Contacts of the helix formed by residues 94 - 119 (chain D) in PDB entry 4LLL
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 94 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LYS* 2.7 30.4 + - + +
76D LEU 3.1 11.7 + - - -
77D ILE 3.4 24.9 - - - +
78D TYR* 3.9 12.8 - - + +
92D GLY 3.7 0.2 + - - -
93D LEU* 1.3 77.3 - - - +
95D THR* 1.3 64.9 + - - +
96D SER* 2.9 15.0 + - - -
97D GLY 3.2 0.9 + - - -
98D ILE* 3.0 22.2 + - - +
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Residues in contact with THR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D THR* 1.3 74.2 - - - +
96D SER* 1.3 62.7 + - - +
98D ILE* 3.2 20.7 + - - +
99D LYS* 3.0 29.5 + - - +
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Residues in contact with SER 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D LYS 5.3 0.5 + - - -
75D LYS* 3.5 11.3 + - - +
76D LEU* 4.2 11.0 - - - +
94D THR* 2.9 12.8 + - - -
95D THR* 1.3 78.0 - - - +
97D GLY* 1.3 63.2 + - - +
99D LYS* 3.4 11.3 + - - +
100D LEU* 3.2 23.6 + - - +
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Residues in contact with GLY 97 (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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37D LEU* 5.0 1.0 - - - +
76D LEU* 3.4 36.3 - - - -
93D LEU* 4.0 9.3 - - - +
94D THR* 3.2 6.2 + - - -
95D THR 3.1 0.8 - - - -
96D SER* 1.3 80.3 + - - +
98D ILE* 1.3 63.1 + - - +
100D LEU* 3.4 5.4 - - - +
101D VAL* 3.1 25.5 + - - +
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Residues in contact with ILE 98 (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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41D TYR* 3.8 19.7 - - + -
44D GLN* 4.8 10.5 - - - +
93D LEU* 3.8 27.1 - - + +
94D THR 3.0 19.8 + - - +
95D THR* 3.2 13.0 + - - +
97D GLY* 1.3 71.7 - - - +
99D LYS* 1.3 60.6 + - + +
100D LEU 3.0 2.0 - - - -
101D VAL* 2.6 26.5 + - - +
102D GLU* 3.0 28.0 + - - +
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Residues in contact with LYS 99 (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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95D THR* 3.0 27.8 + - - +
96D SER* 3.4 9.6 + - - +
98D ILE* 1.3 77.4 - - + +
100D LEU* 1.3 63.8 + - - +
102D GLU* 3.1 17.6 + - - +
103D ALA* 3.0 24.0 + - - +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D PHE* 3.4 44.6 - - + +
29D ILE* 3.8 11.4 - - + -
37D LEU* 3.7 23.6 - - + -
76D LEU* 3.4 32.3 - - + -
96D SER 3.2 13.5 + - - +
97D GLY 3.4 8.5 - - - +
99D LYS* 1.3 78.2 - - - +
101D VAL* 1.3 62.0 + - - +
103D ALA* 3.2 5.0 + - - -
104D PHE* 2.9 36.3 + - + +
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 4.1 15.9 - - + -
38D GLY* 4.4 6.3 - - - -
41D TYR* 3.3 49.4 - - + -
93D LEU* 4.2 4.5 - - + -
97D GLY 3.1 18.8 - - - +
98D ILE 2.6 13.6 + - - +
100D LEU* 1.3 72.9 - - - +
102D GLU* 1.3 55.8 + - - +
104D PHE* 3.4 27.1 - - + -
105D THR* 2.9 42.8 + - - +
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Residues in contact with GLU 102 (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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41D TYR* 3.0 27.5 + - + +
98D ILE* 3.1 31.0 - - + +
99D LYS* 3.1 15.3 + - - +
101D VAL* 1.3 75.5 - - - +
103D ALA* 1.3 60.4 + - - +
105D THR* 3.1 22.1 - - - +
106D SER* 4.2 5.5 + - - -
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Residues in contact with ALA 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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27D PHE* 3.2 30.5 - - + -
99D LYS 3.0 16.2 + - - +
100D LEU* 3.8 4.7 - - - +
102D GLU* 1.3 79.7 - - - +
104D PHE* 1.3 58.4 + - - +
