Contacts of the helix formed by residues 271 - 277 (chain E) in PDB entry 1ZM9
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 ARG 271 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172E GLU* 2.8 35.4 + - - +
175E TYR* 3.2 45.2 + - - -
176E GLN* 3.7 3.8 - - - +
244E LEU 5.5 0.4 - - - +
246E GLY 3.0 28.3 + - - +
247E ASP* 2.8 30.1 + - - +
248E SER 4.0 3.8 - - - +
249E PHE* 3.5 20.1 - - + -
269E LEU 3.6 2.8 + - - -
270E GLU* 1.3 77.1 - - - +
272E ALA* 1.3 64.6 + - + +
273E PHE* 3.1 8.4 + - - +
274E ASN* 3.1 21.1 + - - +
275E MET* 2.8 27.1 + - - +
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Residues in contact with ALA 272 (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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243E ARG 3.4 24.5 - - - +
244E LEU* 4.0 4.6 - - - +
248E SER 2.8 24.1 + - - +
249E PHE* 4.3 2.0 - - - +
250E PHE 5.3 0.7 - - - +
257E TRP* 3.6 26.9 - - + -
270E GLU 3.7 1.2 + - - -
271E ARG* 1.3 72.2 - - + +
273E PHE* 1.3 56.3 + - - +
275E MET* 4.3 2.9 - - - -
276E PHE* 2.9 43.3 + - + +
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Residues in contact with PHE 273 (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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175E TYR* 3.7 20.4 - + + -
178E PHE* 4.4 16.8 - + - -
211E PHE* 4.8 2.7 - + - -
220E PHE* 3.9 23.6 - + - -
222E ILE* 3.2 31.9 - - + -
244E LEU* 3.0 23.5 + - - +
245E TRP* 4.4 9.2 - + - -
271E ARG* 3.1 12.6 - - - +
272E ALA* 1.3 75.2 - - - +
274E ASN* 1.3 64.8 + - - +
275E MET 3.1 0.3 + - - -
277E ILE* 2.7 53.9 + - + +
278E LEU* 3.3 49.5 + - + -
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Residues in contact with ASN 274 (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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171E LYS* 3.0 47.7 + - + +
172E GLU* 3.0 19.6 + - - +
175E TYR* 3.9 8.4 - - - +
270E GLU* 3.6 25.8 - - + +
271E ARG* 3.1 32.4 + - - +
273E PHE* 1.3 74.5 - - - +
275E MET* 1.3 56.9 + - - +
278E LEU* 3.9 13.6 - - - -
279E ASP* 2.9 30.3 + - - +
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Residues in contact with MET 275 (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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250E PHE* 3.2 45.1 - - + +
252E PRO* 4.8 13.2 - - + -
270E GLU* 3.2 30.9 + - + +
271E ARG 2.8 16.0 + - - +
272E ALA* 3.7 4.9 - - - +
274E ASN* 1.3 78.5 - - - +
276E PHE* 1.3 100.3 + - + +
279E ASP* 3.0 22.7 - - - +
280E PRO* 4.0 1.7 - - - +
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Residues in contact with PHE 276 (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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225E PHE* 4.8 2.4 - - - -
229E TYR* 2.7 57.3 + + + -
233E PHE* 3.9 18.8 - + - -
244E LEU* 4.2 10.1 - - + -
250E PHE* 3.6 22.4 - + + -
257E TRP* 3.3 32.3 - + - -
272E ALA* 2.9 25.1 + - - +
275E MET* 1.3 118.2 - - + +
277E ILE* 1.3 65.0 + - + +
280E PRO* 3.4 10.4 - - - +
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Residues in contact with ILE 277 (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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220E PHE* 3.7 29.6 - - + -
222E ILE* 5.4 2.0 - - + -
225E PHE* 3.1 62.0 - - + -
229E TYR* 3.9 6.3 - - + -
244E LEU* 4.4 13.2 - - + -
273E PHE* 2.7 45.6 + - + +
275E MET 3.7 0.6 - - - -
276E PHE* 1.3 89.1 - - + +
278E LEU* 1.3 65.1 + - - +
279E ASP 3.2 1.3 - - - -
280E PRO* 3.3 7.2 - - - +
281E ILE* 3.2 27.3 - - + +
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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