Contacts of the helix formed by residues 113 - 139 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 3.4 9.2 - - - +
56A GLY* 5.0 5.4 - - - -
57A ALA 5.5 1.0 + - - -
112A HIS* 1.3 81.9 - - - +
114A VAL* 1.3 65.7 + - - +
115A GLN* 2.8 46.9 - - - +
116A ASP* 3.2 26.5 + - - +
117A HIS* 3.2 19.6 + - - -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET* 4.3 12.8 - - + -
55A ARG 2.9 37.8 + - - +
56A GLY 3.8 4.7 - - - +
57A ALA 3.4 27.6 - - - +
58A ASN* 4.5 1.3 - - + +
59A PHE* 4.1 11.2 - - - -
62A VAL* 4.2 23.6 - - + -
112A HIS 4.1 1.3 - - - -
113A ASN* 1.3 74.8 - - - +
115A GLN* 1.3 63.6 + - + +
117A HIS* 3.2 4.2 + - - +
118A LEU* 2.8 46.9 + - + +
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 5.3 3.6 + - + +
58A ASN* 5.9 3.0 - - - +
113A ASN* 2.8 24.1 - - - +
114A VAL* 1.3 78.1 - - + +
116A ASP* 1.3 61.2 + - - +
118A LEU* 3.3 12.4 + - - +
119A LYS* 2.9 41.6 + - - +
165A ASN 3.2 21.7 + - - -
166A ILE* 3.3 13.0 - - - +
167A GLU* 2.8 54.0 + - + +
57D ALA* 5.9 0.4 - - - +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.1 28.0 - - + +
112A HIS 4.8 0.5 + - - -
113A ASN* 3.2 32.6 + - - +
115A GLN* 1.3 79.1 - - - +
117A HIS* 1.3 63.3 + - - +
119A LYS* 3.2 15.7 + - - +
120A GLU* 3.0 26.4 + - + +
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Residues in contact with HIS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN* 4.5 5.2 - - - -
50A ALA* 3.4 25.1 - - + -
53A ASN* 3.4 15.1 + - + -
54A MET* 3.6 27.1 - - + -
107A TYR* 2.6 32.4 + + - +
108A PRO 4.9 1.6 - - - -
111A ILE* 3.3 39.9 + - + +
112A HIS* 3.3 25.1 - - - -
113A ASN 3.2 7.1 + - - -
114A VAL 3.2 6.7 + - - +
116A ASP* 1.3 76.3 - - - +
118A LEU* 1.3 57.7 + - - +
120A GLU 3.1 0.5 + - - -
121A LEU* 2.7 41.2 + - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET* 5.0 0.7 - - + -
58A ASN* 5.8 0.9 - - + +
62A VAL* 3.8 27.4 - - + -
65A MET* 5.1 4.0 - - + -
66A LEU* 5.5 0.2 - - + -
114A VAL* 2.8 34.7 + - + +
115A GLN* 3.4 15.0 - - - +
117A HIS* 1.3 77.3 - - - +
119A LYS* 1.3 55.3 + - - +
121A LEU* 4.4 9.6 - - + -
122A ALA* 2.8 26.2 + - - +
162A ILE* 3.3 40.0 - - + +
165A ASN* 3.7 34.8 - - + +
166A ILE* 4.0 10.1 - - + -
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLN* 2.9 32.9 + - - +
116A ASP* 3.7 13.9 + - - +
118A LEU* 1.3 72.4 - - - +
120A GLU* 1.3 67.3 + - + +
122A ALA* 3.4 7.2 + - - +
123A ASP* 3.2 30.0 + - - +
166A ILE* 4.1 32.5 - - + -
167A GLU 5.9 0.4 - - - -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 3.5 24.7 - - + +
108A PRO* 3.9 11.8 - - + +
111A ILE* 3.7 20.7 - - + +
116A ASP* 3.0 17.2 + - + +
117A HIS 3.7 1.6 - - - +
119A LYS* 1.3 77.9 - - + +
121A LEU* 1.3 62.9 + - - +
123A ASP* 3.4 12.2 + - - +
124A ARG* 2.9 57.2 + - - +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.9 27.1 - - + +
47A THR* 4.2 9.6 - - - -
50A ALA* 3.6 32.1 - - + -
54A MET* 4.6 0.9 - - + -
66A LEU* 3.7 32.5 - - + -
107A TYR* 4.0 2.5 - - + +
