Contacts of the helix formed by residues 136 - 159 (chain A) in PDB entry 1EZF
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 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 4.8 7.0 - - - +
134A ASN 3.8 0.6 + - - -
135A LEU* 1.3 74.7 - - - +
137A GLU* 1.3 62.1 + - + +
138A LYS* 3.4 31.6 - - + +
139A TYR* 2.8 38.1 + - + +
140A GLN 3.1 8.7 + - - -
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU 3.4 3.9 + - - -
136A ALA* 1.3 71.7 - - + +
138A LYS* 1.3 58.9 + - - +
140A GLN* 3.6 15.7 - - + +
141A THR* 2.8 37.3 + - - +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 3.4 20.1 + - - -
136A ALA* 3.0 20.5 + - + +
137A GLU* 1.3 81.0 - - - +
139A TYR* 1.3 83.0 + - + +
141A THR* 3.9 6.4 - - - -
142A VAL* 3.5 23.2 + - - +
189A ALA* 3.1 38.2 - - + +
190A SER* 4.7 0.7 - - - +
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Residues in contact with TYR 139 (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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64A GLU* 2.9 47.4 + - + +
65A MET* 5.5 0.7 - - - -
68A ALA* 4.1 15.0 - - + -
135A LEU* 4.4 17.9 - - + -
136A ALA* 2.8 27.0 + - + +
138A LYS* 1.3 95.8 - - + +
140A GLN* 1.3 66.6 + - - +
141A THR 3.2 0.2 - - - -
142A VAL* 3.0 6.1 + - - +
143A ILE* 3.0 27.7 + - + +
186A LEU* 3.6 35.6 - - + +
189A ALA* 3.7 23.6 - - + -
190A SER* 3.2 27.8 - - - -
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Residues in contact with GLN 140 (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 TYR* 3.2 33.7 + - - +
132A PHE* 3.2 36.8 - - + +
133A ARG* 2.8 35.3 + - - +
135A LEU* 2.8 20.2 + - + +
136A ALA 3.1 9.2 + - - +
137A GLU* 3.6 17.1 - - + +
139A TYR* 1.3 74.7 - - - +
141A THR* 1.3 63.4 + - - +
143A ILE* 3.2 1.4 + - - +
144A ALA* 2.9 28.1 + - - +
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 5.0 0.6 + - - -
137A GLU* 2.8 23.4 + - - +
138A LYS* 3.9 8.3 - - - -
140A GLN* 1.3 76.2 - - - +
142A VAL* 1.3 66.1 + - + +
144A ALA* 4.0 3.9 - - - +
145A ASP* 3.2 23.2 + - + +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 5.8 0.4 - - + -
138A LYS 3.5 16.2 - - - +
139A TYR 3.0 7.9 + - - +
141A THR* 1.3 80.6 - - + +
143A ILE* 1.3 64.0 + - + +
145A ASP* 3.4 5.8 + - - +
146A ILE* 3.2 23.6 + - + +
182A GLY* 3.4 35.7 - - - +
185A ARG* 3.9 33.7 - - + +
186A LEU* 3.9 15.0 - - + -
189A ALA* 5.5 2.7 - - + -
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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
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68A ALA 4.1 14.6 - - - +
72A PHE* 3.7 42.2 - - + +
75A VAL* 4.6 8.5 - - + -
104A LEU* 4.7 0.9 - - + -
132A PHE* 3.6 27.4 - - + -
135A LEU* 3.7 29.6 - - + -
139A TYR* 3.0 16.1 + - + +
142A VAL* 1.3 72.4 - - + +
144A ALA* 1.3 64.9 + - - +
146A ILE* 3.3 3.9 + - - +
147A CYS* 3.0 33.2 + - - -
186A LEU* 4.4 13.9 - - + -
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Residues in contact with ALA 144 (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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101A HIS* 3.8 9.5 - - + +
104A LEU* 4.0 21.8 - - + -
105A TYR* 4.3 20.0 - - + +
132A PHE* 4.5 0.6 - - - -
140A GLN 2.9 20.4 + - - +
141A THR* 4.0 4.3 - - - +
143A ILE* 1.3 73.9 - - - +
145A ASP* 1.3 63.3 + - - +
147A CYS* 3.3 2.8 + - - +
148A ARG* 3.0 25.0 + - - +
