Contacts of the strand formed by residues 290 - 295 (chain A) in PDB entry 1Z8G
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 ILE 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A GLY 3.9 9.2 - - - +
289A LYS* 1.3 82.9 - - - +
291A CYS* 1.3 64.9 + - - +
313A ARG* 3.6 64.3 + - + +
314A VAL 3.7 11.2 - - - +
315A PRO* 4.1 12.1 - - + -
341A TYR* 4.9 5.8 - - + +
359A CYS* 5.5 0.5 - - - -
360A GLU 5.8 0.3 + - - -
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Residues in contact with CYS 291 (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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289A LYS* 4.1 8.7 - - - -
290A ILE* 1.3 81.4 - - - +
292A THR* 1.3 64.5 + - - +
313A ARG* 3.2 6.5 - - - +
314A VAL 2.9 31.5 + - - -
316A ILE* 4.1 12.1 - - - -
357A PHE* 3.5 25.8 - - + -
358A VAL 3.1 7.6 - - - +
359A CYS* 2.0 51.8 - - - +
369A TRP* 5.5 2.2 - - - -
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TRP* 3.6 42.0 - - + -
291A CYS* 1.3 77.8 + - - +
293A VAL* 1.3 69.0 + - - +
294A THR* 4.1 8.7 + - + -
311A GLU* 4.3 3.8 - - + +
312A ALA 3.3 19.1 - - - +
313A ARG* 3.8 18.5 - - + -
356A PRO 3.7 0.3 - - - +
357A PHE* 3.3 4.3 - - - -
358A VAL* 2.8 44.0 + - - +
369A TRP* 4.1 8.8 - - - -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 4.0 22.4 - - + +
292A THR* 1.3 74.1 - - - +
294A THR* 1.3 66.8 + - - +
310A GLN 4.1 0.2 - - - +
311A GLU* 3.6 0.5 - - - -
312A ALA* 2.9 47.5 + - + +
314A VAL* 4.2 13.0 - - + +
347A ASP 5.2 0.4 - - - -
348A ALA* 4.3 7.0 - - + +
356A PRO 3.3 12.3 - - - +
357A PHE* 4.3 7.9 - - + -
375A VAL* 3.7 27.4 - - + -
390A TYR* 3.7 23.8 - - + +
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 3.8 8.8 - - - +
174A TRP* 3.7 41.3 - - + +
176A TRP* 5.5 0.2 + - - -
177A GLN* 2.7 30.6 + - - +
292A THR* 4.1 5.4 - - + +
293A VAL* 1.3 82.7 - - - +
295A GLY* 1.3 60.1 + - - +
309A LEU* 4.4 6.7 - - - -
310A GLN 3.1 14.1 - - - +
311A GLU* 3.7 9.4 - - + -
352A ASP* 4.5 3.6 - - - +
355A GLY* 4.5 4.5 - - - -
356A PRO* 3.2 30.4 + - - +
358A VAL* 6.0 0.8 - - + +
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Residues in contact with GLY 295 (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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163A ILE* 3.6 4.7 - - - +
177A GLN* 3.8 8.1 - - - -
189A GLY* 6.2 1.3 - - - -
294A THR* 1.3 76.3 - - - +
296A TRP* 1.3 57.9 + - - -
297A GLY 3.4 0.4 - - - -
309A LEU* 3.4 15.9 - - - +
310A GLN* 3.0 36.5 + - - +
352A ASP* 3.3 19.3 - - - -
355A GLY* 6.2 0.2 - - - -
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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