Contacts of the helix formed by residues 121 - 151 (chain A) in PDB entry 2RER
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 ASP 121 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A MET* 3.7 5.8 - - - -
120A PHE* 1.3 75.5 - - - +
122A ASN* 1.3 63.0 + - - +
123A ALA* 3.4 19.1 + - - +
124A HIS* 2.7 43.5 + - - +
125A MET* 3.0 17.8 + - - +
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Residues in contact with ASN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 3.6 12.0 - - - +
3A ALA* 4.0 23.4 + - + +
112A PHE* 4.4 1.5 - - - -
113A ASP* 2.8 23.8 + - - +
114A MET* 2.8 44.4 + - - +
121A ASP* 1.3 73.6 + - - +
123A ALA* 1.3 57.8 + - - +
125A MET* 4.1 0.9 - - - +
126A THR* 2.7 35.9 + - - -
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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
----------------------------------------------------------
121A ASP* 3.2 16.3 + - - +
122A ASN* 1.3 79.8 - - - +
124A HIS* 1.3 69.9 + - + +
126A THR* 3.4 6.5 + - - -
127A ALA* 3.3 19.4 + - - +
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Residues in contact with HIS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 4.3 17.8 - - + -
121A ASP* 2.7 40.4 + - - +
123A ALA* 1.3 76.9 - - + +
125A MET* 1.3 64.6 + - - +
127A ALA* 3.4 7.7 + - - +
128A HIS* 3.0 22.7 + - - +
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Residues in contact with MET 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 5.5 3.1 - - + -
88A PHE* 3.9 20.2 - - + -
112A PHE* 3.6 26.0 - - + -
114A MET* 3.6 26.2 - - + -
120A PHE* 3.7 29.1 - - + -
121A ASP 3.0 17.2 + - - +
124A HIS* 1.3 74.3 - - - +
126A THR* 1.3 57.4 + - - +
128A HIS* 3.2 21.1 + - + +
129A LEU* 2.7 59.9 + - + +
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.7 9.2 - - - +
4A ARG 3.9 20.0 + - - +
5A THR* 4.1 5.2 - - + +
112A PHE* 3.5 19.5 - - - -
122A ASN 2.7 23.1 + - - -
123A ALA* 3.5 8.0 - - - -
125A MET* 1.3 78.6 - - - +
127A ALA* 1.3 61.8 + - - +
129A LEU* 3.9 1.4 - - - +
130A ASN* 3.0 37.6 + - - +
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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
----------------------------------------------------------
123A ALA 3.3 10.1 + - - +
124A HIS* 3.7 10.3 - - - +
125A MET 3.2 0.6 - - - -
126A THR* 1.3 80.6 - - - +
128A HIS* 1.3 63.0 + - - +
130A ASN* 3.4 7.8 + - - +
131A THR* 3.2 26.9 + - - -
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 4.7 18.9 - + + -
124A HIS 3.0 17.0 + - - +
125A MET* 3.2 24.7 + - + +
127A ALA* 1.3 76.7 - - - +
129A LEU* 1.3 68.7 + - + +
131A THR* 3.4 7.2 + - - +
132A THR* 3.1 47.0 + - + +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 4.1 2.9 - - + -
88A PHE* 5.3 2.2 - - + -
91A MET* 3.8 17.5 - - + -
110A GLN* 3.6 34.1 - - - +
112A PHE* 3.7 21.5 - - + -
125A MET* 2.7 48.8 + - + +
126A THR 4.0 2.9 - - - +
128A HIS* 1.3 76.6 - - + +
130A ASN* 1.3 62.3 + - - +
132A THR* 3.1 9.8 + - - +
133A THR* 2.8 36.6 + - - +
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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
----------------------------------------------------------
5A THR* 3.4 21.2 - - - +
6A ASP 4.4 2.0 + - - +
7A ASN* 2.9 31.6 + - - +
126A THR* 3.0 33.3 + - - +
127A ALA* 3.7 7.0 - - - +
129A LEU* 1.3 76.2 - - - +
131A THR* 1.3 58.6 + - - +
133A THR* 3.8 0.2 - - - -
134A ARG* 2.9 40.8 + - + +
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA 3.2 13.1 + - - -
128A HIS* 3.6 10.5 - - - -