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Residues in contact with ASP 145 (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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141A THR* 3.2 16.9 + - + +
142A VAL* 3.7 5.4 - - - +
143A ILE 3.3 0.2 - - - -
144A ALA* 1.3 79.5 - - - +
146A ILE* 1.3 69.7 + - - +
148A ARG* 3.2 31.8 + - - +
149A ARG* 3.1 54.2 + - - +
185A ARG* 5.2 9.0 + - - -
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Residues in contact with ILE 146 (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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72A PHE* 4.2 19.1 - - + -
76A LEU* 4.7 10.1 - - + -
142A VAL* 3.2 15.7 + - + +
143A ILE 3.3 5.8 + - - +
145A ASP* 1.3 86.4 - - - +
147A CYS* 1.3 53.9 + - - +
149A ARG* 3.4 3.2 + - - +
150A MET* 2.7 41.5 + - + +
178A LEU* 3.3 61.3 - - + +
179A VAL* 4.4 2.0 - - - +
181A ILE* 4.4 7.9 - - + -
182A GLY* 3.8 19.5 - - - +
185A ARG* 5.3 4.7 - - - +
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Residues in contact with CYS 147 (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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72A PHE* 5.1 1.6 - - - -
75A VAL* 3.4 33.0 - - - -
76A LEU* 4.9 13.2 - - - -
79A LEU* 4.1 8.0 - - - +
97A LEU 4.7 1.9 - - - +
100A PHE* 3.9 20.3 - - + -
101A HIS* 4.1 14.4 + - + +
104A LEU* 4.6 3.4 - - + -
143A ILE* 3.0 24.9 + - - +
144A ALA* 3.7 5.8 - - - +
146A ILE* 1.3 75.6 - - - +
148A ARG* 1.3 60.2 + - - +
150A MET* 3.8 4.8 - - - +
151A GLY* 2.9 26.2 + - - -
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Residues in contact with ARG 148 (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 HIS 5.2 3.4 - - - +
101A HIS* 3.6 44.6 - - + +
144A ALA 3.0 16.9 + - - +
145A ASP* 3.2 28.7 + - - +
147A CYS* 1.3 74.9 - - - +
149A ARG* 1.3 90.7 + - - +
151A GLY* 3.1 3.2 + - - -
152A ILE* 3.1 41.1 + - + +
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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
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145A ASP* 3.1 42.0 + - - +
146A ILE* 3.9 1.6 - - - +
148A ARG* 1.3 100.4 - - - +
150A MET* 1.3 61.8 + - - +
152A ILE* 3.5 9.6 + - - +
153A GLY 3.1 16.6 + - - -
174A TYR* 3.6 13.6 - - + -
178A LEU* 3.6 32.6 - - + +
185A ARG* 5.2 9.7 - - - +
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Residues in contact with MET 150 (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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76A LEU* 3.6 30.7 - - + -
79A LEU* 3.4 29.6 - - + -
80A ASP* 3.2 27.8 - - - +
146A ILE* 2.7 25.1 + - + +
147A CYS* 3.8 4.0 - - - +
149A ARG* 1.3 69.4 - - - +
151A GLY* 1.3 55.8 + - - +
153A GLY* 3.0 2.5 + - - -
154A MET* 2.7 52.7 + - + +
174A TYR* 3.0 31.4 - - - +
175A VAL* 4.0 18.6 - - - +
178A LEU* 3.8 2.4 - - + +
179A VAL* 4.5 4.0 - - - -
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Residues in contact with GLY 151 (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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79A LEU* 4.3 4.2 - - - +
97A LEU* 3.1 31.2 - - - +
98A HIS* 4.1 4.3 - - - -
147A CYS 2.9 13.8 + - - -
148A ARG 3.1 3.8 + - - -
150A MET* 1.3 73.1 - - - +
152A ILE* 1.3 66.7 + - - +
154A MET* 3.1 9.7 + - - +
155A ALA* 3.1 24.1 + - - +
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Residues in contact with ILE 152 (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 HIS* 3.6 32.7 + - + +
148A ARG* 3.1 30.8 + - + +
149A ARG* 3.6 9.9 - - - +
151A GLY* 1.3 74.1 - - - +
