Contacts of the helix formed by residues 207 - 216 (chain A) in PDB entry 1OZ2
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 SER 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A MES 3.0 9.6 + - - +
205A CYS* 3.5 7.5 + - - -
206A TRP* 1.3 83.0 - - - +
208A TRP* 1.3 64.5 + - - +
209A GLU* 3.8 7.4 + - - +
210A SER* 3.2 26.5 + - - -
211A TYR* 3.0 23.0 + - - +
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Residues in contact with TRP 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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206A TRP* 3.5 20.9 - + - -
207A SER* 1.3 72.4 - - - +
209A GLU* 1.3 65.0 + - - +
211A TYR* 3.1 19.2 + + - +
212A LEU* 2.9 50.4 + - + +
219A THR* 4.4 1.3 - - + -
454A LYS* 3.6 28.9 - - + -
455A LEU 3.6 27.6 - - - -
456A GLU* 2.8 28.4 + - + -
468A VAL* 3.7 24.7 - - + -
504A ALA* 3.5 22.7 - - + -
505A GLY* 3.6 20.7 - - - +
508A SER* 6.4 0.9 - - - -
514A LEU* 3.7 8.6 - - + +
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Residues in contact with GLU 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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207A SER* 3.3 7.9 + - - +
208A TRP* 1.3 77.3 - - - +
210A SER* 1.3 64.5 + - - +
212A LEU* 3.6 12.7 + - - +
213A GLU* 3.4 36.6 + - - +
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MES 3.6 23.7 - - - -
207A SER* 3.2 17.9 + - - -
208A TRP 3.2 0.4 - - - -
209A GLU* 1.3 79.6 + - - +
211A TYR* 1.3 63.7 + - - +
213A GLU* 3.2 8.2 + - - +
214A GLU* 3.0 31.3 + - - +
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Residues in contact with TYR 211 (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 MES 3.6 5.1 - - + -
206A TRP* 3.3 31.0 - + + -
207A SER 3.0 16.8 + - - +
208A TRP* 3.1 16.8 + + - +
210A SER* 1.3 76.9 - - - +
212A LEU* 1.3 56.8 + - - +
214A GLU* 3.2 17.9 + - - +
215A GLN* 2.9 63.3 + - + +
454A LYS* 3.7 19.9 + - + -
468A VAL* 3.9 9.2 - - + -
484A ASP* 2.6 34.3 + - - +
517A PRO* 3.5 24.9 - - + +
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Residues in contact with LEU 212 (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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208A TRP* 2.9 41.6 + - + +
209A GLU* 4.0 13.5 - - - +
211A TYR* 1.3 76.3 - - + +
213A GLU* 1.4 61.1 + - - +
216A LYS* 2.9 24.6 + - - -
217A ALA* 3.1 47.1 + - + +
218A ILE* 4.0 4.3 - - - +
219A THR* 3.7 36.8 - - + +
454A LYS* 4.6 2.9 - - + -
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Residues in contact with GLU 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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209A GLU* 3.4 31.9 + - - +
210A SER* 3.2 10.7 + - - +
211A TYR 3.2 0.6 - - - -
212A LEU* 1.4 77.6 - - - +
214A GLU* 1.3 65.4 + - + +
215A GLN 3.4 0.3 + - - -
216A LYS* 3.4 28.4 - - - +
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Residues in contact with GLU 214 (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 MES 2.8 63.4 + - - +
210A SER* 3.0 20.9 + - - +
211A TYR* 3.2 14.4 + - - +
213A GLU* 1.3 77.9 - - + +
215A GLN* 1.3 68.8 + - + +
216A LYS* 4.8 4.3 - - - +
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Residues in contact with GLN 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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211A TYR* 2.9 57.7 + - + +
214A GLU* 1.3 83.7 - - + +
216A LYS* 1.3 71.0 + - - +
217A ALA* 3.5 18.7 + - + +
454A LYS* 4.6 7.9 - - - +
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Residues in contact with LYS 216 (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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212A LEU 2.9 8.0 + - - -
213A GLU* 3.4 22.7 - - - +
214A GLU 3.5 4.8 - - - +
215A GLN* 1.3 80.1 - - - +
217A ALA* 1.3 57.8 + - - +
218A ILE* 5.7 0.6 - - - +
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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