7 - - + -
109D PHE* 2.9 48.7 + + + -
110D VAL* 3.4 44.9 + - + +
112D VAL* 1.3 77.3 - - + +
114D GLY* 1.3 67.7 + - - +
115D VAL 3.1 6.5 + - - +
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Residues in contact with GLY 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU 5.2 2.4 - - - +
110D VAL 3.5 4.9 + - - -
111D VAL 3.4 6.6 + - - -
112D VAL 3.0 1.6 - - - -
113D TRP* 1.3 88.9 - - - +
115D VAL* 1.3 65.8 + - - +
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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