106D SER* 3.8 11.6 + - - -
107D ILE* 5.3 0.5 - - - +
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Residues in contact with PHE 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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24D LEU* 3.8 10.8 - - + -
27D PHE* 3.4 30.3 - - + -
29D ILE* 3.6 17.9 - - + -
34D GLY* 3.2 33.4 - - - -
37D LEU* 4.2 6.1 - - + -
38D GLY* 4.3 2.2 - - - -
100D LEU* 2.9 41.3 + - + +
101D VAL* 3.4 37.0 - - + -
103D ALA* 1.3 75.9 - - - +
105D THR* 1.3 73.1 + - - +
106D SER 2.8 7.9 + - - -
107D ILE* 2.9 22.9 + - - +
108D PHE* 3.6 22.5 + + - -
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Residues in contact with THR 105 (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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41D TYR* 6.3 1.6 - - + -
101D VAL* 2.9 29.4 + - + +
102D GLU* 3.1 21.1 - - - +
104D PHE* 1.3 86.7 - - - +
106D SER* 1.3 66.2 + - - +
107D ILE 3.4 0.2 + - - -
108D PHE* 3.5 15.5 + - - +
109D ASP* 3.2 25.4 + - - +
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Residues in contact with SER 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 GLU 4.2 6.8 + - - -
103D ALA* 3.8 14.2 + - - -
104D PHE 2.8 1.1 + - - -
105D THR* 1.3 78.4 - - - +
107D ILE* 1.3 66.3 + - - -
109D ASP* 2.9 21.5 + - - +
110D GLU* 3.1 13.5 + - - +
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Residues in contact with ILE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ALA* 4.8 11.0 - - - +
23D LYS* 3.5 54.7 - - + +
24D LEU* 3.7 20.0 - - + -
26D GLN* 5.1 1.8 - - - +
27D PHE* 3.6 29.4 - - + -
103D ALA 5.3 0.7 - - - +
104D PHE* 2.9 11.2 + - - +
106D SER* 1.3 78.2 - - - +
108D PHE* 1.3 67.6 + - + +
110D GLU* 3.7 6.2 + - - +
111D MET* 3.2 24.0 + - - +
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Residues in contact with PHE 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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6C SER* 5.7 2.0 - - - -
20D ALA* 4.2 13.5 - - + -
24D LEU* 3.7 28.9 - - + -
31D ASN* 4.2 3.4 - - + -
34D GLY 3.9 10.1 - - - -
35D HIS* 3.1 45.1 - + - -
104D PHE* 3.6 40.4 - + - -
105D THR* 3.5 11.4 + - - +
106D SER 3.1 0.2 - - - -
107D ILE* 1.3 82.6 - - + +
109D ASP* 1.3 67.0 + - - +
111D MET* 3.5 19.1 + - + +
112D GLU* 3.1 23.6 + - - +
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Residues in contact with ASP 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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105D THR* 3.2 26.7 + - - +
106D SER* 2.9 9.8 + - - +
108D PHE* 1.3 77.9 - - - +
110D GLU* 1.3 54.6 + - - +
112D GLU* 3.3 7.0 + - - +
113D GLN* 2.7 38.1 + - - +
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Residues in contact with GLU 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 SER 3.1 10.8 + - - +
107D ILE* 3.9 9.4 - - - +
109D ASP* 1.3 76.7 - - - +
111D MET* 1.3 53.3 + - - +
113D GLN* 3.1 5.5 + - - +
114D THR* 2.5 45.3 + - - +
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Residues in contact with MET 111 (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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6C SER* 5.2 9.9 - - - -
138C LEU* 4.9 14.8 - - + +
16D MET* 4.0 38.6 - - + +
19D LYS* 4.3 11.7 - - + -
20D ALA* 4.0 31.6 - - + -
23D LYS* 5.4 8.1 - - + -
35D HIS* 5.8 1.3 - - + +
107D ILE* 3.2 14.6 + - + +
108D PHE* 3.6 24.0 - - + +
109D ASP 3.3 0.2 - - - -
110D GLU* 1.3 76.8 - - - +
112D GLU* 1.3 60.9 - - - +
114D THR* 3.5 7.4 + - - -
115D LEU* 3.1 30.5 + - + +
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Residues in contact with GLU 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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3C PHE 5.0 0.3 - - - +
