Contacts of the helix formed by residues 109 - 136 (chain A) in PDB entry 1EMR
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 ALA 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.5 31.9 - - + -
106A ASN* 2.9 18.8 + - + +
108A SER* 1.3 75.5 + - - +
110A LEU* 1.3 56.2 + - - +
111A SER 3.8 0.9 - - - +
112A LEU* 4.0 14.4 - - + -
113A HIS* 2.7 35.0 + - + -
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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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107A PRO 4.8 5.2 - - - +
108A SER* 2.6 20.0 + - - +
109A ALA* 1.3 72.5 - - - +
111A SER* 1.3 65.2 + - - +
112A LEU 2.7 7.5 + - - -
113A HIS* 3.9 14.9 - - + +
114A SER* 3.0 24.8 + - - -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.2 26.2 - - - -
109A ALA* 4.8 0.2 - - - +
110A LEU* 1.3 78.9 - - - +
112A LEU* 1.3 59.3 + - - +
114A SER* 3.6 3.4 - - - -
115A LYS* 3.1 36.0 + - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.6 3.1 - - + +
44A LEU* 3.7 23.2 - - + +
45A TYR* 3.7 32.5 - - + +
48A ALA* 3.6 28.0 - - + -
49A GLN* 4.2 0.2 - - - +
102A GLN* 4.0 19.3 - - + +
109A ALA* 3.7 16.1 + - + +
110A LEU 2.7 0.8 - - - -
111A SER* 1.3 78.6 - - - +
113A HIS* 1.3 69.7 + - + +
114A SER 2.9 2.5 - - - -
115A LYS* 4.0 1.7 - - + +
116A LEU* 3.0 58.9 + - + +
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Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 5.1 5.2 - - + +
102A GLN* 2.9 43.4 + - + +
103A LYS* 3.6 15.1 + - + -
106A ASN 2.9 26.4 + - - -
107A PRO* 3.6 17.8 + - + -
109A ALA* 2.7 28.8 + - - +
110A LEU* 3.2 17.1 + - + +
112A LEU* 1.3 76.6 - - + +
114A SER* 1.3 65.4 + - - +
116A LEU* 3.3 18.8 - - + +
117A ASN* 3.4 14.7 + - - +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU 3.0 16.3 + - - -
111A SER* 3.6 4.7 - - - -
112A LEU 2.9 1.2 - - - -
113A HIS* 1.3 74.8 - - - +
115A LYS* 1.3 73.6 + - - -
117A ASN* 2.6 22.4 + - - +
118A ALA* 2.7 15.0 + - - +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 5.6 9.6 - - - -
40A ALA* 5.8 6.1 - - + -
41A LEU* 3.9 30.7 - - + +
44A LEU* 4.6 13.0 - - + -
111A SER* 3.1 34.7 + - - +
112A LEU* 4.2 4.9 - - + +
114A SER* 1.3 83.0 - - - +
116A LEU* 1.3 58.5 + - - +
118A ALA* 3.4 13.0 - - + +
119A THR* 2.5 35.3 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.3 20.9 - - + -
95A LEU* 4.7 10.8 - - + +
98A ILE* 4.9 8.5 - - + -
99A THR* 3.5 30.9 + - + +
102A GLN* 4.1 23.3 - - + -
112A LEU* 3.0 53.8 + - + +
113A HIS* 3.3 13.2 - - + +
114A SER 2.7 4.0 + - - -
115A LYS* 1.3 77.0 - - - +
117A ASN* 1.3 62.5 + - - +
119A THR* 3.4 2.8 + - - -
120A ALA* 3.0 20.8 + - - +
167A LEU* 5.0 11.2 - - + -
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Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 3.7 23.6 + - - +
103A LYS* 6.1 1.0 - - - +
113A HIS* 3.7 15.0 + - - +
114A SER* 2.6 12.7 + - - +
116A LEU* 1.3 73.7 - - - +
118A ALA* 1.3 69.3 + - - +
119A THR 2.9 2.5 - - - -
120A ALA* 3.5 9.0 - - - +
121A ASP* 2.9 27.9 + - - +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 2.7 17.5 + - - +
115A LYS* 3.4 21.1 - - + +
117A ASN* 1.3 75.7 - - - +
119A THR* 1.3 61.8 + - - +
121A ASP* 3.4 4.6 + - - +
122A ILE* 3.3 29.9 + - + +
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.5 25.6 - - + -
37A SER* 4.8 8.8 + - - +
