Contacts of the helix formed by residues 201 - 215 (chain A) in PDB entry 1ZIO
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 MET 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 3.4 27.8 - - + -
16A GLN* 3.2 15.6 + - - +
19A LYS* 3.7 23.1 - - - +
142A HIS* 5.9 7.9 - - - -
199A GLN 3.6 0.6 + - - -
200A ASP* 1.3 72.2 - - - +
202A GLU* 1.3 66.7 + - + +
204A VAL* 3.4 1.1 + - - +
205A PHE* 3.1 24.1 + - - +
218A AP5 3.7 44.1 + - + +
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Residues in contact with GLU 202 (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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19A LYS* 2.8 34.0 + - - +
200A ASP* 3.3 9.2 + - - +
201A MET* 1.3 82.5 - - + +
203A LYS* 1.3 59.9 + - - +
205A PHE* 3.4 11.4 + - - +
206A ALA* 3.0 27.0 + - - +
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Residues in contact with LYS 203 (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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199A GLN* 2.9 41.5 - - + +
200A ASP* 3.1 33.8 + - - +
202A GLU* 1.3 76.0 - - - +
204A VAL* 1.3 64.5 + - - +
206A ALA* 3.3 8.7 + - + +
207A ASP* 2.9 49.3 + - - +
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Residues in contact with VAL 204 (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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16A GLN* 3.6 33.9 - - + +
113A ILE* 5.0 5.2 - - + -
195A ILE* 4.0 18.3 - - + +
196A ASN 3.7 18.4 - - - +
197A GLY* 4.0 14.4 - - - +
199A GLN* 3.7 23.8 - - + +
200A ASP 3.0 17.8 + - - +
201A MET 3.7 2.0 - - - +
203A LYS* 1.3 75.8 - - - +
205A PHE* 1.3 64.4 + - - +
207A ASP* 3.2 7.9 + - - +
208A ILE* 3.1 23.9 + - + +
218A AP5 4.6 4.3 - - - +
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Residues in contact with PHE 205 (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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16A GLN* 3.3 21.2 + - - +
19A LYS* 3.7 51.4 - - + -
20A ILE* 3.9 17.7 - - + -
23A ALA* 4.5 7.6 - - + -
24A TYR* 5.9 1.1 - + - -
201A MET 3.1 13.3 + - - +
202A GLU* 3.6 16.6 - - - +
203A LYS 3.2 0.2 - - - -
204A VAL* 1.3 77.2 - - - +
206A ALA* 1.3 57.1 + - - +
208A ILE* 3.1 8.1 + - + +
209A ARG* 2.8 62.9 + - + +
212A LEU* 6.0 0.9 - - + -
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Residues in contact with ALA 206 (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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202A GLU 3.0 17.9 + - - +
203A LYS* 3.7 12.6 - - + +
204A VAL 3.3 0.2 - - - -
205A PHE* 1.3 79.1 - - - +
207A ASP* 1.3 60.3 + - - +
209A ARG* 3.8 6.5 - - - +
210A GLU* 2.8 30.9 + - - +
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Residues in contact with ASP 207 (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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195A ILE* 4.0 24.2 - - + +
196A ASN* 4.7 3.6 + - - +
199A GLN* 2.8 25.8 - - - +
203A LYS* 2.9 38.0 + - - +
204A VAL 3.2 6.3 + - - +
206A ALA* 1.3 77.9 - - - +
208A ILE* 1.3 62.1 + - - +
210A GLU* 3.6 16.5 - - - +
211A LEU* 3.2 20.4 + - - +
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Residues in contact with ILE 208 (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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5A LEU* 4.9 1.1 - - + -
16A GLN* 3.9 39.3 - - + +
20A ILE* 3.9 22.2 - - + -
111A ILE* 4.4 24.5 - - + -
113A ILE* 4.7 5.8 - - + -
195A ILE* 4.1 21.3 - - + -
204A VAL* 3.1 14.0 + - + +
205A PHE* 3.1 11.3 + - + +
207A ASP* 1.3 74.5 - - - +
209A ARG* 1.3 61.4 + - - +
211A LEU* 2.9 11.0 + - - +
212A LEU* 2.8 47.5 + - + +
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Residues in contact with ARG 209 (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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23A ALA* 3.1 35.9 + - - +
24A TYR* 3.4 28.9 + - + +
205A PHE* 2.8 49.9 + - + +
206A ALA* 3.8 7.2 - - - +
208A ILE* 1.3 72.9 - - - +
210A GLU* 1.3 58.2 + - - +
212A LEU* 3.3 5.9 + - + +
213A GLY* 2.9 27.3 + - - -
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Residues in contact with GLU 210 (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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206A ALA 2.8 19.2 + - - +
207A ASP* 3.6 16.4 - - - +
209A ARG* 1.3 75.8 - - - +
211A LEU* 1.3 63.9 + - - +
213A GLY* 3.3 12.1 + - - -
214A GLY 3.9 2.9 + - - -
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Residues in contact with LEU 211 (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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109A TYR* 3.6 29.8 + - + +
111A ILE* 4.0 26.5 - - + -
193A ARG* 3.6 52.7 - - + +
195A ILE* 4.9 12.3 - - + -
207A ASP 3.2 10.1 + - - +
208A ILE* 2.9 9.7 + - - +
210A GLU* 1.3 81.7 - - - +
212A LEU* 1.3 64.0 + - + +
213A GLY 3.1 1.0 + - - -
214A GLY* 3.2 11.3 + - - -
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Residues in contact with LEU 212 (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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1A MET* 4.2 15.4 - - + +
3A LEU* 4.2 19.1 - - + -
20A ILE* 4.6 8.5 - - + -
24A TYR* 3.5 39.6 + - + +
109A TYR* 4.0 25.4 - - + -
111A ILE* 4.0 18.8 - - + -
205A PHE* 6.0 0.4 - - + -
208A ILE* 2.8 34.8 + - + +
209A ARG* 3.3 6.9 + - + +
211A LEU* 1.3 79.9 - - + +
213A GLY* 1.3 62.2 + - - +
215A LEU* 3.0 23.3 + - - +
216A ALA* 4.0 2.1 + - - +
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Residues in contact with GLY 213 (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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24A TYR* 5.0 0.9 + - - -
209A ARG* 2.9 16.6 + - - -
210A GLU* 3.3 5.6 + - - -
211A LEU 3.1 1.2 - - - -
212A LEU* 1.3 77.4 - - - +
214A GLY* 1.3 57.1 + - - +
215A LEU 2.9 5.7 + - - -
216A ALA* 3.1 16.3 + - - +
217A ARG* 3.2 19.0 + - - +
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Residues in contact with GLY 214 (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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109A TYR* 4.2 9.8 + - - -
210A GLU 3.9 4.2 + - - -
211A LEU 3.2 11.7 + - - -
213A GLY* 1.3 74.0 - - - +
215A LEU* 1.3 58.5 + - - +
216A ALA 3.5 0.2 - - - -
217A ARG* 3.5 25.4 - - - +
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Residues in contact with LEU 215 (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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1A MET* 3.4 43.7 - - + -
3A LEU* 4.7 0.2 - - + -
108A ASP* 4.1 27.8 - - + +
109A TYR* 4.0 30.4 + - + +
212A LEU* 3.0 16.0 + - - +
213A GLY 2.9 1.0 + - - -
214A GLY* 1.3 78.8 - - - +
216A ALA* 1.3 61.9 + - - +
217A ARG* 3.2 6.3 + - - +
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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
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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