Contacts of the helix formed by residues 94 - 119 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75O LYS 2.9 19.7 + - - +
76O LEU* 2.5 49.6 + - - +
77O ILE* 4.2 3.4 - - - -
78O TYR* 4.0 20.5 - - - +
92O GLY 3.1 2.6 + - - -
93O LEU* 1.3 74.4 - - - +
95O THR* 1.3 66.4 + - - +
96O SER* 3.5 6.2 + - - +
97O GLY 2.9 10.9 + - - +
98O ILE* 2.9 28.2 + - - +
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Residues in contact with THR 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O THR* 1.3 78.1 + - - +
96O SER* 1.3 59.5 + - - +
98O ILE* 3.2 17.9 + - + +
99O LYS* 2.9 26.1 + - + +
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Residues in contact with SER 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O PHE* 5.7 0.3 - - - -
75O LYS* 3.4 20.6 + - - +
76O LEU* 4.3 11.4 - - - -
94O THR* 3.5 7.0 + - - +
95O THR* 1.3 74.6 - - - +
97O GLY* 1.3 55.4 + - - +
99O LYS* 3.0 9.8 + - - +
100O LEU* 2.6 38.7 + - - +
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Residues in contact with GLY 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LEU* 4.8 1.7 - - - +
76O LEU* 3.6 24.0 - - - +
93O LEU* 3.7 10.8 - - - -
94O THR* 2.9 13.4 + - - +
96O SER* 1.3 80.5 - - - +
98O ILE* 1.3 55.3 + - - +
100O LEU* 3.3 6.8 + - - +
101O VAL* 2.7 39.2 + - - +
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Residues in contact with ILE 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O TYR* 3.7 21.5 - - + +
44O GLN* 5.8 0.7 - - - +
93O LEU* 3.7 24.7 - - + +
94O THR 2.9 21.5 + - - +
95O THR* 3.5 17.0 - - + +
97O GLY* 1.3 77.0 - - - +
99O LYS* 1.3 57.5 + - - +
101O VAL* 3.2 3.4 + - - +
102O GLU* 2.5 50.6 + - - +
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Residues in contact with LYS 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G C 4.6 17.6 + - - -
20G T 5.9 1.0 + - - -
27O PHE* 5.2 10.5 - - + -
95O THR* 2.9 15.0 + - + +
96O SER* 3.2 13.2 - - - +
98O ILE* 1.3 77.2 - - - +
100O LEU* 1.3 63.3 + - - +
102O GLU* 3.3 13.9 + - + +
103O ALA* 3.0 25.1 + - - +
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Residues in contact with LEU 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O PHE* 3.5 48.4 - - + +
29O ILE* 3.7 17.5 - - + -
34O GLY* 5.9 1.1 - - - +
37O LEU* 4.0 13.9 - - + -
76O LEU* 3.7 36.8 - - + -
96O SER 2.6 20.0 + - - +
97O GLY* 3.6 5.6 - - - +
99O LYS* 1.3 70.1 - - - +
101O VAL* 1.3 69.8 + - + +
103O ALA* 3.0 14.1 + - - +
104O PHE* 3.2 41.5 + - + -
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Residues in contact with VAL 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LEU* 3.9 24.5 - - + +
38O GLY* 4.3 11.9 - - - +
41O TYR* 3.5 42.2 - - + -
93O LEU* 4.0 5.6 - - + -
97O GLY 2.7 27.7 + - - +
98O ILE 3.6 0.4 - - - +
100O LEU* 1.3 80.1 - - + +
102O GLU* 1.3 65.1 + - - +
104O PHE* 3.1 11.3 + - + +
105O THR* 3.0 25.6 + - - +
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Residues in contact with GLU 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O TYR* 3.1 25.2 + - + +
98O ILE* 2.5 46.7 + - + +
99O LYS* 3.5 13.9 - - + +
101O VAL* 1.3 76.4 - - - +
103O ALA* 1.3 64.0 + - - +
105O THR* 2.9 20.2 + - - +
106O SER* 3.0 15.3 + - - -
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Residues in contact with ALA 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O LYS* 4.2 11.2 + - - +
27O PHE* 3.8 28.5 - - + -
99O LYS* 3.0 16.4 + - + +
100O LEU 3.0 12.0 + - - +
102O GLU* 1.3 75.5 - - - +
104O PHE* 1.3 57.1 + - + +
106O SER* 2.6 25.4 + - - -
107O ILE* 3.1 14.1 - - - +
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Residues in contact with PHE 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O ALA* 3.8 16.2 - - + -
23O LYS* 3.4 37.7 - - + -
24O LEU* 3.7 30.3 - - + -
27O PHE* 4.7 4.3 - + - -
29O ILE* 4.0 6.3 - - + -
34O GLY* 6.1 0.7 - - - -
100O LEU* 3.2 45.5 + - + -
101O VAL* 3.1 10.2 + - + +
103O ALA* 1.3 81.4 - - + +
105O THR* 1.3 66.4 + - - +
106O SER 3.1 0.2 - - - -
107O ILE* 3.0 16.8 + - + +
108O PHE* 3.1 39.2 + + + -
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Residues in contact with THR 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O TYR* 5.9 3.3 - - - -
101O VAL* 3.0 19.8 + - - +
102O GLU* 2.9 15.7 + - - -
104O PHE* 1.3 71.6 - - - +
106O SER* 1.3 54.6 + - - +
108O PHE* 3.4 7.2 + - - +
109O ASP* 2.6 44.5 + - + +
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Residues in contact with SER 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O GLU 3.0 9.7 + - - -
103O ALA* 2.6 18.3 + - - -
105O THR* 1.3 77.4 - - - +
107O ILE* 1.3 73.0 + - - +
109O ASP* 2.9 6.4 + - - -
110O GLU* 2.4 40.4 + - - +
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Residues in contact with ILE 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O LYS* 4.2 32.3 - - + +
