Contacts of the helix formed by residues 113 - 139 (chain J) in PDB entry 1F33
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 ASN 113 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J ARG* 3.4 8.9 - - - +
56J GLY* 5.1 4.9 - - - -
57J ALA 5.6 0.9 + - - -
112J HIS* 1.3 80.7 - - - +
114J VAL* 1.3 67.9 + - - +
115J GLN* 2.8 47.5 - - - +
116J ASP* 3.2 32.6 + - - +
117J HIS* 3.2 12.5 + - - -
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Residues in contact with VAL 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J MET* 4.3 12.8 - - + -
55J ARG 2.9 37.7 + - - +
56J GLY 3.8 5.8 - - - +
57J ALA 3.4 26.7 - - - +
58J ASN* 5.1 1.1 - - + -
59J PHE* 4.1 11.7 - - - -
62J VAL* 4.2 23.3 - - + -
112J HIS 4.1 1.3 - - - -
113J ASN* 1.3 74.2 + - - +
115J GLN* 1.3 62.6 + - + +
117J HIS* 3.1 4.5 + - - +
118J LEU* 2.8 47.1 + - + +
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Residues in contact with GLN 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J ALA* 5.2 4.6 + - + +
58J ASN* 5.9 3.0 - - - +
113J ASN* 2.8 23.1 - - - +
114J VAL* 1.3 77.2 - - + +
116J ASP* 1.3 61.5 + - - +
118J LEU* 3.3 11.8 + - - +
119J LYS* 3.0 42.7 + - - +
165J ASN 3.2 21.6 + - - -
166J ILE* 3.3 13.7 - - - +
167J GLU* 2.8 52.9 + - + +
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Residues in contact with ASP 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ILE* 4.1 28.5 - - + +
112J HIS 4.9 0.5 + - - -
113J ASN* 3.2 33.3 + - - +
115J GLN* 1.3 78.2 - - - +
117J HIS* 1.3 63.2 + - - +
119J LYS* 3.2 16.0 + - - +
120J GLU* 3.0 26.3 + - + +
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Residues in contact with HIS 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J GLN* 4.5 1.8 - - - -
50J ALA* 3.4 24.8 - - + -
53J ASN* 3.3 19.3 + - + -
54J MET* 3.7 27.6 - - + -
107J TYR* 2.6 32.3 + + - +
108J PRO 4.9 1.6 - - - -
111J ILE* 3.2 39.3 + - + +
112J HIS* 3.4 24.2 - - - -
113J ASN 3.2 7.8 + - - -
114J VAL 3.1 7.6 + - - +
116J ASP* 1.3 77.5 - - - +
118J LEU* 1.3 54.8 + - - +
120J GLU 3.1 0.7 + - - -
121J LEU* 2.7 40.7 + - - +
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Residues in contact with LEU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J MET* 5.0 0.7 - - + -
58J ASN* 5.8 0.4 - - - +
62J VAL* 3.8 28.3 - - + -
65J MET* 5.0 4.3 - - + -
66J LEU* 5.4 0.4 - - + -
114J VAL* 2.8 33.9 + - + +
115J GLN* 3.4 15.3 - - - +
117J HIS* 1.3 76.1 - - - +
119J LYS* 1.3 56.9 + - - +
121J LEU* 3.4 10.5 + - + -
122J ALA* 2.9 25.6 + - - +
162J ILE* 3.3 40.7 - - + +
165J ASN* 3.7 34.3 - - + +
166J ILE* 3.9 10.3 - - + +
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Residues in contact with LYS 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J GLN* 3.0 33.8 + - - +
116J ASP* 3.7 12.7 + - - +
117J HIS 3.2 0.2 - - - -
118J LEU* 1.3 72.5 - - - +
120J GLU* 1.3 67.8 + - + +
122J ALA* 3.3 4.3 + - - +
123J ASP* 3.1 30.4 + - - +
166J ILE* 4.0 37.5 - - + -
167J GLU 5.7 0.4 - - - -
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Residues in contact with GLU 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J TYR* 3.5 22.2 - - + +
108J PRO* 3.9 11.2 - - + +
111J ILE* 3.7 21.3 - - + +
116J ASP* 3.0 17.4 + - + +
117J HIS 3.6 5.2 - - - +
119J LYS* 1.3 77.6 - - - +
121J LEU* 1.3 61.9 + - - +
123J ASP* 3.4 12.7 + - - +
124J ARG* 2.9 56.0 + - - +
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Residues in contact with LEU 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J ILE* 3.9 27.4 - - + +
47J THR* 4.2 9.4 - - - -
50J ALA* 3.6 33.9 - - + -
54J MET* 4.6 1.3 - - + -
66J LEU* 3.7 31.2 - - + -
107J TYR* 4.0 2.7 - - + +
