Contacts of the helix formed by residues 168 - 183 (chain A) in PDB entry 1Z0I
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 GLY 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TYR* 5.6 2.3 - - - +
160A HIS 3.8 14.8 - - - +
161A THR* 3.9 7.8 - - - +
166A ASN 4.2 0.6 + - - -
167A LYS* 1.3 72.7 - - - +
169A ILE* 1.3 57.2 + - - +
170A GLU 3.7 1.1 - - - -
171A GLU* 3.7 12.8 + - - +
172A LEU* 3.2 25.5 + - - +
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Residues in contact with ILE 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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35A LEU* 3.8 25.1 - - + +
38A ARG* 3.9 9.9 - - + -
39A TYR* 3.9 33.9 - - + -
161A THR* 3.9 10.3 - - + -
162A SER 3.7 22.7 - - - +
163A ALA* 3.8 16.8 - - - -
166A ASN* 3.8 21.9 + - - +
167A LYS 3.3 3.3 - - - +
168A GLY* 1.3 75.4 - - - +
170A GLU* 1.3 67.8 + - - +
171A GLU 3.2 1.1 - - - -
172A LEU* 3.3 5.7 + - + +
173A PHE* 3.2 36.2 + - + -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.7 26.7 + - - -
61A LEU* 5.6 4.2 - - - +
166A ASN* 5.4 1.2 + - - -
169A ILE* 1.3 77.2 - - - +
171A GLU* 1.3 61.4 + - - +
173A PHE* 4.2 1.2 - - - +
174A LEU* 3.2 37.3 + - + +
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 5.1 7.4 - - + -
168A GLY* 3.7 13.6 + - - +
169A ILE 3.2 0.8 - - - -
170A GLU* 1.3 78.5 - - - +
172A LEU* 1.3 64.3 + - - +
174A LEU* 4.6 15.9 - - - +
175A ASP* 3.1 36.2 + - + +
178A LYS* 5.5 2.9 + - - -
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Residues in contact with LEU 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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35A LEU* 4.5 7.9 - - + -
96A ILE* 4.3 18.4 - - + -
128A CYS* 3.8 26.9 - - + -
130A VAL* 3.9 22.7 - - + -
159A TYR* 3.8 33.2 - - + -
161A THR* 4.3 17.3 - - + -
168A GLY 3.2 18.1 + - - +
169A ILE* 3.3 5.8 + - - +
171A GLU* 1.3 77.3 - - - +
173A PHE* 1.3 80.2 + - + +
175A ASP* 4.1 1.4 - - - +
176A LEU* 3.2 23.7 + - - +
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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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22A VAL* 4.9 2.2 - - + -
24A LEU* 5.0 3.8 - - + -
35A LEU* 4.6 15.0 - - + -
36A VAL* 5.4 1.1 - - - -
39A TYR* 3.5 63.0 - + + +
61A LEU* 5.4 0.2 - - - -
70A LEU* 4.0 14.4 - - + -
72A ILE* 4.1 30.7 - - + -
96A ILE* 3.5 29.6 - - + -
169A ILE* 3.2 29.9 + - + +
170A GLU 4.4 0.4 - - - +
172A LEU* 1.3 90.0 - - + +
174A LEU* 1.3 59.6 + - - +
176A LEU* 3.9 8.0 - - + +
177A CYS* 3.1 35.4 + - - -
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Residues in contact with LEU 174 (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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39A TYR* 5.1 0.8 + - - -
61A LEU* 4.5 11.9 - - + -
62A ASN 5.7 0.9 - - - +
63A ILE* 3.8 35.2 - - + -
170A GLU* 3.2 31.8 + - + +
171A GLU* 4.1 17.0 - - - +
173A PHE* 1.3 73.8 - - - +
175A ASP* 1.3 60.7 + - - +
177A CYS* 3.4 5.7 + - - +
178A LYS* 3.1 53.0 + - + +
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Residues in contact with ASP 175 (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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157A LYS* 5.2 1.9 - - - +
159A TYR* 2.7 33.4 + - + +
171A GLU* 3.1 32.5 + - - +
172A LEU 4.1 1.1 - - - +
174A LEU* 1.3 73.7 - - - +
176A LEU* 1.3 60.7 + - - +
178A LYS* 3.3 18.0 + - - +
179A ARG* 3.0 42.6 + - - +
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Residues in contact with LEU 176 (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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22A VAL* 4.0 22.2 - - + -
