Contacts of the helix formed by residues 134 - 151 (chain A) in PDB entry 1IZO
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 LEU 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A TRP* 4.3 26.0 - - + -
126A TRP* 4.8 6.1 - - + -
132A VAL* 3.7 5.4 + - - +
133A VAL* 1.3 71.1 - - - +
135A PHE* 1.3 54.0 + - - +
137A GLU* 3.2 4.2 + - + +
138A ALA* 2.7 39.0 + - + +
251A LEU* 4.0 8.5 - - + +
252A VAL* 3.9 22.0 - - + +
255A ALA* 3.6 32.1 - - + -
380A LEU* 5.0 11.0 - - + -
407A GLY 3.7 4.3 - - - +
408A PHE* 3.0 24.6 + - + +
410A MET* 3.9 18.4 - - - -
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Residues in contact with PHE 135 (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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133A VAL* 3.3 2.0 - - + -
134A LEU* 1.3 75.5 - - - +
136A GLU* 1.3 75.8 + - - +
138A ALA* 3.7 2.6 - - - +
139A LYS* 3.0 56.1 + - + +
167A ILE* 3.8 27.6 - - + -
248A SER* 3.2 35.9 - - - -
249A TYR* 3.9 28.3 - + - -
252A VAL* 3.6 8.2 - - + +
403A LEU* 3.7 29.6 - - + -
407A GLY* 3.0 29.1 + - - +
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Residues in contact with GLU 136 (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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133A VAL* 3.0 32.4 + - + +
135A PHE* 1.3 90.5 - - - +
137A GLU* 1.3 64.2 + - + +
139A LYS* 2.9 35.8 + - - +
140A GLU* 3.5 30.4 + - - +
164A ASP* 4.5 0.9 - - - +
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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
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119A TRP* 5.1 1.1 - - + -
125A ARG* 4.1 14.0 + - - -
126A TRP* 3.0 40.0 + - + -
132A VAL* 3.3 34.5 - - + +
133A VAL 2.9 15.3 + - - +
134A LEU* 3.8 5.8 - - - +
136A GLU* 1.3 76.7 - - - +
138A ALA* 1.3 66.6 + - - +
140A GLU* 3.4 6.2 + - - +
141A ILE* 3.1 33.2 + - + +
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Residues in contact with ALA 138 (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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119A TRP* 4.4 12.5 - - + -
134A LEU* 2.7 32.6 + - + +
135A PHE* 3.7 4.3 - - - +
137A GLU* 1.3 74.4 - - - +
139A LYS* 1.3 57.7 + - - +
141A ILE* 3.2 1.7 + - - +
142A LEU* 2.8 45.1 + - + +
248A SER* 3.8 20.4 - - - +
251A LEU* 4.3 11.4 - - + -
252A VAL* 5.5 0.2 - - + -
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Residues in contact with LYS 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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135A PHE* 3.0 46.8 + - + +
136A GLU* 2.9 29.7 + - - +
137A GLU 3.4 0.2 - - - -
138A ALA* 1.3 74.9 - - - +
140A GLU* 1.3 58.6 + - + +
142A LEU* 3.7 1.8 - - - +
143A CYS* 2.9 31.2 + - - +
163A ALA* 3.8 17.0 - - + +
164A ASP* 2.7 31.1 + - - +
167A ILE* 3.6 31.5 - - + +
245A VAL* 3.9 12.1 - - + +
248A SER* 4.0 15.2 - - - +
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Residues in contact with GLU 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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136A GLU* 3.5 19.6 + - - +
137A GLU* 3.4 6.1 + - - +
138A ALA 3.2 0.8 - - - -
139A LYS* 1.3 79.5 - - + +
141A ILE* 1.3 59.6 + - + +
143A CYS* 3.4 1.7 + - - +
144A ARG* 2.9 46.1 + - - +
159A VAL* 3.7 21.2 - - + +
160A LYS* 2.9 54.5 + - + +
163A ALA* 4.3 6.7 - - + -
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Residues in contact with ILE 141 (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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115A MET* 3.6 28.5 - - + -
118A GLU* 3.6 40.4 - - + +
119A TRP* 3.7 32.8 - - + -
122A ALA* 4.7 14.6 - - + -
125A ARG* 5.3 3.1 - - - +
126A TRP* 5.0 0.7 - - + -
137A GLU* 3.1 29.3 + - + +
138A ALA* 3.9 2.9 - - - +
140A GLU* 1.3 75.0 - - + +
142A LEU* 1.3 58.6 + - - +
144A ARG* 3.1 16.9 + - - +
145A VAL* 2.9 34.1 + - - +
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Residues in contact with LEU 142 (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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115A MET* 3.3 34.3 - - + -
138A ALA* 2.8 33.4 + - + +
139A LYS 3.7 2.9 - - - +
141A ILE* 1.3 79.6 - - - +
143A CYS* 1.3 52.5 + - - +
145A VAL* 3.4 1.3 + - + +
146A ALA* 2.7 37.2 + - - +
244A ILE* 3.3 28.9 - - + +
245A VAL* 3.8 14.8 - - - +
247A ILE* 4.3 0.7 - - + -
248A SER* 3.7 27.1 - - - +
251A LEU* 3.7 14.8 - - + -
372A VAL* 4.1 14.8 - - + -