117J HIS 2.7 30.4 + - - +
118J LEU* 3.7 11.9 - - + +
120J GLU* 1.3 71.4 - - - +
122J ALA* 1.3 56.6 + - - +
124J ARG* 3.1 3.4 + - - -
125J TYR* 2.7 50.6 + - + -
162J ILE* 4.1 11.4 - - + -
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Residues in contact with ALA 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J LEU 2.9 18.5 + - - +
119J LYS* 3.3 9.4 + - - +
121J LEU* 1.3 75.8 - - - +
123J ASP* 1.3 57.0 + - - +
125J TYR* 3.3 0.8 + - - -
126J ALA* 2.8 37.2 + - - +
159J LEU* 3.5 11.7 - - + +
162J ILE* 3.9 14.7 - - + +
163J GLU* 4.3 15.7 - - + +
166J ILE* 4.3 11.7 - - + -
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Residues in contact with ASP 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J LYS* 3.1 16.7 + - - +
120J GLU* 3.5 17.4 - - - +
121J LEU 3.1 0.2 - - - -
122J ALA* 1.3 81.9 - - - +
124J ARG* 1.3 70.1 + - - +
126J ALA* 3.2 8.3 + - - +
127J ILE* 3.1 29.9 + - + +
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Residues in contact with ARG 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J LEU* 3.8 19.3 - - + -
46J ILE* 4.2 13.7 - - + +
104J LEU* 3.8 18.7 - - + +
105J LYS* 2.9 55.8 + - - +
106J SER 3.7 3.8 + - - -
107J TYR* 2.9 35.9 - - - +
108J PRO* 3.6 14.3 - - - +
120J GLU* 2.9 40.7 + - - +
121J LEU* 3.1 5.5 + - - +
123J ASP* 1.3 77.4 - - - +
125J TYR* 1.3 65.3 + - - +
127J ILE* 3.2 9.5 + - - +
128J VAL* 3.1 26.5 + - - +
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Residues in contact with TYR 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J LEU* 3.5 34.8 - - + -
47J THR* 2.6 37.7 + - + +
66J LEU* 5.4 0.4 - - + -
69J PHE* 3.6 11.0 - + - +
73J LEU* 3.5 12.2 - - + +
121J LEU* 2.7 44.2 + - + +
122J ALA 3.8 2.9 - - - +
124J ARG* 1.3 72.9 - - - +
126J ALA* 1.3 51.8 + - - +
128J VAL* 3.3 1.0 + - - +
129J ALA* 2.6 39.6 + - - +
155J LEU* 4.2 9.4 - - + +
158J PHE* 3.7 36.1 - + + -
159J LEU* 4.2 13.5 - - + -
162J ILE* 3.5 29.2 - - + -
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Residues in contact with ALA 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ALA 2.8 22.0 + - - +
123J ASP* 3.3 9.0 - - - +
125J TYR* 1.3 74.0 - - - +
127J ILE* 1.3 58.1 + - + +
129J ALA* 4.2 0.2 - - - -
130J ASN* 2.8 47.9 + - - +
159J LEU* 3.9 22.6 - - + +
163J GLU* 5.7 1.1 - - - +
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Residues in contact with ILE 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J GLN* 4.3 10.1 - - - +
103J PRO* 4.5 17.3 - - + +
104J LEU* 3.9 24.0 - - + -
105J LYS* 5.5 2.9 - - + +
123J ASP* 3.1 16.5 + - + +
124J ARG* 3.2 15.0 + - - +
126J ALA* 1.3 78.1 - - + +
128J VAL* 1.3 63.8 + - - +
130J ASN* 4.1 3.6 - - - +
131J ASP* 3.0 28.2 + - + +
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Residues in contact with VAL 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J GLN* 3.4 37.2 - - + +
40J PHE* 3.7 27.8 - - + -
43J LEU* 3.9 17.0 - - + -
104J LEU* 3.9 18.2 - - + -
124J ARG 3.1 12.6 + - - +
125J TYR 3.9 2.5 - - - +
127J ILE* 1.3 75.0 - - - +
129J ALA* 1.3 58.2 + - - +
131J ASP* 3.8 0.3 - - - +
132J VAL* 2.9 32.6 + - - +
155J LEU* 3.5 23.8 - - + -
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Residues in contact with ALA 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125J TYR 2.6 24.6 + - - +
126J ALA* 3.8 5.2 - - - +
128J VAL* 1.3 73.3 - - - +
130J ASN* 1.3 63.1 + - - +
132J VAL* 3.2 10.3 - - - +
133J ARG* 3.0 30.7 + - - +
155J LEU* 3.8 23.3 - - + +
156J ASP* 3.7 18.2 - - - +
159J LEU* 4.4 10.1 - - + -
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Residues in contact with ASN 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J ALA* 2.8 38.9 + - - +
