Contacts of the helix formed by residues 136 - 158 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLU* 4.9 8.1 - - - +
134B ASN 4.0 0.6 + - - -
135B LEU* 1.3 75.3 - - - +
137B GLU* 1.3 66.4 + - - +
138B LYS* 4.2 15.0 - - + -
139B TYR* 2.8 42.7 + - + +
140B GLN* 3.2 8.9 + - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG 5.2 0.2 - - - +
135B LEU 3.5 2.9 + - - +
136B ALA* 1.3 71.5 - - - +
138B LYS* 1.3 63.7 + - - +
140B GLN* 3.2 32.1 + - - +
141B THR* 3.1 28.1 + - - +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 4.2 6.3 + - - -
136B ALA* 4.2 11.4 - - + -
137B GLU* 1.3 78.9 - - - +
139B TYR* 1.3 98.4 + - + +
141B THR* 3.7 7.1 + - - -
142B VAL* 3.4 26.9 + - - +
189B ALA* 2.8 40.0 + - + +
190B SER* 4.1 4.6 + - - +
191B GLU* 5.1 5.5 + - - -
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 2.6 44.8 + - + +
65B MET* 4.8 5.2 - - - -
68B ALA* 4.1 19.7 - - + -
135B LEU* 4.4 15.0 - - + -
136B ALA* 2.8 33.8 + - + +
138B LYS* 1.3 93.0 - - + +
140B GLN* 1.3 67.4 + - - +
142B VAL* 3.2 1.7 + - - +
143B ILE* 3.0 30.5 + - + +
186B LEU* 3.6 44.0 - - + -
189B ALA* 4.0 3.8 - - + -
190B SER* 3.2 28.0 - - - -
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TYR* 3.4 27.2 - - - +
132B PHE* 3.6 41.1 - - + +
133B ARG* 2.9 37.1 + - - +
135B LEU* 3.2 13.2 + - + +
136B ALA 3.2 12.0 + - - +
137B GLU* 3.4 31.0 + - - +
139B TYR* 1.3 78.9 - - - +
141B THR* 1.3 57.7 + - - +
143B ILE* 5.1 0.4 - - - -
144B ALA* 2.9 33.8 + - - +
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Residues in contact with THR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 4.7 5.8 + - - -
137B GLU* 3.1 15.8 + - - +
138B LYS* 3.8 7.5 - - - -
139B TYR 3.2 0.2 - - - -
140B GLN* 1.3 79.6 - - - +
142B VAL* 1.3 63.7 + - + +
144B ALA* 4.0 2.0 - - - +
145B ASP* 3.0 26.9 + - + +
185B ARG* 5.4 5.8 - - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 5.7 0.4 - - + -
138B LYS 3.4 15.0 + - - +
139B TYR 3.2 6.8 + - - +
141B THR* 1.3 78.1 - - + +
143B ILE* 1.3 65.9 + - - +
146B ILE* 3.1 21.1 + - - +
182B GLY* 3.3 35.4 - - - +
185B ARG* 3.3 56.3 + - + +
186B LEU* 3.8 15.0 - - + -
189B ALA* 5.0 4.7 - - + -
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 3.8 22.9 - - - +
72B PHE* 3.7 41.8 - - + +
75B VAL* 4.2 22.0 - - + -
104B LEU* 4.6 0.7 - - + -
132B PHE* 3.8 19.7 - - + -
135B LEU* 4.0 20.9 - - + -
139B TYR* 3.0 23.3 + - + +
140B GLN 3.9 2.7 - - - +
142B VAL* 1.3 75.1 - - + +
144B ALA* 1.3 56.6 + - - +
146B ILE* 3.3 2.1 + - - +
147B CYS* 3.0 29.4 + - - -
186B LEU* 4.3 13.7 - - + -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B HIS* 3.4 16.7 - - + +
104B LEU* 4.0 18.2 - - + -
105B TYR* 3.5 30.3 - - + +
140B GLN 2.9 18.5 + - - +
141B THR* 4.0 2.5 - - - +
143B ILE* 1.3 77.0 - - - +
145B ASP* 1.3 57.2 + - - +
147B CYS 3.1 1.0 + - - -
148B ARG* 2.9 26.9 + - - +
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Residues in contact with ASP 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B THR* 3.0 17.9 + - + +
144B ALA* 1.3 75.8 - - - +
146B ILE* 1.3 61.4 + - - +
148B ARG* 2.7 40.8 + - - +
149B ARG* 3.1 39.4 + - - +
185B ARG* 2.8 34.5 + - - +
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PHE* 4.0 19.7 - - + -
76B LEU* 4.7 0.7 - - + -
142B VAL 3.1 18.3 + - - +
143B ILE 3.7 3.8 - - - +
145B ASP* 1.3 74.8 - - - +
147B CYS* 1.3 60.4 + - - +
149B ARG* 3.4 8.1 + - - +
150B MET* 2.8 47.4 + - + +
178B LEU* 3.6 41.6 - - + +
181B ILE* 4.2 12.1 - - + -
182B GLY* 3.6 24.9 - - - +
185B ARG* 3.7 14.1 - - - +
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Residues in contact with CYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 5.2 1.1 - - - -
75B VAL* 3.1 36.8 - - - -
76B LEU* 4.9 9.9 - - - -
79B LEU* 3.8 15.8 - - - +
97B LEU 4.6 2.8 - - - +
100B PHE* 4.0 21.7 - - + +
101B HIS* 4.2 11.9 + - + -
104B LEU* 4.3 2.9 - - + -
143B ILE* 3.0 21.0 + - - +
144B ALA* 3.5 8.5 - - - +
146B ILE* 1.3 75.8 - - - +
