Contacts of the helix formed by residues 104 - 128 (chain A) in PDB entry 1EQ1
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 PHE 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASN* 5.3 1.2 + - - +
43A LEU* 5.1 0.7 - - - -
44A LYS* 3.5 17.5 - - - +
90A LEU* 5.5 2.3 - - + +
93A ALA* 3.7 20.6 - - + -
96A ASP* 3.1 30.5 - - + -
97A VAL* 3.1 49.9 - - + +
100A GLU* 3.2 27.6 - - + -
101A ALA 5.1 0.4 - - - -
102A ASN* 3.8 2.7 - - + +
103A ALA* 1.3 78.8 - - - +
105A LYS* 1.3 64.6 + - - +
107A LYS* 3.0 50.8 - - + +
108A LEU* 4.0 1.7 + - - +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.4 47.6 + - + +
28A ASN* 4.9 2.8 - - - +
30A LEU* 4.8 7.3 - - + +
31A VAL* 5.5 9.6 - - - +
40A ASN* 5.7 1.0 + - - +
43A LEU* 3.2 39.9 - - + +
47A SER* 5.3 2.9 - - - -
97A VAL* 4.7 0.4 - - - +
102A ASN 5.9 1.3 - - - +
103A ALA* 4.6 7.9 - - - -
104A PHE* 1.3 75.5 - - - +
106A ASP* 1.3 82.5 + - + +
107A LYS 2.9 5.7 + - - -
108A LEU* 3.0 16.5 + - - +
109A GLN* 3.3 19.5 + - - +
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 3.5 18.5 + - + +
104A PHE 3.3 0.6 - - - -
105A LYS* 1.3 90.6 - - + +
107A LYS* 1.3 57.1 + - - +
108A LEU 3.2 0.2 - - - -
109A GLN* 3.8 26.3 + - - +
110A ALA* 2.8 39.7 + - - +
113A GLN* 5.8 0.3 + - - -
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 6.0 4.3 - - + -
90A LEU* 3.7 24.7 - - + +
103A ALA 4.0 4.1 + - - +
104A PHE* 3.0 53.5 + - + +
105A LYS 2.9 0.4 + - - -
106A ASP* 1.3 80.5 - - - +
108A LEU* 1.3 56.3 + - - +
110A ALA* 3.9 3.8 - - - +
111A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.2 6.5 - - + -
47A SER* 2.9 51.1 - - - +
50A VAL* 3.0 18.4 - - + -
51A LEU* 3.5 12.3 - - + -
54A LEU* 5.2 0.4 - - + -
87A ALA* 5.7 0.2 - - - -
90A LEU* 3.0 23.9 - - + +
104A PHE 4.0 1.3 + - - +
105A LYS* 3.0 9.1 + - - +
107A LYS* 1.3 76.9 - - - +
109A GLN* 1.3 67.3 + - - +
110A ALA 3.1 1.6 - - - -
111A ALA* 2.8 13.4 + - + -
112A VAL* 2.8 32.8 + - + +
155A VAL* 3.5 7.2 - - + -
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Residues in contact with GLN 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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23A PHE* 3.7 4.9 - - + -
24A SER* 3.1 35.3 + - - +
27A PHE* 3.5 46.0 - - + +
28A ASN* 5.2 3.1 + - - +
105A LYS* 3.3 18.7 + - - +
106A ASP* 3.8 19.8 + - - +
108A LEU* 1.3 79.1 - - - +
110A ALA* 1.3 61.3 + - - +
112A VAL 3.6 0.2 + - - -
113A GLN* 3.3 33.4 + - - +
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Residues in contact with ALA 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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106A ASP* 2.8 25.7 + - - +
107A LYS* 4.1 3.8 - - - +
109A GLN* 1.3 77.5 - - - +
111A ALA* 1.3 62.3 + - - +
112A VAL 3.3 0.4 + - - -
113A GLN* 3.8 12.3 + - - +
114A THR* 3.4 23.2 + - - +
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Residues in contact with ALA 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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86A THR* 2.6 37.1 + - - +
87A ALA* 4.3 6.5 - - - -
89A GLU* 5.0 6.7 - - + +
90A LEU* 4.4 6.1 - - + -
107A LYS 3.0 19.2 + - - +
108A LEU* 2.8 10.9 + - + +
110A ALA* 1.3 75.5 - - - +
112A VAL* 1.3 59.2 + - - +
114A THR* 2.3 27.8 + - - -
115A THR* 3.4 5.5 + - - -
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Residues in contact with VAL 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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20A GLN* 5.2 1.6 - - + -
23A PHE* 3.1 43.1 - - + -
27A PHE* 5.0 1.6 - - + -
50A VAL* 5.2 5.6 - - + -
54A LEU* 4.7 16.2 - - + -
108A LEU* 2.8 43.3 + - + +
109A GLN* 4.5 0.2 - - - -
111A ALA* 1.3 75.5 - - + +
113A GLN* 1.3 65.5 + - - +
114A THR 2.8 6.3 + - - -
