Contacts of the helix formed by residues 266 - 271 (chain E) in PDB entry 1FZB
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 TRP 266 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265E LYS* 1.3 73.6 - - - +
267E ASP* 1.3 77.1 + - - +
269E TYR* 3.2 15.8 + - - +
270E LYS* 3.3 17.0 + - + +
296E ASN* 5.4 0.2 - - - +
334E GLU* 3.0 31.3 + - + -
337E LYS* 4.7 12.3 - - + -
338E TYR* 3.5 35.7 - + - -
375E PHE* 3.3 39.3 - + + -
377E THR* 3.2 40.6 - - + +
379E ASP* 2.7 14.6 + - - +
380E ARG* 3.3 59.0 - - + +
382E ASN* 4.1 3.8 - - - -
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Residues in contact with ASP 267 (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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265E LYS* 4.7 1.0 - - - +
266E TRP* 1.3 85.9 - - - +
268E PRO* 1.3 62.8 - - + +
270E LYS* 2.9 26.0 + - - +
271E GLN* 2.9 54.3 + - + +
379E ASP* 4.9 0.2 + - - -
380E ARG* 5.7 0.7 + - - -
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Residues in contact with PRO 268 (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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264E ARG* 3.8 32.3 - - + +
265E LYS* 3.3 21.5 - - + +
267E ASP* 1.3 94.3 - - + +
269E TYR* 1.3 53.1 + - - +
271E GLN* 4.5 4.3 - - + -
272E GLY* 2.7 41.4 + - - +
273E PHE* 3.3 16.0 - - + -
136F GLN* 6.0 1.6 - - - +
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Residues in contact with TYR 269 (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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262E PHE* 2.4 33.6 + - - +
264E ARG* 3.4 20.0 - - + -
265E LYS 3.5 17.0 - - - -
266E TRP* 3.2 9.5 + - + +
267E ASP 3.1 0.6 - - - -
268E PRO* 1.3 80.1 - - - +
270E LYS* 1.3 51.1 + - - +
273E PHE* 3.5 20.9 - + - -
293E TRP* 2.8 36.6 + + - +
295E GLY* 3.0 2.6 - - - -
296E ASN* 2.5 43.3 + - - +
375E PHE* 3.8 14.4 - + + -
377E THR* 3.6 9.4 - - + -
401E GLY* 3.2 24.7 + - - -
413E ASN* 3.6 32.8 - - - +
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Residues in contact with LYS 270 (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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266E TRP* 3.3 15.3 + - - +
267E ASP* 2.9 32.4 + - - +
269E TYR* 1.3 77.3 - - - +
271E GLN* 1.3 75.2 + - - +
295E GLY* 3.3 2.6 - - - -
296E ASN* 3.1 23.7 + - - +
297E ASP* 3.4 31.9 + - - +
298E LYS* 4.8 1.0 + - - +
334E GLU* 3.4 30.7 + - - +
338E TYR* 3.1 28.7 - - + +
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Residues in contact with GLN 271 (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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267E ASP* 3.0 36.6 + - + +
268E PRO* 4.5 2.0 - - + -
270E LYS* 1.3 88.6 - - - +
272E GLY* 1.3 67.3 + - - +
294E LEU 3.2 12.3 - - - +
295E GLY* 3.6 0.2 - - - -
297E ASP* 5.4 1.6 - - - +
298E LYS* 3.6 16.6 - - - -
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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