148B ARG* 1.3 56.9 + - - +
150B MET* 3.8 1.6 - - - +
151B GLY* 2.9 27.2 + - - -
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU 5.7 0.4 - - - -
98B HIS 5.0 4.7 - - - +
101B HIS* 3.7 42.8 - - + +
144B ALA 2.9 13.0 + - - +
145B ASP* 2.7 35.3 + - - +
147B CYS* 1.3 76.9 - - - +
149B ARG* 1.3 81.0 + - - +
151B GLY* 3.5 1.3 + - - -
152B ILE* 3.1 52.9 + - + +
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ASP* 3.1 33.9 + - - +
146B ILE* 3.8 9.8 - - - +
148B ARG* 1.3 94.6 - - - +
150B MET* 1.3 67.2 + - - +
152B ILE* 3.3 11.9 + - - +
153B GLY* 3.1 18.9 + - - -
173B HIS* 5.2 3.2 + - - -
174B TYR* 4.1 7.9 - - + -
178B LEU* 3.3 40.3 - - + +
181B ILE* 4.7 11.7 - - - +
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.7 34.1 - - + -
79B LEU* 3.8 15.3 - - + -
80B ASP* 4.6 9.9 - - - +
146B ILE* 2.8 20.1 + - + +
147B CYS* 3.8 3.8 - - - +
149B ARG* 1.3 76.2 - - - +
151B GLY* 1.3 57.2 + - - +
153B GLY* 3.1 3.1 + - - -
154B MET* 2.8 53.8 + - + +
174B TYR* 3.2 27.2 - - - +
175B VAL* 4.2 6.7 - - - +
178B LEU* 3.6 22.8 - - + +
179B VAL* 3.8 19.1 - - + -
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 4.3 2.4 - - - +
97B LEU* 3.2 32.9 - - - +
98B HIS* 4.3 1.3 - - - -
147B CYS 2.9 14.5 + - - -
148B ARG 3.9 0.9 - - - -
149B ARG 3.3 0.2 - - - -
150B MET* 1.3 76.8 - - - +
152B ILE* 1.3 62.7 + - - +
154B MET* 3.3 12.0 + - - -
155B ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B HIS* 3.7 27.6 + - + +
148B ARG* 3.1 46.0 + - + +
149B ARG* 3.5 9.2 - - + +
150B MET 3.3 0.2 - - - -
151B GLY* 1.3 74.8 - - - +
153B GLY* 1.3 65.3 + - - +
155B ALA* 3.3 3.3 + - - +
156B GLU* 3.1 28.8 + - + +
174B TYR* 5.2 3.4 - - + +
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG 3.1 11.1 + - - -
150B MET 3.5 2.7 - - - -
152B ILE* 1.3 77.3 - - - +
154B MET* 1.3 61.4 + - - +
156B GLU* 3.0 22.2 + - - +
157B PHE* 3.2 10.7 + - - -
171B TYR* 6.2 0.2 - - - -
174B TYR* 3.4 42.4 - - - -
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Residues in contact with MET 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 3.3 33.9 - - + +
80B ASP* 4.5 7.2 - - - +
83B GLU* 3.5 40.0 - - + +
97B LEU* 3.3 33.9 - - + -
150B MET* 2.8 41.7 + - + +
151B GLY* 3.9 6.3 - - - +
153B GLY* 1.3 72.0 - - - +
155B ALA* 1.3 62.0 + - - +
157B PHE* 3.4 5.9 + - - +
158B LEU* 3.3 26.9 + - - +
171B TYR* 5.5 1.3 - - - -
174B TYR* 4.7 2.0 - - + -
175B VAL* 4.3 12.6 - - + -
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 4.4 16.7 - - + +
97B LEU* 3.9 17.2 - - + +
98B HIS* 3.8 26.2 - - + +
151B GLY 3.0 18.1 + - - +
152B ILE 3.6 4.0 - - - +
154B MET* 1.3 77.6 - - - +
156B GLU* 1.3 61.1 + - - +
158B LEU* 3.4 21.0 + - - +
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ILE* 3.1 16.2 + - + +
153B GLY* 3.0 23.6 + - - +
155B ALA* 1.3 78.3 - - - +
157B PHE* 1.3 66.4 + - + +
158B LEU 3.7 0.2 + - - -
159B ASP 4.8 1.6 + - - -
160B LYS* 3.2 36.8 + - - +
170B LYS* 5.9 2.4 + - - +
174B TYR* 2.7 33.8 + - - -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU* 5.5 0.4 - - - +
153B GLY 3.2 18.8 + - - +
154B MET 3.4 4.2 + - - +
155B ALA 3.2 0.2 - - - -
156B GLU* 1.3 81.0 - - + +
158B LEU* 1.3 65.4 + - - +
159B ASP 3.3 2.5 - - - -
160B LYS* 2.9 56.0 + - - +
162B VAL* 4.2 5.6 - - + -
167B GLU* 3.3 50.9 - - + -
170B LYS* 3.9 9.4 - - + -
171B TYR* 3.6 42.8 - + + -
174B TYR* 3.7 28.0 - + - -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU* 4.5 16.4 - - + +
86B MET* 5.6 8.7 - - + +
90B VAL* 4.3 20.0 - - + -
93B LYS* 3.8 36.6 - - + +
94B VAL* 3.9 27.6 - - + -
97B LEU* 4.1 14.6 - - + -
154B MET 3.3 20.0 + - - +
155B ALA* 3.4 14.4 + - - +
156B GLU 3.4 0.8 - - - -
157B PHE* 1.3 77.1 - - - +
159B ASP* 1.3 64.2 + - + +
160B LYS 3.8 0.3 + - - -
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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) + - + + + + + -
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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