41A LEU* 3.7 16.8 - - + +
95A LEU* 4.2 12.6 - - + -
115A LYS* 2.5 24.0 + - - +
116A LEU 3.8 3.4 - - - -
118A ALA* 1.3 75.3 - - - +
120A ALA* 1.3 71.2 + - - +
122A ILE* 3.9 5.0 - - - +
123A LEU* 3.0 27.8 + - + +
170A TYR* 3.5 18.8 - - + +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLY* 5.7 4.0 - - - +
95A LEU* 4.3 15.4 - - + +
99A THR* 6.1 0.4 - - - +
116A LEU 3.0 15.8 + - - +
117A ASN* 3.1 12.5 + - - +
119A THR* 1.3 73.8 - - - +
121A ASP* 1.3 65.0 + - - +
123A LEU* 2.8 18.7 + - - +
124A ARG* 2.9 37.7 + - - +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 2.9 11.7 + - - +
118A ALA* 3.4 12.1 - - - +
120A ALA* 1.3 80.4 - - - +
122A ILE* 1.3 70.4 + - + +
124A ARG* 3.2 36.8 + - - +
125A GLY* 3.3 8.8 + - - -
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Residues in contact with ILE 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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30A GLN* 4.1 22.8 + - + +
33A GLN* 4.6 23.3 - - + +
34A LEU* 3.2 44.4 - - + +
118A ALA* 3.3 21.4 + - + +
119A THR* 4.0 2.9 - - - +
121A ASP* 1.3 82.4 - - + +
123A LEU* 1.3 66.3 + - - +
125A GLY* 3.0 13.7 + - - +
126A LEU* 3.2 9.0 + - - +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.8 30.7 - - + -
88A VAL* 3.7 24.4 - - + +
91A LEU* 3.6 19.1 - - + -
92A GLY* 3.3 37.7 - - - +
95A LEU* 4.1 8.1 - - + -
119A THR* 3.0 25.3 + - + +
120A ALA* 2.8 13.9 + - - +
122A ILE* 1.3 75.7 - - - +
124A ARG* 1.3 61.4 + - + +
126A LEU* 2.8 20.3 + - - +
127A LEU* 3.0 12.3 + - - +
170A TYR* 4.6 9.2 - - + -
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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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120A ALA* 2.9 38.0 + - - +
121A ASP* 3.3 30.2 + - - +
123A LEU* 1.3 75.8 - - - +
125A GLY* 1.3 63.2 + - - +
127A LEU* 3.0 20.8 + - + +
128A SER* 3.2 14.3 + - - -
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Residues in contact with GLY 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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30A GLN* 3.5 17.3 - - - -
121A ASP 3.3 5.3 + - - -
122A ILE* 3.0 8.6 + - - -
124A ARG* 1.3 76.7 - - - +
126A LEU* 1.3 63.7 + - - +
127A LEU 3.0 0.9 + - - -
128A SER* 3.0 8.6 + - - -
129A ASN* 2.9 25.7 + - - -
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Residues in contact with LEU 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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27A ILE* 4.0 9.0 - - + +
30A GLN* 3.2 42.6 + - + +
31A LEU* 3.2 38.6 - - + +
34A LEU* 4.7 5.4 - - + -
84A LEU* 3.8 20.9 - - + -
88A VAL* 3.4 28.3 - - + +
122A ILE 3.2 7.5 + - - +
123A LEU* 2.8 16.6 + - - +
125A GLY* 1.3 72.1 - - - +
127A LEU* 1.3 65.8 + - - +
129A ASN* 3.7 3.6 - - - +
130A VAL* 3.1 31.0 + - + +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.3 42.6 - - + +
88A VAL* 3.5 25.3 - - + +
89A VAL* 4.2 15.3 - - + -
123A LEU 3.0 8.6 + - - +
124A ARG* 3.0 14.5 + - + +
126A LEU* 1.3 77.8 - - - +
128A SER* 1.3 63.6 + - - +
129A ASN 2.9 0.7 + - - -
130A VAL* 3.8 0.7 - - - +
131A LEU* 2.8 32.9 + - + +
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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 ARG 3.2 7.3 + - - -
125A GLY* 3.0 9.7 + - - -
127A LEU* 1.3 82.2 - - - +