94A GLY* 4.3 0.2 - - - -
95A ALA 4.7 2.2 - - - +
96A ILE* 3.8 35.4 - - + -
126A CYS* 3.7 36.6 - - + +
128A CYS* 3.8 17.7 - - - -
159A TYR* 4.5 0.4 + - - -
172A LEU 3.2 18.8 + - - +
173A PHE* 3.9 9.4 - - + +
175A ASP* 1.3 76.2 + - - +
177A CYS* 1.3 63.8 + - - +
179A ARG* 3.1 11.6 + - - +
180A MET* 3.0 38.0 + - + +
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Residues in contact with CYS 177 (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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20A PHE* 4.1 1.7 - - - -
61A LEU* 4.4 10.5 - - - -
63A ILE* 3.6 21.8 - - + -
68A VAL* 4.1 18.4 - - + -
70A LEU* 3.8 37.7 - - - -
173A PHE* 3.1 26.0 + - - +
174A LEU* 3.6 2.5 - - - +
176A LEU* 1.3 76.1 - - - +
178A LYS* 1.3 61.2 + - - +
180A MET* 3.5 11.9 + - - +
181A ILE* 3.1 29.5 + - + +
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Residues in contact with LYS 178 (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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63A ILE* 4.1 24.7 - - + -
171A GLU* 5.5 3.4 + - - -
174A LEU* 3.1 44.2 + - + +
175A ASP* 3.6 15.9 + - - +
176A LEU 3.3 0.2 - - - -
177A CYS* 1.3 72.9 - - - +
179A ARG* 1.3 65.3 + - + +
181A ILE* 3.3 10.7 + - - +
182A GLU* 3.1 22.7 + - - +
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Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A CYS* 3.7 28.1 - - - +
127A LEU 2.9 40.8 + - - +
128A CYS* 3.1 19.6 - - - -
155A GLY 5.2 3.0 + - - -
156A ALA* 4.9 3.6 - - - +
157A LYS* 4.1 15.0 - - - +
159A TYR* 3.1 29.8 + - - -
175A ASP* 3.0 25.3 + - - +
176A LEU* 3.5 11.1 - - - +
178A LYS* 1.3 75.4 - - + +
180A MET* 1.3 61.4 + - - +
182A GLU* 3.4 16.2 + - - +
183A THR* 3.5 9.2 + - - +
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Residues in contact with MET 180 (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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20A PHE* 3.8 44.2 - - + -
22A VAL* 3.9 13.9 - - + -
70A LEU* 4.2 7.0 - - + -
93A ASN* 3.7 16.6 - - + +
94A GLY* 3.5 29.6 - - - -
126A CYS* 3.8 24.2 - - + -
176A LEU* 3.0 34.1 + - + +
177A CYS* 3.7 16.4 - - - +
179A ARG* 1.3 75.7 - - - +
181A ILE* 1.3 61.3 + - - +
183A THR 3.3 19.8 - - - +
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Residues in contact with ILE 181 (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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18A TYR* 3.7 40.7 + - + +
20A PHE* 3.7 18.4 - - + -
63A ILE* 4.4 16.6 - - + +
66A LYS* 6.0 2.0 - - + -
68A VAL* 4.0 24.0 - - + -
177A CYS 3.1 21.7 + - - +
178A LYS* 3.3 11.2 + - - +
180A MET* 1.3 75.7 - - - +
182A GLU* 1.3 64.4 + - - +
183A THR* 3.5 0.9 + - - -
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Residues in contact with GLU 182 (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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178A LYS 3.1 12.8 + - - +
179A ARG* 3.4 10.9 + - - +
181A ILE* 1.3 76.8 - - - +
183A THR* 1.3 61.6 + - - +
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Residues in contact with THR 183 (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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124A GLU 4.6 9.3 - - - +
126A CYS* 4.3 9.9 - - - -
179A ARG 3.5 8.4 + - - +
180A MET* 3.3 22.5 - - - +
181A ILE 3.3 2.1 - - - -
182A GLU* 1.3 82.9 - - - +
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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