115A THR* 2.8 28.4 + - - +
116A VAL* 3.6 5.8 + - + +
152A ALA* 5.1 11.2 - - + +
155A VAL* 5.2 1.6 - - + -
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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
----------------------------------------------------------
20A GLN* 3.7 35.0 + - - +
21A LYS* 6.1 0.2 - - - -
23A PHE* 3.7 7.6 - - + -
24A SER* 3.9 14.1 + - - -
106A ASP* 5.8 0.6 + - - -
109A GLN* 3.3 31.5 + - - +
110A ALA* 4.1 11.1 - - - +
112A VAL* 1.3 78.7 - - - +
114A THR* 1.3 61.0 + - + +
116A VAL* 3.5 17.7 + - - +
117A GLN* 3.9 7.6 + - - +
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Residues in contact with THR 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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86A THR* 2.4 17.6 + - - +
110A ALA 3.4 12.4 + - - +
111A ALA* 2.3 34.0 + - - -
112A VAL 2.8 0.2 + - - -
113A GLN* 1.3 74.4 - - + +
115A THR* 1.3 50.1 + - - -
116A VAL 2.5 6.9 + - - -
117A GLN* 2.5 37.0 + - + +
118A GLU* 3.2 13.2 + - - +
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Residues in contact with THR 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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54A LEU* 4.4 14.3 - - + +
57A PHE* 3.9 16.6 - - + -
83A VAL* 4.5 5.6 - - + -
86A THR* 3.6 14.4 + - - +
87A ALA* 4.7 1.0 - - - +
111A ALA 3.4 12.1 + - - -
112A VAL* 2.8 18.0 + - - +
114A THR* 1.3 78.6 + - - +
116A VAL* 1.3 60.8 + - + +
118A GLU* 3.5 18.3 + - - +
119A SER* 3.6 10.7 + - - -
148A PHE* 3.4 34.1 - - + -
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Residues in contact with VAL 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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13A GLU* 3.9 12.6 - - + +
16A ALA* 4.5 6.3 - - + +
17A LYS* 3.0 46.4 - - + +
20A GLN* 3.3 35.2 - - + +
112A VAL* 3.9 7.2 - - + +
113A GLN 3.5 14.1 - - - +
114A THR 2.5 5.1 + - - -
115A THR* 1.3 74.2 - - - +
117A GLN* 1.3 68.6 + - - +
118A GLU 3.1 1.8 - - - -
119A SER* 3.1 20.3 + - - -
120A GLN 3.6 3.3 + - - -
148A PHE* 6.1 0.4 - - - -
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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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13A GLU* 5.1 1.4 + - - -
113A GLN 3.9 5.2 + - - -
114A THR* 2.5 24.0 + - + +
116A VAL* 1.3 79.2 - - - +
118A GLU* 1.3 61.8 + - + +
120A GLN* 3.2 32.2 + - + +
121A LYS* 3.7 4.0 + - - +
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Residues in contact with GLU 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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78A GLN* 5.0 0.2 - - - +
79A ALA* 5.2 5.9 - - + +
82A ASN* 2.6 65.8 + - - +
83A VAL* 2.9 28.7 + - + -
86A THR* 4.1 4.0 - - + +
114A THR* 3.6 15.5 - - - +
115A THR* 3.6 10.1 - - - +
116A VAL 3.1 0.4 - - - -
117A GLN* 1.3 76.4 - - + +
119A SER* 1.3 63.1 + - - +
120A GLN 2.9 6.9 + - - -
121A LYS* 3.0 21.8 + - - +
122A LEU* 3.2 12.7 + - - +
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Residues in contact with SER 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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12A MET* 4.1 7.3 + - - +
13A GLU* 3.7 29.8 + - - +
16A ALA* 4.6 3.3 - - - +
115A THR 3.6 8.6 + - - -
116A VAL* 3.1 14.4 + - - -
118A GLU* 1.3 78.8 - - - +
120A GLN* 1.3 55.9 + - - +
121A LYS 3.4 0.2 - - - -
122A LEU* 4.5 6.6 - - - +
123A ALA* 2.7 31.5 + - - +
148A PHE* 4.0 23.7 - - - -
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Residues in contact with GLN 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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13A GLU* 3.1 31.3 + - - +
116A VAL 3.6 1.6 + - - -
117A GLN* 3.2 27.1 + - + +
