Contacts of the helix formed by residues 118 - 149 (chain O) in PDB entry 1NF6
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 ASP 118 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O ARG* 5.2 0.8 - - - +
9O LYS* 5.9 0.3 - - - -
12O VAL* 3.4 31.0 - - + +
66O ARG* 3.1 24.6 + - - -
70O LEU* 3.9 8.9 - - - +
113O CYS* 2.7 20.7 + - - +
116O GLN 4.3 3.8 - - - +
117O GLY* 1.3 72.8 - - - +
119O ILE* 1.3 57.6 + - - +
120O VAL* 3.7 1.9 + - - +
121O THR* 3.0 29.0 + - - -
122O ALA* 3.0 27.4 + - - +
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Residues in contact with ILE 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O CYS 5.7 0.4 - - - +
114O LYS* 6.0 5.2 - - + +
117O GLY* 3.7 15.4 + - - +
118O ASP* 1.3 71.4 + - - +
120O VAL* 1.3 62.8 + - + +
122O ALA* 3.2 7.7 + - + +
123O ARG* 2.8 47.9 + - + +
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Residues in contact with VAL 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O ARG* 3.9 34.8 - - - +
69O GLU* 5.1 2.5 - - - +
118O ASP* 3.5 1.2 + - - +
119O ILE* 1.3 78.2 - - + +
121O THR* 1.3 62.2 + - - +
123O ARG* 3.3 10.3 + - - +
124O LEU* 3.0 20.8 + - + +
127O ARG* 5.4 0.3 + - - -
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Residues in contact with THR 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O VAL* 3.4 23.9 - - + +
16O LEU* 3.6 27.6 - - + -
66O ARG* 2.5 33.1 + - + +
113O CYS* 3.5 11.4 - - - -
118O ASP* 3.0 24.6 + - - -
120O VAL* 1.3 74.1 - - - +
122O ALA* 1.3 66.6 + - - +
124O LEU* 3.1 8.3 + - + +
125O PHE* 3.1 22.9 + - + -
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Residues in contact with ALA 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O LEU* 4.1 21.8 - - + +
113O CYS* 3.8 20.8 - - + +
114O LYS* 4.7 6.7 - - + -
118O ASP 3.0 19.5 + - - +
119O ILE* 3.2 10.5 + - + +
121O THR* 1.3 78.1 - - - +
123O ARG* 1.3 62.1 + - + +
125O PHE* 3.1 5.5 + - - +
126O GLU* 3.0 28.7 + - - +
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Residues in contact with ARG 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O ILE* 2.8 32.7 + - + +
120O VAL* 3.3 11.9 + - - +
122O ALA* 1.3 73.9 - - + +
124O LEU* 1.3 60.0 + - - +
126O GLU* 2.5 49.5 + - - +
127O ARG* 3.0 82.8 + - - +
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Residues in contact with LEU 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O LEU* 4.4 4.5 - - + -
62O ASN* 3.9 37.5 - - + +
63O PHE* 3.9 19.5 - - + -
66O ARG* 3.9 22.2 - - + -
120O VAL* 3.0 13.7 + - + +
121O THR* 3.5 8.1 - - - +
122O ALA 3.1 0.2 - - - -
123O ARG* 1.3 75.4 - - - +
125O PHE* 1.3 63.5 + - - +
127O ARG* 3.7 10.7 + - + +
128O ILE* 3.2 43.5 + - + +
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Residues in contact with PHE 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O VAL* 4.0 10.3 - - + -
16O LEU* 3.9 18.8 - - + -
19O ALA* 3.5 24.5 - - + -
63O PHE* 3.3 30.1 - + - -
106O TYR* 3.7 37.9 - + + +
109O PHE* 3.8 19.7 - - + -
110O LEU* 4.2 18.8 - - + -
113O CYS* 4.0 19.3 - - - -
121O THR* 3.1 19.4 + - + -
122O ALA 3.1 7.5 + - - +
124O LEU* 1.3 75.0 - - - +
