Contacts of the strand formed by residues 382 - 386 (chain A) in PDB entry 1RY2
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 ALA 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A LYS* 3.9 3.0 - - - +
149A LYS* 3.6 18.4 - - + +
150A ALA 3.5 7.0 - - - +
152A ILE* 3.9 25.8 - - + -
355A ASP 3.1 14.1 + - - +
356A VAL* 3.5 6.9 - - + -
357A PHE* 2.8 30.6 + - - +
376A PRO* 4.9 0.2 - - - -
381A CYS* 1.3 80.9 - - - +
383A THR* 1.3 60.3 + - - +
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Residues in contact with THR 383 (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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150A ALA 3.0 16.0 + - - +
151A ILE* 3.5 11.4 - - + +
152A ILE* 3.0 23.7 + - - -
203A ILE* 5.8 2.0 - - + -
356A VAL* 5.8 0.2 - - - -
357A PHE* 3.4 7.1 + - - +
359A THR 5.6 0.2 + - - -
371A TYR 4.5 1.0 + - - -
372A VAL* 3.5 33.9 + - - +
373A VAL* 5.2 0.2 - - - -
376A PRO* 3.5 25.5 - - + +
377A LEU* 4.1 22.2 - - + -
381A CYS 4.1 0.2 + - - -
382A ALA* 1.3 73.5 - - - +
384A LEU* 1.3 62.1 + - - +
385A VAL* 3.9 4.9 + - + -
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Residues in contact with LEU 384 (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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152A ILE* 3.2 27.1 - - + +
154A GLU* 4.3 16.6 - - + -
356A VAL* 4.4 6.5 - - + -
357A PHE 2.9 17.6 + - - +
358A PHE* 3.9 30.1 - - + -
359A THR 4.7 0.5 + - - +
372A VAL* 3.7 19.9 - - - +
383A THR* 1.3 73.2 + - - +
385A VAL* 1.3 70.7 + - - +
386A PHE* 4.0 6.5 + - + +
401A ILE* 4.4 5.8 - - + +
405A HIS* 4.0 23.1 - - + -
407A VAL* 3.4 33.2 - - + -
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Residues in contact with VAL 385 (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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151A ILE* 3.3 32.1 - - + -
152A ILE 2.8 10.1 + - - +
153A PHE* 2.8 37.7 - - + -
154A GLU 2.8 11.6 + - - -
198A MET* 3.5 44.4 - - + +
199A VAL 3.9 9.6 - - - +
200A PRO* 5.0 0.7 - - + -
203A ILE* 4.3 18.4 - - + -
372A VAL* 5.3 6.7 - - + +
383A THR* 4.3 7.9 - - + +
384A LEU* 1.3 75.3 - - - +
386A PHE* 1.3 58.4 + - - +
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Residues in contact with PHE 386 (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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154A GLU* 3.3 25.4 - - + +
155A GLY 3.5 3.1 - - - -
198A MET* 3.6 19.4 - - - +
358A PHE* 4.0 22.8 - + + -
360A ALA* 6.2 0.7 - - + -
384A LEU* 4.0 4.9 + - + -
385A VAL* 1.3 73.9 - - - +
387A GLU* 1.3 58.5 + - - +
388A GLY* 3.3 44.4 + - - +
389A THR 3.5 16.2 - - - -
397A ARG* 3.3 42.2 - - + -
398A TYR* 3.8 27.1 - + - -
401A ILE* 4.1 12.6 - - + -
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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