118A GLU 2.9 0.6 - - - -
119A SER* 1.3 78.4 - - - +
121A LYS* 1.3 66.7 + - - +
123A ALA* 3.7 0.7 - - - +
124A LYS* 3.1 38.8 + - + +
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Residues in contact with LYS 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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75A ALA* 5.2 5.1 + - - +
78A GLN* 3.1 36.6 + - - +
79A ALA* 5.0 7.8 - - + +
82A ASN* 4.8 2.8 - - - +
117A GLN 3.7 3.9 + - - +
118A GLU* 3.0 15.7 + - - +
120A GLN* 1.3 82.1 - - - +
122A LEU* 1.3 59.2 + - - +
124A LYS* 4.0 2.6 - - - +
125A GLU* 3.0 46.2 + - - +
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Residues in contact with LEU 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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61A LEU* 3.5 28.9 - - + -
75A ALA* 5.1 2.5 - - + +
76A LEU* 3.5 16.6 - - + -
79A ALA* 3.1 33.4 - - + +
118A GLU 3.2 11.5 + - - +
119A SER* 4.5 5.2 - - - +
121A LYS* 1.3 77.1 - - - +
123A ALA* 1.3 65.7 + - - +
125A GLU* 4.0 5.8 - - + -
126A VAL* 3.2 29.5 + - + +
141A ILE* 3.1 32.4 - - + +
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Residues in contact with ALA 123 (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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9A PHE* 4.6 10.7 - - - +
10A GLU* 3.9 24.7 + - + +
12A MET* 6.0 0.7 - - + -
13A GLU* 3.9 15.9 - - + +
119A SER* 2.7 23.8 + - - +
120A GLN 3.7 3.8 - - - +
121A LYS 3.2 0.2 - - - -
122A LEU* 1.3 80.7 - - - +
124A LYS* 1.3 67.6 + - - +
126A VAL* 3.9 1.4 - - - +
127A ALA* 3.0 27.0 + - - +
141A ILE* 6.3 2.2 - - - -
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Residues in contact with LYS 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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10A GLU* 3.9 23.5 - - - +
13A GLU* 4.8 8.2 + - - -
14A LYS* 5.3 5.9 - - - +
120A GLN* 3.1 34.5 + - + +
121A LYS* 4.2 2.5 - - - +
123A ALA* 1.3 85.4 - - - +
125A GLU* 1.3 72.1 + - - +
127A ALA* 3.2 17.4 + - + +
128A SER* 3.4 10.7 + - - -
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Residues in contact with GLU 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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75A ALA* 4.1 27.5 - - + +
76A LEU* 6.0 1.1 - - + -
121A LYS* 3.0 39.8 + - - +
122A LEU* 3.7 11.0 - - + +
124A LYS* 1.3 84.2 - - - +
126A VAL* 1.3 66.3 + - + +
128A SER* 3.2 19.0 + - - -
129A ASN 4.6 0.2 + - - -
131A GLU* 5.4 3.8 - - - +
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Residues in contact with VAL 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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8A ALA* 6.0 0.3 - - - -
9A PHE* 3.2 41.5 - - + -
76A LEU* 4.8 5.8 - - + -
122A LEU* 3.2 38.3 + - + +
123A ALA 4.5 1.3 - - - +
125A GLU* 1.3 75.5 - - + +
127A ALA* 1.3 64.7 + - - +
128A SER 3.2 0.4 + - - -
129A ASN* 3.4 18.8 + - - +
134A ASN* 5.1 11.0 - - - +
137A LEU* 5.2 15.0 - - + -
141A ILE* 4.1 14.1 - - + -
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Residues in contact with ALA 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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8A ALA* 5.4 4.3 - - - +
9A PHE 5.7 0.2 - - - +
10A GLU* 3.4 30.1 - - + +
123A ALA 3.0 21.2 + - - +
124A LYS* 3.3 17.3 - - + +
125A GLU 3.1 0.4 - - - -
126A VAL* 1.3 77.3 - - - +
128A SER* 1.3 69.8 + - - +
129A ASN* 3.1 8.1 + - - +
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS 3.4 7.5 + - - -
125A GLU* 3.2 17.2 + - - -
127A ALA* 1.3 79.2 - - - +
129A ASN* 1.3 70.9 + - - +
130A MET* 3.1 33.4 + - - +
131A GLU* 5.6 2.5 - - - -
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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