Contacts of the helix formed by residues 158 - 173 (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 GLU 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A PRO 4.4 3.3 - - - +
154A LEU* 3.9 16.1 - - + +
155A LYS* 2.7 54.8 + - - +
157A THR* 1.3 73.2 + - - +
159A VAL* 1.3 65.2 + - - +
160A LYS 3.4 2.2 - - - -
161A GLU* 3.0 17.6 + - - +
162A ARG* 2.9 57.7 + - + +
193A TRP* 3.8 11.1 + - - -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU* 3.7 40.2 - - + +
143A CYS* 4.2 2.8 - - + -
144A ARG* 3.9 16.6 - - + +
154A LEU* 4.0 27.3 - - + +
155A LYS 3.3 3.6 + - - +
156A GLU* 3.5 45.9 + - - +
158A GLU* 1.3 75.8 - - - +
160A LYS* 1.3 62.5 + - + +
162A ARG* 3.2 1.6 + - - +
163A ALA* 2.9 31.7 + - - +
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Residues in contact with LYS 160 (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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140A GLU* 2.9 46.7 + - - +
144A ARG* 5.7 0.8 - - - +
156A GLU* 4.4 24.4 + - - +
157A THR 5.4 4.3 - - - +
158A GLU 3.2 1.0 + - - -
159A VAL* 1.3 84.2 - - + +
161A GLU* 1.3 53.4 + - - +
163A ALA* 3.7 0.7 - - - +
164A ASP* 2.7 48.4 + - - +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR 5.1 3.7 + - - +
158A GLU* 3.0 19.8 + - - +
160A LYS* 1.3 78.7 - - - +
162A ARG* 1.3 87.8 + - - +
164A ASP* 3.8 6.6 - - - +
165A ASP* 3.1 38.2 + - - +
189A ARG* 5.6 6.4 - - - +
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Residues in contact with ARG 162 (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* 3.9 13.9 - - - -
154A LEU* 3.8 12.6 - - + -
158A GLU* 2.9 45.6 + - + +
159A VAL 3.9 2.7 - - - +
161A GLU* 1.3 97.5 + - - +
163A ALA* 1.3 66.3 + - - +
165A ASP* 3.2 15.2 + - - +
166A PHE* 3.0 30.5 + - + -
189A ARG* 3.9 16.6 + - - +
190A ALA* 4.7 1.2 - - - +
193A TRP* 3.5 69.7 - - + +
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Residues in contact with ALA 163 (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* 3.8 38.4 - - + +
140A GLU* 4.3 8.3 - - + +
143A CYS* 3.7 13.6 - - + -
159A VAL 2.9 16.9 + - - +
160A LYS 3.7 4.0 - - - +
162A ARG* 1.3 78.0 - - - +
164A ASP* 1.3 62.9 + - - +
166A PHE* 3.2 7.2 + - - +
167A ILE* 3.1 26.7 + - - +
245A VAL* 4.3 1.7 - - - +
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Residues in contact with ASP 164 (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* 4.5 1.2 - - - +
139A LYS* 2.7 36.5 + - - +
160A LYS* 2.7 34.1 + - - +
161A GLU* 3.8 7.3 - - - +
163A ALA* 1.3 74.7 - - - +
165A ASP* 1.3 58.1 + - - +
167A ILE* 3.5 2.0 + - - +
168A ASP* 3.0 39.1 + - - +
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Residues in contact with ASP 165 (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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161A GLU* 3.1 27.3 + - - +
162A ARG* 3.2 15.8 + - - +
164A ASP* 1.3 76.9 - - - +
166A PHE* 1.3 67.5 + - + +
168A ASP* 3.4 4.0 + - - +
169A MET* 3.3 26.6 + - + +
186A ALA* 3.4 22.0 - - + +
189A ARG* 3.0 55.4 + - - +
190A ALA* 4.6 5.0 + - + -
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Residues in contact with PHE 166 (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* 4.1 16.8 - - - -
147A CYS* 5.1 2.2 - - - -
162A ARG 3.0 26.2 + - - -
163A ALA* 3.2 6.0 + - - +
165A ASP* 1.3 77.4 - - + +
167A ILE* 1.3 63.4 + - - +
169A MET* 3.2 27.8 + - + +
170A VAL* 3.3 16.4 + - - +
190A ALA* 4.7 4.7 - - + -
193A TRP* 3.9 28.0 - + - -
238A ILE* 4.3 19.1 - - + -
241A LEU* 3.7 28.7 - - + -
242A ARG* 3.7 34.9 - - + +
245A VAL* 4.0 29.2 - - + -