127J ILE* 4.1 3.1 - - - +
129J ALA* 1.3 73.6 - - - +
131J ASP* 1.3 63.9 + - - +
133J ARG* 2.4 37.2 + - - +
134J LYS* 3.3 45.2 + - - +
159J LEU* 5.3 4.8 - - - +
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Residues in contact with ASP 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ARG* 2.8 40.1 + - - -
36J GLN* 3.7 2.5 - - - +
39J GLN* 3.0 26.9 + - - +
103J PRO* 5.4 0.5 - - - +
127J ILE* 3.0 21.3 + - + +
128J VAL 3.8 2.9 - - - +
130J ASN* 1.3 76.7 - - - +
132J VAL* 1.3 64.4 + - - +
134J LYS* 3.0 11.5 + - - +
135J ALA* 3.0 16.5 + - - +
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Residues in contact with VAL 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J GLN* 3.6 28.7 + - - +
40J PHE* 4.3 19.7 - - + -
128J VAL 2.9 25.5 + - - +
129J ALA* 3.2 12.1 - - - +
131J ASP* 1.3 73.8 + - - +
133J ARG* 1.3 66.8 + - - +
135J ALA* 3.2 10.0 + - - +
136J ILE* 3.4 13.6 + - - +
148J LEU* 3.9 35.2 - - + +
151J ALA* 4.6 0.4 - - + -
152J SER* 4.0 20.4 - - - +
155J LEU* 4.8 2.9 - - + -
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Residues in contact with ARG 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J ALA* 3.0 19.7 + - - +
130J ASN* 2.4 36.6 + - - +
131J ASP 3.2 0.2 - - - -
132J VAL* 1.3 76.4 - - - +
134J LYS* 1.3 66.0 + - + +
136J ILE* 3.4 24.2 - - + +
137J GLY 4.4 0.5 + - - -
152J SER* 3.7 17.3 - - - +
156J ASP* 2.6 45.6 + - - -
159J LEU* 6.2 0.8 - - - +
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Residues in contact with LYS 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J ASN* 3.3 35.8 + - - +
131J ASP* 3.0 9.2 + - - +
133J ARG* 1.3 80.5 - - + +
135J ALA* 1.3 67.3 + - - +
136J ILE 3.0 3.4 + - - -
137J GLY* 3.1 11.6 + - - -
138J GLU* 3.2 14.0 + - - +
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Residues in contact with ALA 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J LEU* 3.9 16.2 - - + +
35J ARG* 4.3 3.8 - - - +
36J GLN* 3.6 23.3 - - - +
131J ASP 3.0 8.1 + - - +
132J VAL* 3.2 10.1 + - - +
134J LYS* 1.3 77.6 - - - +
136J ILE* 1.3 57.5 + - - +
138J GLU* 3.1 13.9 + - - +
139J ALA* 2.9 31.2 + - - +
148J LEU* 3.7 16.2 - - + +
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Residues in contact with ILE 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J VAL 3.4 9.2 - - - +
133J ARG* 3.4 20.4 - - + +
134J LYS 3.0 0.6 - - - -
135J ALA* 1.3 77.6 - - - +
137J GLY* 1.3 64.0 + - - +
139J ALA* 3.2 20.3 + - - +
145J ALA* 4.0 14.7 - - + +
148J LEU* 3.9 20.9 - - + -
149J THR* 3.4 42.4 - - + +
152J SER* 3.7 19.7 - - - +
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Residues in contact with GLY 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J ARG 4.4 0.8 + - - -
134J LYS 3.1 7.0 + - - -
136J ILE* 1.3 81.2 - - - +
138J GLU* 1.3 59.2 + - - +
139J ALA 3.2 6.1 + - - +
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Residues in contact with GLU 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J LEU* 3.6 28.6 - - + +
35J ARG* 3.8 13.9 + - - -
134J LYS* 3.2 13.8 + - - +
135J ALA* 3.1 12.4 + - - +
137J GLY* 1.3 76.4 - - - +
139J ALA* 1.3 61.6 + - - +
140J LYS* 3.5 10.9 + - - +
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Residues in contact with ALA 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J LEU* 4.0 15.3 - - + -
135J ALA 2.9 10.5 + - - +
136J ILE 3.3 17.6 - - - +
137J GLY 3.2 5.2 - - - +
138J GLU* 1.3 76.5 - - - +
140J LYS* 1.3 65.5 + - - +
141J ASP 4.4 2.2 - - - +
144J THR* 4.4 5.6 - - + -
145J ALA* 3.9 30.1 - - + +
148J LEU* 4.1 6.1 - - + -
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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