126O GLU* 1.3 60.9 + - - +
128O ILE* 3.6 1.9 - - - +
129O ILE* 2.8 38.8 + - + +
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Residues in contact with GLU 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O LEU* 4.0 31.1 - - + +
114O LYS* 5.0 6.9 + - - -
122O ALA* 3.0 15.8 + - - +
123O ARG* 2.5 52.3 + - - +
124O LEU 3.3 0.2 - - - -
125O PHE* 1.3 80.5 - - - +
127O ARG* 1.3 60.9 + - + +
129O ILE* 3.3 11.0 + - - +
130O GLU* 3.4 23.3 + - - +
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Residues in contact with ARG 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120O VAL 5.4 0.2 + - - -
123O ARG* 3.0 71.4 + - - +
124O LEU* 4.2 9.8 - - + +
126O GLU* 1.3 75.7 - - - +
128O ILE* 1.3 64.0 + - + +
130O GLU* 3.6 14.7 + - - +
131O GLU* 3.2 28.3 + - - +
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Residues in contact with ILE 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O HIS* 3.9 39.7 - - + +
62O ASN* 4.7 5.2 - - + +
63O PHE* 3.4 34.1 - - + -
106O TYR* 3.6 31.4 - - + -
124O LEU* 3.2 33.3 + - + +
125O PHE* 3.2 4.7 + - - +
127O ARG* 1.3 77.2 - - + +
129O ILE* 1.3 60.1 + - - +
131O GLU* 3.4 9.5 + - - +
132O GLU* 3.0 25.9 + - + +
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Residues in contact with ILE 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O ILE* 3.8 24.4 - - + +
106O TYR* 3.7 23.8 - - + +
107O SER* 3.6 32.8 - - - +
110O LEU* 3.9 23.8 - - + -
125O PHE 2.8 25.2 + - - +
126O GLU* 3.7 6.1 - - - +
127O ARG 3.3 0.4 - - - -
128O ILE* 1.3 75.8 - - - +
130O GLU* 1.3 62.2 + - + +
132O GLU* 3.1 9.5 + - - +
133O GLN* 2.9 28.7 + - + +
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Residues in contact with GLU 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126O GLU* 3.4 17.5 + - - +
127O ARG* 3.8 16.7 - - - +
129O ILE* 1.3 79.9 - - + +
131O GLU* 1.3 61.9 + - + +
133O GLN* 3.4 9.9 + - - +
134O ALA* 3.1 19.1 + - - +
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Residues in contact with GLU 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O ASP* 4.7 1.2 - - - -
58O ARG* 3.7 19.9 + - - -
59O HIS* 2.7 35.9 + - + +
127O ARG* 3.2 18.6 - - - +
128O ILE* 3.4 9.6 + - - +
129O ILE 3.2 0.4 - - - -
130O GLU* 1.3 76.5 - - + +
132O GLU* 1.3 55.1 + - - +
134O ALA* 2.8 28.5 + - - +
135O HIS* 3.0 19.0 + - + -
172P VAL* 3.8 29.6 - - + +
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Residues in contact with GLU 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O GLU* 4.0 5.3 - - - +
56O GLU* 4.2 1.2 - - - +
59O HIS* 3.3 19.3 - - - -
99O GLU* 3.1 15.4 - - - +
102O THR* 3.0 28.0 - - + +
103O ILE* 3.6 20.3 - - + +
106O TYR* 4.0 16.2 - - + -
128O ILE* 3.0 26.7 + - + +
129O ILE* 3.3 9.4 - - - +
131O GLU* 1.3 73.9 - - - +
133O GLN* 1.3 57.5 + - - +
135O HIS* 3.2 3.8 + - - -
136O LEU* 3.0 27.9 + - - +
200O FE 1.9 33.3 - - - -
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Residues in contact with GLN 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O ILE* 3.8 19.4 - - + +
129O ILE* 2.9 13.8 + - + +
130O GLU* 3.5 13.0 - - - +
132O GLU* 1.3 75.5 - - - +