117A HIS 2.7 30.7 + - - +
118A LEU* 3.6 12.6 - - + +
120A GLU* 1.3 71.7 - - - +
122A ALA* 1.3 57.6 + - - +
124A ARG* 3.1 4.5 + - - -
125A TYR* 2.8 50.4 + - + -
162A ILE* 4.1 11.7 - - + -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU 2.8 18.9 + - - +
119A LYS* 3.5 9.2 - - - +
121A LEU* 1.3 75.8 - - - +
123A ASP* 1.3 59.4 + - - +
125A TYR* 4.5 0.7 - - - -
126A ALA* 2.8 33.2 + - - +
159A LEU* 3.5 9.9 - - + +
162A ILE* 3.8 15.0 - - + +
163A GLU* 4.3 21.1 - - + +
166A ILE* 4.3 6.5 - - + -
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Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 3.2 15.8 + - - +
120A GLU* 3.6 15.7 - - - +
121A LEU 3.2 0.2 - - - -
122A ALA* 1.3 79.3 - - - +
124A ARG* 1.3 69.3 + - - +
126A ALA* 3.3 7.1 + - - +
127A ILE* 3.1 31.0 + - + +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.8 18.8 - - + -
46A ILE* 4.2 13.2 - - + +
104A LEU* 3.8 19.4 - - + +
105A LYS* 2.9 54.5 + - - +
106A SER 3.7 3.6 + - - -
107A TYR* 2.9 35.1 - - - +
108A PRO* 3.6 13.9 - - - +
120A GLU* 2.9 42.4 + - - +
121A LEU* 3.1 6.0 + - - +
123A ASP* 1.3 77.3 - - - +
125A TYR* 1.3 65.8 + - - +
127A ILE* 3.2 9.8 + - - +
128A VAL* 3.1 26.7 + - - +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.6 35.9 - - + -
47A THR* 2.6 38.3 + - + +
66A LEU* 5.5 0.4 - - + -
69A PHE* 3.6 15.1 - + - +
73A LEU* 3.5 11.2 - - + +
121A LEU* 2.8 41.4 + - + +
122A ALA 3.9 2.7 - - - +
124A ARG* 1.3 72.8 - - - +
126A ALA* 1.3 53.4 + - - +
128A VAL* 3.6 0.7 - - - +
129A ALA* 2.6 40.8 + - + +
155A LEU* 4.2 9.1 - - + +
158A PHE* 3.7 37.5 - + + -
159A LEU* 4.2 12.8 - - + -
162A ILE* 3.5 24.5 - - + -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA 2.8 19.6 + - - +
123A ASP* 3.5 7.9 - - - +
125A TYR* 1.3 77.6 - - - +
127A ILE* 1.3 58.4 + - + +
129A ALA* 4.2 0.2 - - - -
130A ASN* 2.8 47.8 + - - +
159A LEU* 3.9 23.7 - - + +
163A GLU* 5.7 1.8 - - - +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 4.3 11.0 - - - +
103A PRO* 4.5 17.7 - - + +
104A LEU* 3.8 24.2 - - + -
105A LYS* 5.6 2.7 - - + +
123A ASP* 3.1 19.5 + - + +
124A ARG* 3.2 12.3 + - - +
126A ALA* 1.3 77.1 - - + +
128A VAL* 1.3 59.3 + - - +
130A ASN* 4.0 3.7 - - - +
131A ASP* 3.0 31.4 + - + +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 3.3 35.6 - - + +
40A PHE* 3.6 28.3 - - + -
43A LEU* 4.0 17.9 - - + -
104A LEU* 3.9 17.5 - - + -
124A ARG 3.1 15.3 + - - +
125A TYR 3.9 0.9 - - - +
127A ILE* 1.3 72.4 - - - +
129A ALA* 1.3 66.3 + - - +
131A ASP* 3.8 0.2 - - - +
132A VAL* 2.9 24.4 + - - +
155A LEU* 3.5 22.9 - - + -
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR 2.6 24.4 + - - +
126A ALA* 3.8 5.6 - - - +
128A VAL* 1.3 73.4 - - - +
130A ASN* 1.3 62.6 + - - +
132A VAL* 3.2 7.1 - - - +
133A ARG* 3.0 30.4 + - - +
155A LEU* 3.8 25.3 - - + +
156A ASP* 3.7 18.2 - - - +
159A LEU* 4.4 10.5 - - + -
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Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA* 2.8 37.8 + - - +