20O ALA* 5.5 0.9 - - - -
23O LYS* 3.6 34.3 - - + +
103O ALA 3.1 15.7 - - - +
104O PHE* 3.0 13.2 + - + +
106O SER* 1.3 85.2 + - - +
108O PHE* 1.3 67.0 + - + +
110O GLU* 3.7 8.0 + - + +
111O MET* 3.2 29.0 + - + +
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Residues in contact with PHE 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O MET* 5.3 9.6 - - + -
19O LYS* 6.4 0.4 - - + -
20O ALA* 4.3 28.7 - - + -
104O PHE* 3.1 38.5 + + + -
105O THR* 3.7 7.2 - - - +
107O ILE* 1.3 80.5 - - + +
109O ASP* 1.3 61.2 + - - +
110O GLU 3.1 1.6 - - - -
111O MET* 2.8 36.5 + - - +
112O GLU* 3.3 8.7 + - - +
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Residues in contact with ASP 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105O THR* 2.6 32.0 + - + +
106O SER* 3.5 6.5 - - - +
108O PHE* 1.3 72.6 - - - +
110O GLU* 1.3 59.2 + - - +
111O MET 3.6 0.2 + - - -
112O GLU* 4.0 4.0 + - - +
113O GLN* 3.8 19.2 + - - +
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Residues in contact with GLU 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O SER* 2.4 27.3 + - - +
107O ILE* 3.8 9.2 - - + +
109O ASP* 1.3 74.9 - - - +
111O MET* 1.3 58.4 + - - +
113O GLN* 3.4 5.6 + - - +
114O THR* 2.8 32.6 + - - -
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Residues in contact with MET 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O GLU* 4.5 3.4 - - + +
16O MET* 3.5 56.1 - - + +
19O LYS* 3.5 32.5 - - + -
107O ILE* 3.2 18.4 + - + +
108O PHE* 2.8 24.2 + - + +
110O GLU* 1.3 78.9 - - - +
112O GLU* 1.3 56.4 + - - +
114O THR* 3.4 6.5 + - - -
115O LEU* 3.0 27.4 + - - +
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Residues in contact with GLU 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M SER* 5.3 14.1 - - - +
108O PHE 3.3 8.8 + - - +
109O ASP* 4.6 4.9 - - - +
110O GLU 3.4 0.2 - - - -
111O MET* 1.3 79.5 - - - +
113O GLN* 1.3 58.1 + - - +
115O LEU* 3.2 6.9 + - - +
116O VAL* 3.0 29.3 + - - +
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Residues in contact with GLN 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O ASP 3.8 12.9 + - - +
110O GLU* 3.4 9.1 + - - +
111O MET 3.3 0.4 - - - -
112O GLU* 1.3 77.8 - - - +
114O THR* 1.3 61.7 + - - +
116O VAL* 3.7 6.4 + - - +
117O SER* 3.2 23.9 + - - -
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Residues in contact with THR 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137M SER* 5.3 2.6 - - - -
110O GLU 2.8 19.7 + - - -
111O MET* 3.9 7.0 - - - -
112O GLU 3.3 0.2 - - - -
113O GLN* 1.3 76.2 - - - +
115O LEU* 1.3 59.2 + - - +
117O SER* 4.1 6.5 - - - -
118O GLN* 3.4 19.8 + - - +
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Residues in contact with LEU 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134M MET* 4.2 24.3 - - + +
111O MET 3.0 17.6 + - - +
112O GLU* 3.5 8.5 - - - +
113O GLN 3.2 0.4 - - - -
114O THR* 1.3 74.9 - - - +
116O VAL* 1.3 64.6 + - - +
117O SER 3.2 1.6 - - - -
118O GLN* 3.0 17.4 + - - +
119O LEU* 3.0 12.1 + - - +
124O ASN* 5.9 0.2 - - - +
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Residues in contact with VAL 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O GLU 3.0 16.5 + - - +
113O GLN* 4.1 6.7 - - - +
115O LEU* 1.3 74.7 - - - +
117O SER* 1.3 60.5 + - - +
119O LEU 2.7 26.0 - - - +
120O SER* 4.0 3.1 + - - -
121O GLU* 4.3 10.8 + - + +
124O ASN* 5.0 9.6 - - + -
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Residues in contact with SER 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O GLN 3.2 16.6 + - - -
114O THR* 4.1 6.5 - - - -
115O LEU 3.2 0.2 - - - -
116O VAL* 1.3 79.8 - - - +
118O GLN* 1.3 62.8 + - - +
119O LEU* 3.4 2.1 + - - -
120O SER* 4.8 1.2 + - - -
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Residues in contact with GLN 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133M LYS* 4.6 16.3 - - - +
134M MET* 4.8 8.3 - - - -
137M SER* 4.0 25.1 - - - -
114O THR 3.4 13.9 + - - +
115O LEU* 3.0 13.3 + - - +
117O SER* 1.3 80.2 - - - +
119O LEU* 1.3 58.4 + - - +
120O SER 4.3 0.4 + - - -
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Residues in contact with LEU 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M ASN* 5.0 11.7 - - + +
133M LYS* 5.0 9.2 - - + -
134M MET* 4.3 22.0 - - + -
115O LEU 3.0 8.8 + - - +
116O VAL* 2.7 20.8 - - - +
117O SER 4.5 0.4 - - - -
118O GLN* 1.3 79.3 - - - +
120O SER* 1.3 66.2 + - - +
123O GLU* 6.0 2.0 - - + -
124O ASN* 3.5 15.6 - - + +
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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
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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