Contacts of the strand formed by residues 382 - 385 (chain A) in PDB entry 2ADU
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 HIS 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A PRO* 3.7 29.5 + - + +
222A GLY* 4.7 5.4 - - - -
231A HIS* 3.3 33.4 + - + -
232A TYR 3.9 2.0 - - - -
233A THR* 3.4 33.4 - - + +
380A CYS* 3.3 5.8 - - - -
381A SER* 1.3 93.3 + - - +
383A TYR* 1.3 69.5 + - - +
415A PHE 3.5 4.7 - - - +
444A TYR* 2.9 47.4 + - + +
906A R20 3.6 31.5 - + + -
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Residues in contact with TYR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A CYS* 3.7 14.5 + - - +
381A SER* 3.4 28.3 - - - -
382A HIS* 1.3 77.6 - - - +
384A MET* 1.3 64.8 + - - +
414A ALA* 3.3 2.3 - - - +
415A PHE* 2.9 59.8 + + + -
417A ARG* 3.5 35.4 + - + -
429A LEU* 5.7 0.3 - - - +
432A LEU* 3.6 39.7 - - + +
436A CYS* 3.9 18.8 - - - -
441A VAL* 4.0 3.4 - - + -
442A ASP 3.5 5.2 - - - -
443A PRO* 4.0 19.7 - - + -
444A TYR* 4.4 2.7 - - - -
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Residues in contact with MET 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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337A ARG* 6.1 3.6 - - + -
338A ILE* 3.8 23.1 - - + +
339A HIS* 5.5 2.7 - - + +
383A TYR* 1.3 78.5 - - - +
385A LYS* 1.3 70.8 + - - +
386A ASN 3.6 0.2 + - - -
387A PHE* 6.5 1.6 - - + -
412A THR 3.2 28.0 - - - +
413A LEU* 4.0 0.9 - - - -
414A ALA* 3.6 27.6 - - + +
415A PHE* 4.2 6.1 - - - -
441A VAL* 4.1 3.8 - - - +
442A ASP* 2.7 39.3 + - - +
444A TYR* 3.5 31.1 + - + +
906A R20 3.7 17.3 - - + -
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Residues in contact with LYS 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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384A MET* 1.3 89.9 - - - +
386A ASN* 1.3 73.6 + - - +
387A PHE* 3.1 5.4 + - - +
389A VAL* 5.0 11.9 + - + -
390A GLY 5.4 8.2 + - - -
391A HIS* 6.3 0.2 - - - +
403A LEU* 4.4 12.8 - - + -
406A ILE* 4.7 9.4 - - + -
407A ASN* 2.7 33.5 + - - +
411A GLY* 3.7 27.8 + - - +
412A THR* 4.4 14.1 - - + +
413A LEU 5.0 0.8 + - - -
415A PHE* 4.6 5.5 - - - -
440A ILE* 3.3 27.1 - - + +
441A VAL* 4.2 5.6 - - + +
442A ASP* 4.7 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