Contacts of the helix formed by residues 97 - 122 (chain A) in PDB entry 1P4X
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 SER 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASN* 4.7 1.1 - - - +
95A SER* 4.1 1.0 - - - -
96A ILE* 1.3 76.1 - - - +
98A GLU* 1.3 54.8 + - - +
99A GLU* 3.4 9.7 + - - +
100A GLN* 3.0 38.3 + - - +
101A ARG* 2.8 32.6 + - - +
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Residues in contact with GLU 98 (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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49A ASN* 4.8 8.4 + - - +
97A SER* 1.3 73.6 - - - +
99A GLU* 1.3 59.2 + - - +
101A ARG* 3.6 13.1 + - - +
102A GLU* 2.9 44.9 + - + +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A SER* 3.1 8.5 - - - +
98A GLU* 1.3 80.9 - - - +
100A GLN* 1.3 61.6 + - + +
102A GLU* 3.5 9.3 + - - +
103A LYS* 3.4 17.8 + - - +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 3.4 24.6 + - - +
79A TYR 3.2 12.7 - - - +
80A ILE* 3.3 19.9 + - - +
81A SER* 3.2 26.1 + - - -
95A SER* 3.3 15.9 + - - +
96A ILE* 3.5 2.8 - - + -
97A SER* 3.0 39.5 + - - +
99A GLU* 1.3 75.7 - - + +
101A ARG* 1.3 64.1 + - - +
102A GLU 3.0 2.0 - - - -
103A LYS* 3.0 6.0 + - - +
104A ILE* 2.9 27.6 + - - +
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Residues in contact with ARG 101 (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 3.3 12.3 + - - -
44A PHE* 3.1 41.0 + - + +
46A GLN* 3.1 12.7 + - - +
47A GLN* 4.1 4.6 + - - -
48A GLU 3.0 30.1 + - - -
49A ASN* 4.2 17.7 - - - +
96A ILE* 3.6 29.6 - - + +
97A SER 2.8 15.4 + - - +
98A GLU* 4.0 16.8 - - - +
100A GLN* 1.3 78.1 - - - +
102A GLU* 1.3 61.3 + - - +
104A ILE* 3.6 6.3 - - + +
105A ALA* 2.9 27.1 + - + +
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Residues in contact with GLU 102 (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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98A GLU* 2.9 37.4 + - + +
99A GLU* 3.6 10.3 - - - +
100A GLN 3.0 0.8 - - - -
101A ARG* 1.3 83.3 - - - +
103A LYS* 1.3 65.3 + - - +
104A ILE 3.1 0.2 - - - -
105A ALA* 3.3 10.0 + - - +
106A GLU* 3.1 25.8 + - - +
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Residues in contact with LYS 103 (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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77A HIS* 3.6 18.0 + - - +
78A SER* 3.9 24.7 - - - +
79A TYR* 3.4 35.8 + - + +
99A GLU 3.4 8.8 + - - +
100A GLN* 3.0 10.4 + - - +
102A GLU* 1.3 78.8 - - - +
104A ILE* 1.3 62.4 + - - +
106A GLU* 3.2 24.9 + - - +
107A ARG* 3.2 22.4 + - - +
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Residues in contact with ILE 104 (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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40A LEU* 3.6 36.8 - - + +
43A LEU* 4.6 6.7 - - + -
44A PHE* 3.9 19.1 - - + -
79A TYR* 3.4 39.9 - - + +
80A ILE* 4.1 10.5 - - + -
96A ILE* 3.9 26.0 - - + -
100A GLN 2.9 15.3 + - - +
101A ARG* 3.6 8.7 - - + +
103A LYS* 1.3 74.9 - - - +
105A ALA* 1.3 60.8 + - - +
107A ARG* 3.0 5.5 + - - +
108A VAL* 2.8 28.5 + - + +
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Residues in contact with ALA 105 (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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44A PHE* 3.5 31.9 - - + -
101A ARG* 2.9 19.3 + - + +
102A GLU* 3.3 14.6 + - - +
104A ILE* 1.3 73.3 - - - +
106A GLU* 1.3 65.0 + - - +
108A VAL* 3.2 3.8 + - - +
109A THR* 2.7 29.4 + - - +
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Residues in contact with GLU 106 (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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102A GLU 3.1 10.0 + - - +