134O ALA* 1.3 62.8 + - - +
136O LEU* 3.7 19.6 - - - +
137O THR* 3.0 43.3 + - - +
140O GLU* 5.7 1.6 + - - -
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Residues in contact with ALA 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130O GLU 3.1 11.1 + - - +
131O GLU* 2.8 13.4 + - - +
133O GLN* 1.3 77.2 - - - +
135O HIS* 1.3 60.0 + - + +
137O THR* 3.9 5.2 - - - -
138O TYR* 3.3 19.8 + - - +
171P PHE* 3.8 10.8 - - + -
172P VAL* 3.9 21.3 - - + -
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Residues in contact with HIS 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O ILE* 3.8 26.4 - - + +
55O ASP* 2.6 46.2 + - + +
56O GLU* 3.4 11.7 + - - -
59O HIS* 4.1 5.8 - + - -
99O GLU* 3.4 17.9 - - - +
131O GLU 3.0 11.7 + - - -
132O GLU* 3.2 7.1 + - - +
133O GLN 3.3 0.2 - - - -
134O ALA* 1.3 74.0 - - - +
136O LEU* 1.3 61.0 + - - +
138O TYR* 3.2 4.9 + - - +
139O TYR* 2.9 43.3 + - + -
200O FE 2.1 28.6 - - - -
171P PHE* 3.8 11.9 - + - -
172P VAL* 3.5 6.7 - - + +
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Residues in contact with LEU 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O ALA* 3.2 34.8 - - + +
99O GLU* 4.0 12.0 - - + +
100O ASP* 4.1 21.3 - - + +
103O ILE* 3.8 17.9 - - + -
132O GLU 3.0 16.7 + - - +
133O GLN* 3.6 25.1 - - - +
135O HIS* 1.3 74.4 - - - +
137O THR* 1.3 59.9 + - - +
139O TYR* 3.3 3.1 + - - +
140O GLU* 2.9 59.6 + - + +
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Residues in contact with THR 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133O GLN* 3.0 32.3 + - - +
134O ALA* 3.9 6.5 - - - -
136O LEU* 1.3 73.1 - - - +
138O TYR* 1.3 66.0 + - - +
140O GLU* 3.8 10.7 + - - +
141O ASN* 3.0 42.7 + - - +
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Residues in contact with TYR 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O GLU* 5.9 0.2 - - - +
45O LEU* 3.6 27.1 + - - +
48O ASN* 3.3 40.6 + - + +
49O MET* 5.3 1.6 - - + -
52O ILE* 3.6 24.2 - - + -
92O TYR* 4.3 5.7 + + - -
134O ALA 3.3 6.8 + - - +
135O HIS 3.2 7.7 + - - +
137O THR* 1.3 81.1 - - - +
139O TYR* 1.3 79.0 + + - +
141O ASN* 3.3 6.4 + - + +
142O ILE* 3.0 55.3 + - + +
171P PHE* 3.5 33.2 - + + -
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Residues in contact with TYR 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 3.7 11.2 - + - -
49O MET* 3.4 26.7 - - + -
52O ILE* 3.1 40.8 - - + +
92O TYR* 3.7 27.9 - + - +
95O ASP* 3.3 35.0 - - + -
96O ALA* 3.8 17.7 - - + +
99O GLU* 3.7 28.5 - - + -
135O HIS* 2.9 27.8 + - + +
136O LEU 3.8 3.8 - - - +
138O TYR* 1.3 86.2 - + - +
140O GLU* 1.3 57.2 + - - +
142O ILE* 3.6 1.7 + - - +
143O GLY* 2.9 25.8 + - - -
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Residues in contact with GLU 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O ALA* 4.1 17.7 - - + +
100O ASP* 5.9 0.2 - - - +
133O GLN* 5.7 1.2 + - - -
136O LEU* 2.9 42.4 + - + +
137O THR* 3.8 11.3 + - - +
139O TYR* 1.3 73.9 - - - +
141O ASN* 1.3 56.5 + - - +
143O GLY* 3.1 2.8 + - - -
144O SER* 2.7 36.7 + - - -