127A ILE* 4.2 3.7 - - - +
129A ALA* 1.3 74.5 - - - +
131A ASP* 1.3 62.9 + - - +
133A ARG* 2.4 37.9 + - - +
134A LYS* 3.3 45.5 + - - +
159A LEU* 5.2 4.7 - - - +
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ARG* 2.8 41.5 + - - -
36A GLN* 3.7 2.0 - - - +
39A GLN* 3.0 26.2 + - - +
103A PRO* 5.4 0.3 - - - +
127A ILE* 3.0 21.7 + - + +
128A VAL 3.8 2.7 - - - +
130A ASN* 1.3 74.4 - - - +
132A VAL* 1.3 67.5 + - - +
134A LYS* 3.0 11.8 + - - +
135A ALA 3.0 16.5 + - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 3.7 28.9 + - - +
40A PHE* 4.3 20.0 - - + -
128A VAL 2.9 19.7 + - - +
129A ALA* 3.2 16.2 - - - +
131A ASP* 1.3 74.0 - - - +
133A ARG* 1.3 66.6 + - - +
135A ALA* 3.2 10.2 + - - +
136A ILE* 3.3 14.4 + - - +
148A LEU* 3.9 35.4 - - + +
151A ALA* 4.7 0.7 - - + -
152A SER* 3.9 21.5 - - - +
155A LEU* 4.8 2.5 - - + -
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Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 3.0 19.9 + - - +
130A ASN* 2.4 37.2 + - - +
131A ASP 3.2 0.2 - - - -
132A VAL* 1.3 76.4 - - - +
134A LYS* 1.3 66.7 + - + +
136A ILE* 3.4 24.9 - - + +
137A GLY 4.4 0.7 + - - -
152A SER* 3.6 17.0 - - - +
156A ASP* 2.6 47.1 + - - -
159A LEU* 6.1 1.0 - - - +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASN* 3.3 34.8 + - - +
131A ASP* 3.0 9.9 + - - +
133A ARG* 1.3 79.9 - - + +
135A ALA* 1.3 66.7 + - - +
136A ILE 3.0 3.5 + - - -
137A GLY* 3.2 11.6 + - - -
138A GLU* 3.2 14.5 + - - +
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.9 15.4 - - + +
35A ARG* 4.4 3.8 - - - +
36A GLN* 3.6 22.7 - - - +
131A ASP 3.0 8.9 + - - +
132A VAL* 3.2 10.3 + - - +
134A LYS* 1.3 77.0 - - - +
136A ILE* 1.3 57.1 + - - +
138A GLU* 3.1 13.5 + - - +
139A ALA* 2.8 31.7 + - - +
148A LEU* 3.8 16.8 - - + +
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL 3.4 9.0 - - - +
133A ARG* 3.4 21.5 - - + +
134A LYS 3.0 0.2 - - - -
135A ALA* 1.3 79.9 - - - +
137A GLY* 1.3 62.0 + - - +
139A ALA* 3.2 18.2 + - - +
145A ALA* 4.0 14.4 - - + +
148A LEU* 3.9 21.5 - - + +
149A THR* 3.4 43.5 - - + +
152A SER* 3.7 19.3 - - - +
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ARG 4.4 0.8 + - - -
134A LYS* 3.2 7.8 + - - +
136A ILE* 1.3 82.4 - - - +
138A GLU* 1.3 60.8 + - - +
139A ALA 3.4 4.7 + - - +
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.6 29.5 - - + +
35A ARG* 3.9 12.2 + - - -
134A LYS* 3.2 14.2 + - - +
135A ALA* 3.1 12.3 + - - +
137A GLY* 1.3 76.6 - - - +
139A ALA* 1.3 62.5 + - - +
140A LYS* 3.5 11.6 + - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.0 15.5 - - + -
135A ALA 2.8 11.0 + - - +
136A ILE 3.4 17.4 - - - +
137A GLY 3.2 5.5 - - - +
138A GLU* 1.3 75.9 - - - +
140A LYS* 1.3 64.0 + - - +
141A ASP 4.4 1.8 - - - +
144A THR* 4.4 5.8 - - + -
145A ALA* 4.0 30.5 - - - +
148A LEU* 4.1 5.8 - - + -
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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