Contacts of the helix formed by residues 146 - 158 (chain E) in PDB entry 3IZ0
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 LYS 146 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145E THR* 1.3 86.1 - - - +
147E PHE* 1.3 65.6 - - - +
148E GLU* 3.2 21.0 + - - +
149E GLU* 3.4 40.4 + - + +
150E GLU* 3.1 24.6 + - + +
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Residues in contact with PHE 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E VAL* 3.6 24.7 - - + -
125E PHE* 5.4 2.0 - + - -
126E LEU* 3.6 38.8 - - + -
142E LEU* 4.5 13.7 - - + -
143E PRO 5.5 3.8 - - - +
145E THR 3.6 2.3 - - - -
146E LYS* 1.3 74.2 - - - +
148E GLU* 1.3 78.0 + - + +
149E GLU 3.0 5.4 - - - -
150E GLU* 4.2 7.2 - - - -
151E VAL* 2.9 33.8 + - + +
169E MET* 3.2 43.7 - - + -
170E TYR* 4.4 12.6 - + - -
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E LYS* 3.4 25.4 + - - +
147E PHE* 1.3 95.8 + - + +
149E GLU* 1.3 73.2 + - - +
152E PRO* 3.2 21.5 - - - +
166E LYS* 3.9 29.6 + - + +
169E MET* 3.7 24.8 - - + +
170E TYR* 3.2 46.7 + - + +
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Residues in contact with GLU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E LYS* 3.4 50.6 + - + +
147E PHE 3.0 0.2 - - - -
148E GLU* 1.3 84.5 + - - +
150E GLU* 1.3 63.3 + - - +
152E PRO* 3.3 5.1 - - - +
153E ARG* 3.1 45.9 + - - +
166E LYS* 3.1 30.8 + - + +
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Residues in contact with GLU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E TYR* 4.3 2.3 + - - +
142E LEU* 5.7 4.0 - - + -
143E PRO* 4.5 27.8 - - + +
145E THR 5.6 0.4 - - - +
146E LYS* 3.1 18.0 + - + +
147E PHE* 3.1 6.7 + - - +
149E GLU* 1.3 73.6 - - - +
151E VAL* 1.3 69.2 + - + +
153E ARG* 2.4 37.5 + - - +
154E ILE* 2.9 56.2 + - + +
111F CYS* 5.3 7.8 - - - -
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Residues in contact with VAL 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E PHE* 4.0 13.5 - - + -
126E LEU* 4.1 22.0 - - + -
129E PHE* 3.9 33.4 - - + -
142E LEU* 4.8 4.0 - - + -
147E PHE* 2.9 23.3 + - + +
150E GLU* 1.3 72.6 - - + +
152E PRO* 1.4 68.3 - - + +
154E ILE* 3.2 2.3 + - - +
155E PHE* 3.1 45.1 + - + -
169E MET* 3.6 23.1 - - + -
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Residues in contact with PRO 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E GLU 3.2 30.5 - - - +
149E GLU 3.3 7.9 - - - +
151E VAL* 1.4 92.6 - - + +
153E ARG* 1.3 61.7 + - - +
155E PHE* 3.2 3.5 + - - +
156E LYS* 3.0 22.6 + - - +
164E LEU* 3.5 38.6 - - + +
165E SER 4.5 2.2 - - - +
166E LYS 5.0 0.4 - - - +
169E MET* 3.6 19.1 - - + -
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Residues in contact with ARG 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E GLU* 3.1 37.9 + - - +
150E GLU* 2.4 65.1 + - - +
152E PRO* 1.3 78.8 - - - +
154E ILE* 1.3 59.0 + - + +
156E LYS* 3.1 10.9 + - + +
157E ASP* 2.8 50.3 + - - +
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Residues in contact with ILE 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E PHE* 3.9 20.6 - - + -
133E TYR* 3.4 50.9 - - + +
140E TYR* 3.4 23.8 - - + +
150E GLU* 2.9 38.2 + - + +
151E VAL 3.2 6.3 + - - +
153E ARG* 1.3 74.6 - - + +
155E PHE* 1.3 66.4 + - - +
157E ASP* 3.2 8.2 + - + +
158E LEU* 3.0 30.2 + - + +
110F LEU* 6.1 0.2 - - + -
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Residues in contact with PHE 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E PHE* 5.3 2.9 - + - -
129E PHE* 3.6 25.6 - + - -
151E VAL* 3.1 31.9 + - + -
152E PRO 3.8 4.5 - - - +
154E ILE* 1.3 77.6 - - + +
156E LYS* 1.3 63.2 + - - +
158E LEU* 3.4 7.7 + - + +
159E GLY 3.4 3.6 + - - -
160E TYR* 3.0 51.6 + + + +
164E LEU* 3.6 28.0 - - + -
184E ALA* 3.3 39.9 - - + -
185E LEU* 4.4 10.1 - - + -
187E TRP* 4.1 13.9 - + - -
188E LEU* 4.1 21.5 - - + -
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Residues in contact with LYS 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E PRO 3.0 13.4 + - - +
153E ARG* 3.4 13.5 - - + +
155E PHE* 1.3 76.7 - - - +
157E ASP* 1.3 65.3 + - - +
159E GLY* 2.8 23.0 + - - -
160E TYR 4.7 7.5 - - - +
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Residues in contact with ASP 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ARG* 2.8 43.9 + - - +
154E ILE* 3.2 8.7 + - - +
156E LYS* 1.3 79.3 - - - +
158E LEU* 1.3 59.2 + - - +
159E GLY 3.3 0.6 + - - -
42F PRO* 4.5 20.0 - - + +
43F GLU* 6.0 1.4 - - - +
85F PHE* 5.2 5.4 - - - +
110F LEU* 3.9 39.0 - - + +
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Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E PHE* 6.2 0.7 - - + -
133E TYR* 4.2 2.9 - - + -
136E LEU* 3.8 22.7 - - + -
154E ILE* 3.0 35.2 + - + +
155E PHE* 3.8 9.0 - - + +
156E LYS 3.1 0.4 - - - -
157E ASP* 1.3 77.6 - - - +
159E GLY* 1.3 59.8 + - - +
160E TYR 3.6 0.2 - - - -
187E TRP* 3.5 16.7 - - + -
188E LEU* 3.6 31.9 - - + -
191E CYS* 5.3 0.9 - - - -
81F GLY 4.3 2.5 - - - -
82F PHE* 3.3 44.6 - - + +
85F PHE* 4.6 4.3 - - + -
110F LEU* 3.7 29.6 - - + -
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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