Contacts of the strand formed by residues 473 - 480 (chain A) in PDB entry 2AYN
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ARG* 3.4 38.4 - - - +
341A LYS* 4.2 18.4 - - - +
343A LEU* 3.7 37.2 - - + +
424A THR* 3.3 15.8 - - - +
425A HIS 3.3 22.6 + - - +
465A LEU* 3.4 9.6 - - - +
467A GLY* 3.9 15.0 - - - -
469A GLY 4.3 7.6 - - - +
470A ASP* 6.1 0.4 - - - -
471A TRP 3.7 9.0 - - - +
472A HIS* 1.3 81.5 - - - +
474A ALA* 1.3 74.5 + - + +
475A TYR* 4.4 0.5 - - - +
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Residues in contact with ALA 474 (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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327A MET* 3.5 20.3 - - + +
329A ARG* 3.9 4.0 + - - -
348A PHE* 3.9 19.1 - - + -
422A VAL* 3.5 23.8 - - + -
423A LEU 3.9 0.2 - - - -
424A THR* 3.5 9.3 + - - -
465A LEU* 3.0 12.7 + - + +
473A ILE* 1.3 84.8 - - - +
475A TYR* 1.3 58.9 + - - +
477A LEU* 3.8 19.7 - - + -
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Residues in contact with TYR 475 (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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198A ASP* 3.1 33.2 + - - -
199A ALA* 4.7 1.8 - - + -
200A ASN* 3.1 31.0 - - + +
326A GLN* 3.6 20.5 + - + -
327A MET* 3.0 42.3 + - - -
328A VAL* 5.3 0.2 - - - -
329A ARG* 5.0 3.4 - - + +
330A PHE* 3.7 35.7 - + + -
423A LEU* 2.9 12.0 + - + +
425A HIS* 4.3 15.3 - - + +
435A TYR* 3.9 21.5 - + - -
473A ILE 3.4 1.3 + - - +
474A ALA* 1.3 74.7 - - - +
476A VAL* 1.3 68.9 + - + +
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Residues in contact with VAL 476 (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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121A CYS* 5.4 0.3 - - - -
200A ASN* 3.2 31.9 - - + +
203A TRP* 3.7 31.6 - - + -
273A GLN* 5.5 0.2 - - - +
324A THR* 4.2 12.6 - - + -
325A ILE 3.3 9.9 - - - +
326A GLN* 4.8 2.0 - - - -
421A ALA 4.2 0.2 - - - +
422A VAL* 3.4 6.2 - - - +
423A LEU* 2.9 48.6 + - + +
475A TYR* 1.3 95.5 - - + +
477A LEU* 1.3 70.9 + - - +
478A LEU* 4.0 1.0 + - + +
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Residues in contact with LEU 477 (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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285A LEU* 4.2 3.8 - - + -
323A LEU 3.8 0.7 - - - +
324A THR* 3.7 1.6 - - - -
325A ILE* 2.8 40.2 + - + +
327A MET* 3.6 27.8 - - + -
348A PHE* 3.9 34.5 - - + -
419A LEU* 3.8 13.2 - - + -
421A ALA 4.2 1.1 - - - -
422A VAL* 3.9 20.6 - - + -
474A ALA* 3.8 27.1 - - + -
476A VAL* 1.3 76.7 - - - +
478A LEU* 1.3 61.0 + - - +
479A TYR* 3.8 24.7 - - + -
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Residues in contact with LEU 478 (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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121A CYS* 4.1 9.9 - - + +
122A ILE* 5.7 0.4 - - - -
124A SER* 3.6 25.1 - - - +
125A VAL* 4.2 9.0 - - + -
203A TRP* 4.3 27.1 - - + -
246A PHE* 5.7 3.6 - - + -
322A TYR* 4.2 16.2 - - + -
323A LEU 3.7 8.3 - - - +
324A THR* 5.0 4.9 - - + +
419A LEU* 3.5 4.6 - - - +
420A GLN* 2.7 43.7 + - - +
421A ALA* 3.2 25.9 + - + +
476A VAL 5.3 0.9 - - - +
477A LEU* 1.3 75.3 - - - +
479A TYR* 1.3 68.1 + - - +
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Residues in contact with TYR 479 (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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285A LEU* 3.7 16.5 - - + +
322A TYR* 3.4 3.1 - - - -
323A LEU* 2.8 42.8 + - + +
325A ILE* 3.9 14.4 - - + -
348A PHE* 3.7 8.1 - - - +
349A PRO* 2.5 46.3 + - - +
350A LEU 4.2 1.8 - - - -
352A LEU* 3.6 35.0 - - + -
417A TYR* 3.5 19.9 - - + -
418A ASP* 4.0 2.2 - - - -
419A LEU* 3.2 44.2 - - + +
477A LEU* 3.8 20.6 - - + -
478A LEU* 1.3 76.2 - - - +
480A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 480 (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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321A ALA 3.7 4.0 - - - -
322A TYR* 3.6 12.1 - - - -
417A TYR* 3.1 6.5 - - - -
418A ASP 2.4 45.8 + - - -
420A GLN* 3.9 12.4 - - - +
479A TYR* 1.3 74.8 - - - +
481A PRO* 1.3 70.9 - - - +
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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