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Residues in contact with ILE 167 (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* 3.8 17.3 - - + -
139A LYS* 3.6 26.7 - - + +
163A ALA 3.1 16.2 + - - +
164A ASP* 4.0 3.6 - - - +
166A PHE* 1.3 75.3 - - - +
168A ASP* 1.3 59.0 + - - +
170A VAL* 3.0 5.7 + - + -
171A ASP* 2.7 37.9 + - + +
245A VAL* 3.8 20.6 - - + +
246A ALA* 4.3 2.9 - - - +
248A SER* 3.7 22.7 - - - +
249A TYR* 3.7 29.2 - - + +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 3.0 26.6 + - - +
165A ASP* 3.7 13.6 - - - +
166A PHE 3.3 0.6 - - - -
167A ILE* 1.3 78.3 - - - +
169A MET* 1.3 60.3 + - - +
171A ASP* 3.6 7.2 + - - +
172A ALA* 3.2 25.5 + - - +
179A ARG 4.5 1.2 - - - +
182A LYS* 3.7 53.1 + - + +
183A GLY* 3.4 5.5 + - - -
186A ALA* 4.0 4.0 - - + +
189A ARG* 4.8 4.0 + - - -
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Residues in contact with MET 169 (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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77A SER 3.6 15.0 - - - +
78A LEU* 4.0 14.6 + - - +
165A ASP* 3.3 22.0 + - + +
166A PHE* 3.2 18.5 + - + +
167A ILE 3.1 0.4 - - - -
168A ASP* 1.3 76.2 - - - +
170A VAL* 1.3 66.6 + - - +
172A ALA* 3.3 10.4 + - - +
173A PHE 3.6 7.3 + - - -
183A GLY* 4.1 8.7 - - - +
186A ALA* 4.0 4.0 - - + +
187A ARG* 3.6 54.5 - - - +
190A ALA* 3.4 32.5 - - + -
238A ILE* 4.6 4.5 - - + -
242A ARG* 4.0 14.6 - - - -
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Residues in contact with VAL 170 (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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78A LEU* 4.0 6.7 - - - -
166A PHE 3.5 13.2 - - - +
167A ILE* 3.0 10.0 + - + +
169A MET* 1.3 77.6 - - - +
171A ASP* 1.3 61.5 + - - +
172A ALA 3.2 1.0 + - - -
173A PHE* 3.1 31.0 - - + -
242A ARG* 3.8 11.7 - - + +
246A ALA* 3.9 13.5 - - + -
249A TYR* 3.6 29.4 - - + +
289A PHE* 4.3 3.8 - - + -
401A PRO* 3.5 7.7 - - + +
601A PAM 3.4 41.1 - - + +
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Residues in contact with ASP 171 (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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167A ILE* 2.7 25.2 + - + +
168A ASP* 3.9 7.2 - - - +
170A VAL* 1.3 72.3 - - - +
172A ALA* 1.3 58.5 + - - +
173A PHE 3.5 0.4 - - - -
175A ALA* 4.0 0.3 - - - +
179A ARG* 3.1 52.1 + - + +
249A TYR* 3.2 18.0 + - - +
399A ARG* 2.9 41.8 + - - -
401A PRO* 3.8 9.2 - - - +
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Residues in contact with ALA 172 (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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77A SER* 4.1 9.4 - - - -
168A ASP 3.2 17.0 + - - +
169A MET 3.8 4.0 - - - +
170A VAL 3.1 1.2 - - - -
171A ASP* 1.3 77.6 - - - +
173A PHE* 1.3 65.0 - - - +
174A GLY 3.2 3.3 + - - -
175A ALA* 3.2 9.6 + - - +
179A ARG 3.4 20.9 - - - +
180A HIS* 3.1 36.9 + - - +
183A GLY* 3.6 9.0 - - - -
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Residues in contact with PHE 173 (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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73A ARG* 3.4 13.9 + - - -
74A VAL* 4.7 9.8 - - + +
77A SER* 4.2 10.5 + - - -
78A LEU* 3.8 36.1 - - + -
169A MET 3.6 3.0 + - - -
170A VAL* 3.1 24.7 + - + +
171A ASP 3.5 0.2 - - - -
172A ALA* 1.3 78.2 - - - +
174A GLY* 1.3 75.2 + - - +
180A HIS* 5.4 0.2 - - - -
289A PHE 4.0 7.0 - - - -
291A PRO* 3.6 26.9 - - + -
400A MET* 3.5 28.9 - - + -
401A PRO* 3.6 31.0 - - + -
601A PAM 3.8 45.9 - - + +
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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