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Residues in contact with CYS 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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139A LYS 2.9 18.6 + - - +
140A GLU* 3.8 3.8 - - - +
142A LEU* 1.3 76.7 - - - +
144A ARG* 1.3 62.7 + - - +
146A ALA* 4.5 1.6 - - - -
147A CYS* 3.2 33.8 + - - -
154A LEU* 3.7 12.9 - - - +
159A VAL* 4.2 4.0 - - + +
162A ARG* 3.9 15.0 - - - -
163A ALA* 3.7 32.1 - - + -
166A PHE* 4.1 15.3 - - - -
245A VAL* 3.5 14.5 - - + +
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Residues in contact with ARG 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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118A GLU* 3.3 36.6 + - - +
125A ARG* 4.1 23.6 - - - +
140A GLU* 2.9 25.0 + - - +
141A ILE* 3.4 22.5 - - - +
143A CYS* 1.3 78.1 - - - +
145A VAL* 1.3 63.4 + - - +
147A CYS* 3.5 1.9 + - - +
148A TYR* 3.1 24.7 + - - +
154A LEU* 3.9 10.5 - - + +
156A GLU* 3.0 36.5 + - - +
159A VAL* 3.9 26.6 - - + +
160A LYS* 5.7 1.0 - - - +
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Residues in contact with VAL 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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111A LEU* 3.7 27.6 - - + +
114A LEU* 3.6 31.4 - - + +
115A MET* 3.6 23.8 - - + -
118A GLU* 3.8 24.7 - - + +
141A ILE 2.9 20.0 + - - +
142A LEU* 3.8 2.9 - - + +
144A ARG* 1.3 73.1 - - - +
146A ALA* 1.3 67.8 + - - +
148A TYR* 3.2 5.5 + - - +
149A TRP* 2.9 24.1 + - - +
244A ILE* 5.8 2.2 - - + -
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Residues in contact with ALA 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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111A LEU* 4.7 0.4 - - - -
142A LEU 2.7 24.0 + - - +
143A CYS* 4.0 6.1 - - - +
145A VAL* 1.3 73.1 - - - +
147A CYS* 1.3 60.4 + - - +
149A TRP* 3.6 7.0 - - - -
150A ALA* 3.0 30.5 + - - +
241A LEU* 3.8 17.7 - - + +
244A ILE* 3.8 39.4 - - + +
245A VAL* 4.9 1.1 - - + -
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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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143A CYS* 3.2 27.0 + - - +
144A ARG 3.9 2.5 - - - +
146A ALA* 1.3 78.4 - - - +
148A TYR* 1.3 58.7 + - - +
150A ALA* 3.4 1.5 + - - -
151A GLY 2.9 6.1 + - - -
152A VAL* 2.5 69.8 + - + +
154A LEU* 4.1 20.2 - - + -
166A PHE* 5.1 2.2 - - - -
193A TRP* 4.1 16.6 - - - -
241A LEU* 4.4 11.7 - - - -
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Residues in contact with TYR 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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110A ARG* 4.2 14.5 + - - -
114A LEU* 4.1 30.3 - - + -
144A ARG 3.1 18.6 + - - +
145A VAL* 3.7 4.5 - - - +
147A CYS* 1.3 73.8 - - - +
149A TRP* 1.3 63.8 + - - +
151A GLY* 2.8 20.4 + - - -
152A VAL 4.7 2.5 - - - -
212A THR* 5.8 0.2 - - - +
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Residues in contact with TRP 149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.2 36.6 - - + -
103A MET* 5.3 1.1 - - + -
107A HIS* 3.3 34.2 + + + +
110A ARG* 3.9 25.3 - - + +
111A LEU* 3.4 36.7 - - + +
114A LEU* 3.8 12.1 - - + -
145A VAL 2.9 16.6 + - - +
146A ALA 3.6 15.5 - - - -
148A TYR* 1.3 79.3 - - - +
150A ALA* 1.3 71.2 + - + +
151A GLY 3.5 0.3 + - - -
212A THR* 3.9 18.1 - - - +
213A ALA* 4.5 7.4 - - + -
240A VAL* 3.7 31.2 - - + -
241A LEU* 5.5 0.2 - - + -
244A ILE* 3.7 13.9 - - + -
368A ILE* 4.7 4.3 - - + -
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Residues in contact with ALA 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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146A ALA 3.0 20.2 + - - +
147A CYS 3.8 3.8 - - - +
149A TRP* 1.3 83.0 - - + +
151A GLY* 1.3 58.8 - - - +
152A VAL* 3.9 15.5 - - + -
212A THR* 3.6 7.1 + - - -
213A ALA* 3.8 25.1 - - + +
214A LEU* 3.0 31.4 + - - +
237A LEU* 4.5 0.4 - - + -
241A LEU* 4.0 11.2 - - + -
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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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147A CYS 3.4 0.4 - - - -
148A TYR* 2.8 15.8 + - - -
149A TRP 3.2 1.0 + - - -
150A ALA* 1.3 81.1 - - - +
152A VAL* 1.3 59.7 + - - +
153A PRO* 3.5 11.7 - - - +
206A LEU* 5.3 1.7 - - - +
207A LYS 5.1 6.2 - - - +
212A THR* 4.7 9.0 - - - -
214A LEU* 4.1 12.8 - - - +
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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
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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