4C THR* 3.2 26.7 - - + +
5C TYR* 2.8 42.4 + - - +
6C SER* 4.0 3.3 + - - -
108D PHE 3.1 11.4 + - - +
109D ASP* 3.4 10.8 - - - +
111D MET* 1.3 78.0 - - - +
113D GLN* 1.3 54.7 + - + +
115D LEU* 2.9 9.9 + - - +
116D VAL* 2.7 56.2 + - + +
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Residues in contact with GLN 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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109D ASP 2.7 21.9 + - - +
110D GLU* 3.8 4.9 - - - +
112D GLU* 1.3 71.5 - - - +
114D THR* 1.3 63.0 + - - +
116D VAL* 3.9 10.4 - - - +
117D SER* 3.2 21.3 + - - -
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Residues in contact with THR 114 (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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137C SER* 4.8 23.3 + - - +
138C LEU* 5.9 2.0 - - + -
110D GLU* 2.5 30.7 + - - +
111D MET* 3.5 9.5 - - - -
113D GLN* 1.3 73.2 - - - +
115D LEU* 1.3 62.4 + - + +
117D SER* 2.6 26.7 + - - +
118D GLN* 4.0 1.4 + - - +
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Residues in contact with LEU 115 (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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5C TYR* 3.9 35.3 - - + -
6C SER 5.5 0.2 - - - +
9C PHE* 4.8 2.0 - - + -
134C MET* 3.9 40.7 - - + +
137C SER* 4.0 12.3 - - - +
138C LEU* 3.8 27.6 - - + -
16D MET* 3.9 27.1 - - - -
111D MET* 3.1 19.3 - - + +
112D GLU* 2.9 7.4 + - - +
114D THR* 1.3 75.5 - - + +
116D VAL* 1.3 65.6 + - - +
117D SER 3.0 2.3 + - - -
118D GLN* 3.5 14.9 + - - +
119D LEU* 4.2 3.6 + - - +
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Residues in contact with VAL 116 (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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5C TYR* 3.9 17.5 - - + -
112D GLU* 2.7 48.2 + - + +
113D GLN* 4.2 7.6 - - - +
115D LEU* 1.3 71.4 - - - +
117D SER* 1.3 64.5 + - - +
119D LEU* 3.0 26.0 + - - +
124D ASN* 4.8 13.7 - - + -
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Residues in contact with SER 117 (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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113D GLN 3.2 14.3 + - - -
114D THR* 2.6 23.5 + - - +
115D LEU 3.0 0.6 - - - -
116D VAL* 1.3 80.4 - - - +
118D GLN* 1.3 65.1 + - - +
119D LEU 3.4 4.5 + - - +
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Residues in contact with GLN 118 (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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133C LYS* 5.9 7.6 - - + -
134C MET* 5.6 8.3 - - + -
137C SER* 5.4 7.6 - - - +
114D THR 4.0 1.1 + - - +
115D LEU 3.5 9.5 + - - +
116D VAL 3.2 0.8 - - - -
117D SER* 1.3 86.6 + - - +
119D LEU* 1.3 60.1 + - - +
120D SER 4.0 0.7 + - - -
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Residues in contact with LEU 119 (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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5C TYR* 4.7 4.7 - - + +
134C MET* 6.5 0.4 - - - -
115D LEU 4.2 2.2 + - - +
116D VAL* 3.0 21.0 + - - +
117D SER 3.8 4.3 - - - +
118D GLN* 1.3 82.8 - - - +
120D SER* 1.3 61.6 + - - +
121D GLU 4.1 0.3 + - - -
123D GLU* 4.2 5.8 - - + -
124D ASN* 3.3 37.4 - - + +
127D MET* 6.2 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
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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) + - + + + + + -
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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