153A GLY* 1.3 58.9 + - - +
155A ALA* 3.4 3.1 + - - +
156A GLU* 2.9 37.3 + - + +
174A TYR* 5.0 5.8 - - + +
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Residues in contact with GLY 153 (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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149A ARG 3.1 4.8 + - - -
150A MET 3.0 8.2 + - - -
152A ILE* 1.3 78.1 - - - +
154A MET* 1.3 64.0 + - - +
156A GLU* 3.3 4.4 + - - +
157A PHE* 3.3 26.5 + - - +
171A TYR* 4.9 1.5 - - - -
174A TYR* 3.4 41.3 - - - -
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Residues in contact with MET 154 (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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79A LEU* 3.2 37.7 - - + +
80A ASP* 4.4 2.2 - - - +
83A GLU* 3.2 60.5 - - + +
97A LEU* 3.5 22.4 - - + +
150A MET* 2.7 57.4 + - + +
151A GLY* 3.1 5.4 + - - +
153A GLY* 1.3 71.6 - - - +
155A ALA* 1.3 64.1 + - - +
157A PHE* 3.3 3.6 + - - +
158A LEU* 3.0 23.4 + - - +
171A TYR* 5.1 4.0 - - - -
174A TYR* 4.9 0.4 - - - +
175A VAL* 4.2 9.2 - - + -
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Residues in contact with ALA 155 (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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94A VAL* 4.3 15.6 - - + +
97A LEU* 3.5 16.5 - - + +
98A HIS* 3.3 38.8 - - + +
151A GLY 3.1 9.4 + - - +
152A ILE 3.6 2.2 - - - +
154A MET* 1.3 76.7 - - - +
156A GLU* 1.3 64.3 + - - +
158A LEU* 3.1 19.5 + - - +
159A ASP* 4.1 6.9 - - - +
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Residues in contact with GLU 156 (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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152A ILE* 2.9 23.7 + - + +
153A GLY 3.4 6.3 - - - +
155A ALA* 1.3 78.0 - - - +
157A PHE* 1.3 66.1 + - + +
158A LEU 3.7 0.2 + - - -
159A ASP* 4.1 6.4 - - - +
160A LYS* 3.3 41.7 + - - +
170A LYS* 2.8 27.6 + - - -
174A TYR* 2.9 28.0 + - - -
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Residues in contact with PHE 157 (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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153A GLY 3.3 17.3 + - - +
154A MET 3.7 1.3 - - - +
155A ALA 3.2 0.6 - - - -
156A GLU* 1.3 97.0 - - + +
158A LEU* 1.3 63.5 + - - +
159A ASP 3.4 2.2 - - - -
160A LYS* 3.2 35.1 - - + +
162A VAL* 3.9 28.7 - - + +
167A GLU* 3.4 53.6 - - + -
170A LYS* 3.7 18.6 - - + -
171A TYR* 3.6 35.0 - + + -
174A TYR* 3.8 9.0 - + - -
230A PHE* 6.0 1.9 - - - -
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Residues in contact with LEU 158 (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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83A GLU* 4.6 11.4 - - + +
86A MET* 4.7 9.9 - - + -
90A VAL* 4.0 30.9 - - + +
93A LYS* 3.7 50.9 - - + +
94A VAL* 4.3 11.7 - - + -
97A LEU* 3.9 14.8 - - + -
154A MET 3.0 14.5 + - - +
155A ALA 3.1 9.5 + - - +
157A PHE* 1.3 79.7 - - - +
159A ASP* 1.3 60.0 + - + +
160A LYS 3.9 0.7 + - - +
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Residues in contact with ASP 159 (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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90A VAL* 4.6 23.7 - - + +
155A ALA 4.1 5.6 - - - +
156A GLU 4.1 9.9 - - - +
158A LEU* 1.3 75.3 - - + +
160A LYS* 1.3 62.0 + - - +
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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