103A LYS* 3.2 36.2 + - - +
105A ALA* 1.3 77.7 - - - +
107A ARG* 1.3 66.3 + - + +
109A THR* 2.8 26.5 + - - -
110A LEU* 2.9 13.1 + - - +
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Residues in contact with ARG 107 (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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30A VAL* 4.7 4.8 - - - +
31A ASP* 5.7 1.0 - - - +
32A MET* 3.3 43.1 - - - +
37A PHE* 3.8 18.1 - - + -
40A LEU* 3.8 22.7 - - + -
79A TYR* 3.0 32.1 + - + +
103A LYS* 3.2 10.9 + - - +
104A ILE* 3.0 10.2 + - - +
106A GLU* 1.3 84.5 - - + +
108A VAL* 1.3 56.4 + - - +
110A LEU* 3.3 23.5 + - - +
111A PHE* 3.1 23.2 + - - +
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Residues in contact with VAL 108 (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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37A PHE* 5.3 0.9 - - - +
40A LEU* 3.8 35.2 - - + +
41A THR* 4.0 9.9 - - + +
44A PHE* 4.0 25.4 - - + -
45A HIS* 5.0 0.9 - - - +
104A ILE* 2.8 23.5 + - + +
105A ALA* 3.2 7.6 + - - +
107A ARG* 1.3 72.5 - - - +
109A THR* 1.3 60.3 + - - +
111A PHE* 3.4 7.1 + - - +
112A ASP* 3.0 29.7 + - - +
133A SER* 3.5 27.8 - - - +
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Residues in contact with THR 109 (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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105A ALA* 2.7 20.0 + - - +
106A GLU* 2.8 14.3 + - - -
108A VAL* 1.3 74.7 - - - +
110A LEU* 1.3 63.8 + - - +
112A ASP* 3.3 13.0 + - + +
113A GLN* 3.2 25.1 + - - +
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Residues in contact with LEU 110 (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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30A VAL* 5.9 2.2 - - + -
37A PHE* 4.6 3.8 - - + -
106A GLU 2.9 10.4 + - - +
107A ARG* 3.4 41.1 - - - +
109A THR* 1.3 76.2 - - - +
111A PHE* 1.3 65.1 + - - +
113A GLN* 3.1 17.6 + - + +
114A ILE* 2.9 44.2 + - + +
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Residues in contact with PHE 111 (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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22A PHE* 4.0 22.9 - + - -
26A VAL* 6.1 0.9 - - + -
34A ILE* 5.0 3.8 - - + -
37A PHE* 3.5 59.2 - + + +
38A ILE* 4.7 3.8 - - + -
41A THR* 3.7 21.5 - - - -
107A ARG 3.1 5.5 + - - +
108A VAL* 3.6 10.8 - - - +
109A THR 3.3 0.2 - - - -
110A LEU* 1.3 80.6 - - - +
112A ASP* 1.3 62.4 + - - +
114A ILE* 3.1 11.9 + - + +
115A ILE* 2.9 39.0 + - + +
133A SER* 3.8 13.0 - - - -
136A PHE* 3.8 42.4 - + + -
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Residues in contact with ASP 112 (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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108A VAL* 3.0 21.8 + - - +
109A THR* 3.4 17.7 - - + +
111A PHE* 1.3 77.5 - - - +
113A GLN* 1.3 56.2 + - - +
115A ILE* 3.3 4.5 + - - +
116A LYS* 3.0 26.4 + - - +
131A LYS 4.8 3.5 - - - +
132A ASP* 3.4 13.8 - - + +
133A SER* 2.9 37.8 + - - +
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Residues in contact with GLN 113 (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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109A THR* 3.2 11.8 + - - +
110A LEU* 3.1 20.7 + - + +
112A ASP* 1.3 77.9 - - - +
114A ILE* 1.3 59.8 + - - +
116A LYS* 3.2 11.7 + - + +
117A GLN* 2.8 63.4 + - + +
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Residues in contact with ILE 114 (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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22A PHE* 4.0 21.3 - - + -
26A VAL* 4.2 20.4 - - + -
30A VAL* 4.4 18.6 - - + -
37A PHE* 4.2 24.5 - - + -