129A LEU 3.3 0.2 - - - -
130A ASN* 1.3 79.7 - - - +
132A THR* 1.3 67.3 + - + +
134A ARG* 3.9 4.6 - - - +
135A ALA* 3.1 23.6 + - + +
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Residues in contact with THR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 3.6 23.6 + - - +
128A HIS* 3.1 39.2 + - + +
129A LEU* 3.1 21.1 + - - +
131A THR* 1.3 76.6 - - + +
133A THR* 1.3 61.5 + - - +
135A ALA* 3.3 6.3 + - - +
136A ASN* 2.9 35.0 + - - -
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Residues in contact with THR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 5.9 0.2 - - - +
7A ASN* 3.6 24.5 - - + +
108A TRP* 4.1 20.3 - - + +
110A GLN* 4.1 20.1 + - - -
129A LEU* 2.8 25.0 + - - +
130A ASN 3.8 2.7 - - - -
132A THR* 1.3 79.6 + - - +
134A ARG* 1.3 58.7 + - - +
136A ASN* 3.2 7.6 + - - +
137A MET* 2.8 50.1 + - - +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 3.4 27.5 + - + +
130A ASN* 2.9 27.3 + - - +
131A THR* 3.9 5.4 - - - +
133A THR* 1.3 78.6 - - - +
135A ALA* 1.3 63.1 + - - +
137A MET* 3.4 6.0 + - - +
138A GLU* 3.1 40.9 + - - +
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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
----------------------------------------------------------
33A SER* 6.2 0.2 - - - -
131A THR* 3.1 20.1 + - + +
132A THR* 3.6 7.6 - - - +
134A ARG* 1.3 76.6 - - - +
136A ASN* 1.3 63.6 + - - +
138A GLU* 3.5 7.1 + - - +
139A ARG* 3.1 24.5 + - - +
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Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU 4.6 1.0 - - - +
32A PHE* 3.7 30.8 - - + -
33A SER* 3.3 32.1 + - - -
34A GLU* 3.4 30.6 + - - +
108A TRP* 4.5 4.4 - - + -
132A THR 2.9 23.4 + - - +
133A THR* 3.2 6.8 + - - +
135A ALA* 1.3 75.3 - - - +
137A MET* 1.3 60.4 + - - +
139A ARG* 3.2 5.5 + - - +
140A ILE* 2.9 37.0 + - + +
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Residues in contact with MET 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 3.5 26.2 - - - +
8A SER 4.5 3.4 - - - +
9A ILE* 3.6 33.5 - - + +
11A VAL* 5.7 0.2 - - - +
106A MET* 3.4 28.3 - - + +
108A TRP* 3.7 44.9 - - + +
133A THR* 2.8 39.6 + - - +
134A ARG* 3.9 5.8 - - - +
136A ASN* 1.3 73.2 - - - +
138A GLU* 1.3 58.6 + - - +
140A ILE* 3.9 6.0 - - - +
141A LYS* 3.0 29.8 + - - +
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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
----------------------------------------------------------
9A ILE* 3.7 19.7 - - + -
134A ARG* 3.1 32.3 + - - +
135A ALA* 3.8 6.9 - - - +
137A MET* 1.3 78.1 - - - +
139A ARG* 1.3 60.8 + - - +
141A LYS* 3.4 5.7 + - + +
142A LYS* 3.2 22.0 + - - +
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 2.7 31.3 + - - +
31A LEU 2.8 23.3 + - - +
32A PHE 4.7 1.9 - - - -
33A SER* 3.5 26.0 + - - -
135A ALA 3.1 17.5 + - - +
136A ASN* 3.7 6.5 - - - +
138A GLU* 1.3 75.4 - - - +
140A ILE* 1.3 63.7 + - - +
142A LYS* 3.4 6.8 + - + +
143A ILE* 3.1 42.3 + - + +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 5.6 0.7 - - + -
21A VAL* 5.2 0.2 - - + -
22A THR* 3.8 18.2 - - + -
31A LEU* 4.0 30.1 - - + +
32A PHE* 3.8 27.1 - - + -
106A MET* 5.0 6.7 - - - -
108A TRP* 3.5 32.1 - - + -
136A ASN 2.9 18.7 + - - +
137A MET* 3.9 4.3 - - - +
139A ARG* 1.3 73.8 - - - +
141A LYS* 1.3 64.8 + - - +
143A ILE* 3.7 7.0 - - - +
144A ILE* 2.9 46.6 + - + +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.6 22.2 - - + -
10A VAL* 2.8 26.9 + - - +
11A VAL* 4.1 19.7 - - + -