129A ASN* 1.3 59.9 + - - +
131A LEU* 3.6 6.6 - - - +
132A CYS* 2.7 31.6 + - - +
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Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.9 22.8 - - + +
26A GLN* 2.7 34.9 + - - +
27A ILE* 4.2 15.7 - - + +
30A GLN* 2.6 31.3 + - - +
125A GLY* 2.9 16.0 + - - +
126A LEU* 4.1 2.5 - - - +
127A LEU 2.9 1.0 + - - -
128A SER* 1.3 78.6 - - - +
130A VAL* 1.3 62.9 + - - +
131A LEU 2.9 4.9 - - - -
132A CYS* 3.0 5.6 + - - +
133A ARG* 3.0 23.6 + - - +
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Residues in contact with VAL 130 (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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27A ILE* 4.5 11.9 - - + -
81A LEU* 3.2 49.6 - - + +
84A LEU* 3.4 29.4 - - + -
85A TYR* 4.0 15.7 - - + +
88A VAL* 6.4 0.7 - - + -
126A LEU* 3.1 25.8 + - + +
127A LEU 4.0 1.3 - - - +
129A ASN* 1.3 73.2 - - - +
131A LEU* 1.3 60.8 + - - +
133A ARG* 3.3 2.8 + - - +
134A LEU* 2.9 35.8 + - + +
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Residues in contact with LEU 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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85A TYR* 3.9 25.5 - - + +
127A LEU* 2.8 22.6 + - + +
128A SER* 3.6 7.0 - - - +
130A VAL* 1.3 76.4 - - - +
132A CYS* 1.3 60.0 + - - +
134A LEU* 2.9 23.1 + - + +
135A CYS* 2.9 45.9 + - + +
140A VAL* 5.8 0.2 - - + -
141A GLY 5.3 6.3 - - - +
143A VAL* 4.5 11.4 - - + -
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Residues in contact with CYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.1 17.0 - - + +
128A SER 2.7 22.3 + - - +
129A ASN* 3.0 5.8 + - - +
131A LEU* 1.3 74.7 - - - +
133A ARG* 1.3 58.8 + - - +
135A CYS* 4.8 3.4 - - - +
136A SER* 2.7 40.5 + - - +
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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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23A LEU* 4.2 18.0 - - + +
24A MET* 3.2 33.6 - - - +
77A GLU* 3.3 30.9 + - - -
81A LEU* 3.9 21.8 - - + -
129A ASN 3.0 12.1 + - - +
130A VAL 3.7 7.9 - - - +
131A LEU 3.2 0.2 - - - -
132A CYS* 1.3 78.2 - - - +
134A LEU* 1.3 63.1 + - - +
136A SER* 3.9 5.1 + - - -
137A LYS* 3.7 11.6 - - - +
138A TYR* 3.5 31.9 - - + +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 5.0 2.7 - - + +
81A LEU* 3.3 42.8 - - + +
82A VAL* 5.0 4.3 - - + +
85A TYR* 4.3 8.5 - - + -
130A VAL* 2.9 42.0 + - + +
131A LEU* 2.9 25.8 + - + +
133A ARG* 1.3 79.0 - - + +
135A CYS* 1.3 63.7 + - - +
136A SER 2.9 15.7 + - - +
138A TYR* 3.6 7.2 - - + +
139A HIS 3.5 3.1 + - - -
140A VAL* 3.4 42.6 + - + +
143A VAL* 4.7 6.5 - - + -
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Residues in contact with CYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 2.9 29.9 + - + +
132A CYS* 5.1 2.9 - - - +
134A LEU* 1.3 75.3 - - - +
136A SER* 1.3 59.5 + - - +
139A HIS* 4.8 2.3 + - - -
140A VAL* 4.2 2.2 + - - +
141A GLY* 3.3 45.2 + - - +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A CYS* 2.7 31.1 + - - -
133A ARG* 3.9 4.3 - - - -
134A LEU 2.9 4.3 + - - +
135A CYS* 1.3 79.4 - - - +
137A LYS* 1.3 58.0 + - - +
138A TYR 2.6 19.2 + - - -
139A HIS* 3.0 14.4 + - - -
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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