110A LEU* 2.9 39.4 + - + +
111A PHE* 3.1 14.3 + - + +
113A GLN* 1.3 75.3 - - - +
115A ILE* 1.3 58.8 + - - +
117A GLN* 3.5 8.7 + - - +
118A PHE* 2.9 28.9 + - - +
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Residues in contact with ILE 115 (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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18A TYR* 4.1 8.3 - - - +
22A PHE* 4.2 17.5 - - + -
111A PHE* 2.9 28.3 + - + +
112A ASP 3.6 5.8 - - - +
114A ILE* 1.3 77.2 - - - +
116A LYS* 1.3 58.9 + - - +
118A PHE* 3.3 1.4 + - - +
119A ASN* 2.7 48.3 + - - +
130A PRO* 3.7 15.5 - - + +
131A LYS 3.9 11.4 - - - -
132A ASP* 3.5 4.7 - - - +
133A SER* 3.5 31.4 - - - +
136A PHE* 3.7 29.2 - - + -
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Residues in contact with LYS 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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112A ASP 3.0 14.1 + - - +
113A GLN* 3.2 15.5 + - + +
115A ILE* 1.3 77.5 - - - +
117A GLN* 1.3 67.7 + - + +
119A ASN* 3.2 10.7 + - - +
120A LEU* 3.0 48.2 + - + +
131A LYS 4.9 5.6 + - - +
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Residues in contact with GLN 117 (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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113A GLN* 2.8 52.4 + - + +
114A ILE* 4.0 6.2 - - - +
116A LYS* 1.3 74.8 - - + +
118A PHE* 1.3 65.2 + - - +
120A LEU* 3.4 13.4 + - + +
121A ALA* 3.2 23.2 + - - +
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Residues in contact with PHE 118 (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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18A TYR* 3.5 34.5 - + - -
21A ARG* 3.7 14.6 - - + -
22A PHE* 3.6 53.8 - + + -
25A LYS* 3.8 33.9 - - + +
26A VAL* 4.5 6.7 - - + -
114A ILE 2.9 19.1 + - - +
115A ILE 3.7 2.9 - - - +
117A GLN* 1.3 77.1 - - - +
119A ASN* 1.3 62.2 + - - +
121A ALA* 3.2 5.7 + - - +
122A ASP* 2.9 60.6 + - + +
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Residues in contact with ASN 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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18A TYR* 2.7 34.3 + - - -
115A ILE* 2.7 31.7 + - - +
116A LYS* 3.2 8.8 + - - +
118A PHE* 1.3 78.6 - - - +
120A LEU* 1.3 61.8 + - + +
122A ASP* 3.2 11.5 - - - +
124A SER* 2.9 27.1 + - - -
129A ILE* 3.9 16.6 - - + +
130A PRO 3.3 21.0 + - - +
131A LYS* 4.4 8.5 + - - +
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Residues in contact with LEU 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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116A LYS* 3.0 42.6 + - + +
117A GLN* 3.7 13.5 - - + +
118A PHE 3.2 0.2 - - - -
119A ASN* 1.3 79.9 - - + +
121A ALA* 1.3 60.9 + - - +
122A ASP 3.6 3.5 + - - +
124A SER* 4.9 1.9 + - - -
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Residues in contact with ALA 121 (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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25A LYS* 3.5 28.3 + - - +
117A GLN 3.2 11.1 + - - +
118A PHE 3.2 4.1 + - - +
120A LEU* 1.3 79.1 - - + +
122A ASP* 1.3 58.8 + - - +
123A GLN 4.3 0.2 + - - -
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Residues in contact with ASP 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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18A TYR* 4.4 4.5 - - - -
21A ARG* 2.9 47.2 + - - +
118A PHE* 2.9 44.1 + - + +
119A ASN* 3.2 7.0 - - - +
120A LEU 3.2 4.6 - - - +
121A ALA* 1.3 80.9 - - - +
123A GLN* 1.3 59.2 + - - +
124A SER* 2.3 37.6 + - - +
129A ILE* 5.6 0.7 - - - +
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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