Contacts of the helix formed by residues 206 - 213 (chain E) in PDB entry 1ZBQ
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 PRO 206 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A LYS* 6.2 3.1 - - - -
271A ALA* 4.3 11.0 - - + -
204E VAL 4.3 3.6 - - - +
205E MET* 1.3 88.2 - - + +
207E GLU* 1.3 65.7 + - - +
208E ASP* 3.2 18.2 - - - +
209E LEU* 2.9 32.1 + - + +
210E VAL* 3.1 10.0 + - - +
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Residues in contact with GLU 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ALA* 3.1 27.3 + - + +
272A ASN* 4.1 14.6 - - - +
205E MET 3.8 1.0 + - - -
206E PRO* 1.3 72.6 - - - +
208E ASP* 1.3 61.0 + - - +
210E VAL* 3.4 11.6 + - - +
211E GLU* 3.2 23.0 + - - +
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Residues in contact with ASP 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LYS* 4.6 19.4 - - - +
271A ALA* 3.2 25.4 + - - +
273A TRP* 6.0 0.9 - - + +
274A LYS* 5.9 7.2 - - + +
206E PRO* 3.2 26.8 - - - +
207E GLU* 1.3 72.0 + - - +
209E LEU* 1.3 57.4 + - - +
211E GLU* 3.6 7.1 + - - +
212E ALA* 3.1 27.3 + - - +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E MET* 4.0 20.4 - - + -
206E PRO* 2.9 33.0 + - + +
208E ASP* 1.3 81.4 + - - +
210E VAL* 1.3 60.2 + - - +
212E ALA* 3.0 4.0 + - - +
213E LEU* 2.8 40.1 + - + +
296F ILE* 3.8 48.7 - - + -
299F LEU* 3.9 19.1 - - + -
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Residues in contact with VAL 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E GLY* 3.2 35.7 + - - +
198E SER* 4.1 3.1 - - - +
202E GLN* 4.0 34.8 - - + +
205E MET* 3.5 39.0 - - + +
206E PRO 3.1 14.1 + - - +
207E GLU* 3.5 11.7 - - - +
209E LEU* 1.3 75.4 - - - +
211E GLU* 1.3 62.2 + - - +
213E LEU 3.8 5.7 + - - +
214E LYS* 5.3 0.5 - - - -
215E PRO* 5.7 0.3 - - - +
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Residues in contact with GLU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LYS* 5.5 11.4 - - + -
207E GLU 3.2 10.9 + - - +
208E ASP* 3.6 11.7 - - - +
209E LEU 3.2 0.2 - - - -
210E VAL* 1.3 80.5 - - - +
212E ALA* 1.3 62.0 + - - +
213E LEU 4.6 0.2 - - - -
214E LYS* 3.5 24.4 - - - +
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Residues in contact with ALA 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E ASP 3.1 17.0 + - - +
209E LEU* 3.0 6.7 + - - +
211E GLU* 1.3 75.4 - - - +
213E LEU* 1.3 58.8 + - - +
214E LYS* 3.0 13.7 + - - +
217E TYR* 3.3 19.1 + - - -
299F LEU* 3.7 27.9 - - + +
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Residues in contact with LEU 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ASN* 3.9 31.0 - - + +
196E ALA* 3.3 4.0 - - - +
197E GLY* 2.7 28.6 + - - +
205E MET* 3.8 27.6 - - - -
209E LEU* 2.8 34.5 + - + +
210E VAL 3.9 2.9 - - - +
211E GLU 3.5 0.2 - - - -
212E ALA* 1.3 68.7 - - - +
214E LYS* 1.3 64.2 + - - +
215E PRO* 3.6 1.2 - - - +
217E TYR* 4.8 0.4 - - - -
240E GLY 4.6 0.9 - - - -
241E ALA* 3.8 37.0 - - + +
295F ILE* 4.7 4.0 - - + -
296F ILE* 4.4 13.2 - - + -
299F LEU* 4.3 7.2 - - + -
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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