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Residues in contact with ASN 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137O THR* 3.0 39.8 + - - +
138O TYR* 3.7 6.5 - - + +
140O GLU* 1.3 76.6 - - - +
142O ILE* 1.3 66.9 + - + +
144O SER* 2.9 18.2 + - - -
145O HIS* 3.0 33.4 + - + +
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Residues in contact with ILE 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O LEU* 4.1 12.1 - - + -
92O TYR* 3.6 34.8 - - + -
138O TYR* 3.0 58.9 + - + +
139O TYR 3.9 0.2 - - - +
141O ASN* 1.3 78.3 - - + +
143O GLY* 1.3 62.6 + - - +
145O HIS* 3.3 9.3 + - + +
146O ILE* 3.1 37.3 + - + +
153O TYR* 3.5 22.8 - - + +
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Residues in contact with GLY 143 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O TYR* 4.0 17.0 - - - +
93O GLU* 5.6 0.7 - - - -
139O TYR 2.9 16.0 + - - -
140O GLU* 3.1 5.4 + - - -
142O ILE* 1.3 78.3 - - - +
144O SER* 1.3 60.6 + - - +
146O ILE* 3.6 3.9 + - - +
147O LYS* 3.3 23.6 + - - +
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Residues in contact with SER 144 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O GLU 2.7 17.3 + - - -
141O ASN* 2.9 12.3 + - - -
143O GLY* 1.3 74.5 - - - +
145O HIS* 1.3 69.5 + - - +
147O LYS* 3.2 5.6 + - - +
148O ASN* 2.9 41.3 + - - +
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Residues in contact with HIS 145 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141O ASN* 3.0 36.8 + - + +
142O ILE* 3.9 6.1 - - + +
144O SER* 1.3 79.4 - - - +
146O ILE* 1.3 58.7 + - - +
148O ASN* 4.7 2.8 + - - +
149O LEU* 2.7 50.7 + - + +
150O GLY 3.4 0.3 + - - -
153O TYR* 4.0 44.2 - + + +
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Residues in contact with ILE 146 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O LEU* 5.2 1.3 - - + -
88O VAL* 3.6 30.7 - - + +
89O PRO* 4.5 24.9 - - + -
92O TYR* 3.9 11.2 - - + -
142O ILE* 3.1 37.6 + - + +
143O GLY* 4.3 3.1 - - - +
145O HIS* 1.3 76.2 - - - +
147O LYS* 1.3 59.5 + - - +
150O GLY* 3.0 31.7 + - - +
153O TYR* 4.0 20.4 - - + -
154O LEU* 4.4 16.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 147 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O GLY 3.3 16.5 + - - +
144O SER* 3.2 6.4 + - - +
146O ILE* 1.3 82.7 - - - +
148O ASN* 1.3 65.7 + - - +
150O GLY* 4.6 1.2 + - - -
----------------------------------------------------------
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Residues in contact with ASN 148 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O SER* 2.9 39.4 + - - +
145O HIS* 4.4 2.3 + - - +
147O LYS* 1.3 85.1 - - - +
149O LEU* 1.3 71.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 149 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145O HIS* 2.7 37.0 + - + +
148O ASN* 1.3 85.0 - - + +
150O GLY* 1.3 64.8 + - - +
151O ASP 3.4 0.7 + - - -
152O THR* 3.2 26.6 + - - -
153O TYR* 3.7 31.6 - - + +
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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
------------------------------------------------------------
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