12A ASN* 3.4 14.5 + - - +
137A MET 3.0 19.7 + - - +
138A GLU* 3.5 7.0 - - + +
139A ARG 3.3 0.2 - - - -
140A ILE* 1.3 78.6 - - - +
142A LYS* 1.3 57.1 + - - +
144A ILE* 3.9 0.7 - - - +
145A GLU* 2.5 76.9 + - - +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU 3.2 11.0 + - - +
139A ARG* 3.6 10.1 - - - +
140A ILE 3.3 0.2 - - - -
141A LYS* 1.3 79.9 - - - +
143A ILE* 1.3 61.2 + - + +
145A GLU* 3.4 10.3 + - - +
146A ASP* 2.8 70.4 + - - +
149A ARG* 5.5 4.2 - - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 5.2 2.7 - - + -
30A GLU 3.9 4.5 - - - +
31A LEU* 3.9 30.7 - - + +
139A ARG* 3.1 54.5 + - + +
140A ILE* 3.7 4.9 - - - +
142A LYS* 1.3 79.0 - - + +
144A ILE* 1.3 65.9 + - + +
146A ASP* 3.3 9.0 + - - +
147A ARG* 3.1 44.0 + - + +
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.5 26.2 - - + -
13A ALA* 3.8 14.8 - - + -
17A LEU* 3.8 17.6 - - + +
18A VAL* 4.0 22.7 - - + -
21A VAL* 3.8 26.0 - - + -
22A THR* 4.0 16.4 - - + -
140A ILE* 2.9 39.6 + - + +
141A LYS 3.9 0.2 - - - +
143A ILE* 1.3 77.0 - - + +
145A GLU* 1.3 57.9 + - - +
147A ARG* 3.2 8.8 + - - +
148A HIS* 2.9 26.9 + - - +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.0 4.9 - - + -
12A ASN* 2.8 44.9 + - + +
13A ALA* 5.1 0.2 - - - -
141A LYS* 2.5 68.8 + - - +
142A LYS* 3.8 7.3 - - - +
144A ILE* 1.3 75.7 - - - +
146A ASP* 1.3 59.8 + - - +
148A HIS* 3.5 7.2 - - - +
149A ARG* 2.8 41.7 + - + +
----------------------------------------------------------
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Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 2.8 58.1 + - - +
143A ILE* 3.6 6.8 - - - +
145A GLU* 1.3 76.2 - - - +
147A ARG* 1.3 79.9 + - - +
149A ARG* 3.3 19.9 + - - +
150A GLU* 3.1 32.8 + - + +
----------------------------------------------------------
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.6 15.9 - - + -
21A VAL* 5.7 5.6 - - + -
143A ILE* 3.1 37.8 + - + +
144A ILE* 3.2 8.5 + - - +
146A ASP* 1.3 87.2 - - - +
148A HIS* 1.3 62.9 + - - +
150A GLU* 2.8 53.9 + - - +
151A GLY* 3.5 4.9 + - - -
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Residues in contact with HIS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN 3.6 20.1 + - - -
13A ALA* 4.0 10.0 - - + -
14A PRO* 3.6 29.7 - - + +
17A LEU* 3.7 17.1 - - + +
144A ILE 2.9 15.9 + - - +
145A GLU* 3.5 5.2 - - - +
147A ARG* 1.3 78.4 - - - +
149A ARG* 1.3 68.4 + - + +
151A GLY* 3.3 12.4 + - - -
152A GLN* 3.4 40.2 + - + +
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN 6.1 0.2 - - - +
142A LYS* 5.5 3.8 - - - +
145A GLU* 2.8 29.1 + - + +
146A ASP* 3.3 19.9 + - - +
148A HIS* 1.3 80.3 - - + +
150A GLU* 1.3 61.6 + - + +
152A GLN* 3.2 33.4 + - - +
153A ARG* 4.0 12.9 - - - +
----------------------------------------------------------
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASP* 3.1 26.1 + - + +
147A ARG* 2.8 51.3 + - - +
148A HIS 3.2 0.2 - - - -
149A ARG* 1.3 78.5 - - + +
151A GLY* 1.3 57.6 + - - +
152A GLN 3.1 5.1 + - - -
153A ARG* 3.6 16.3 + - - +
154A THR* 4.2 8.1 + - - -
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Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG 3.5 5.1 + - - -
148A HIS 3.3 9.2 + - - -
150A GLU* 1.3 77.5 - - - +
152A GLN* 1.3 58.9 + - - +
154A THR* 4.9 2.0 - - - -
155A PRO* 2.6 31.8 - - - +
----------------------------------------------------------
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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