Contacts of the strand formed by residues 416 - 426 (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 TYR 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A MET* 3.5 24.0 - - + -
352A LEU 3.0 14.8 - - - +
353A ASP* 3.7 24.7 - - + +
370A ARG* 3.3 58.9 + - + +
371A SER* 5.1 0.5 + - - -
374A LYS* 4.5 22.9 - - + +
413A ASN* 3.5 18.5 + - - -
414A CYS 4.2 1.0 + - - -
415A GLY* 1.3 76.2 - - - -
417A TYR* 1.3 74.2 + - - +
482A ARG* 4.0 47.6 + - + +
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Residues in contact with TYR 417 (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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319A LEU* 3.5 14.4 - - + +
320A PRO* 2.4 51.0 + - - +
321A ALA 3.1 20.4 - - - -
323A LEU* 3.8 20.9 - - + -
351A MET* 3.3 12.6 - - - +
352A LEU* 3.1 32.9 + - + -
354A MET* 3.6 37.0 - - + -
413A ASN* 3.7 13.6 + - - -
415A GLY 5.0 0.9 - - - -
416A TYR* 1.3 84.4 - - - +
418A ASP* 1.3 62.4 + - - +
419A LEU 4.2 0.4 - - - -
479A TYR* 3.5 26.5 - - + -
480A GLY 3.1 15.5 - - - +
481A PRO 4.4 2.7 - - - -
482A ARG* 4.6 1.6 - - - -
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Residues in contact with ASP 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 2.6 27.6 - - - +
351A MET* 3.8 8.9 - - - +
417A TYR* 1.3 72.8 - - - +
419A LEU* 1.3 66.7 + - - +
420A GLN* 2.9 10.2 + - - +
440A LYS* 6.0 8.7 - - - +
480A GLY* 2.4 31.2 + - - +
481A PRO 3.2 15.6 - - - +
482A ARG* 3.7 27.2 - - - +
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Residues in contact with LEU 419 (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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348A PHE* 3.5 35.4 - - + -
349A PRO 4.0 5.2 - - - +
350A LEU* 3.0 21.4 + - + +
418A ASP* 1.3 67.9 - - - +
420A GLN* 1.3 62.6 + - - +
421A ALA 3.9 4.9 - - - +
422A VAL* 3.9 16.4 - - + -
440A LYS* 4.2 7.7 - - - +
446A TRP* 3.2 19.2 - - + -
462A ILE* 4.2 9.9 - - + -
477A LEU* 3.8 22.7 - - + -
478A LEU 3.6 17.5 - - - +
479A TYR* 3.2 35.6 - - + -
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Residues in contact with GLN 420 (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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124A SER* 3.2 37.1 + - - +
125A VAL* 3.7 12.8 - - - +
126A PRO* 4.5 4.4 - - - +
322A TYR* 3.2 32.7 + - - -
418A ASP 2.9 13.8 + - - +
419A LEU* 1.3 71.4 - - - +
421A ALA* 1.3 60.3 + - - +
439A VAL* 5.0 0.7 - - - -
440A LYS* 3.1 24.9 + - - +
446A TRP* 3.1 21.2 - - - -
478A LEU* 2.7 17.3 + - + +
480A GLY* 3.9 12.3 - - - +
481A PRO* 4.7 3.0 - - - +
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Residues in contact with ALA 421 (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* 3.6 33.4 - - + -
124A SER* 4.2 11.7 - - - +
419A LEU* 3.9 0.9 - - - +
420A GLN* 1.3 77.7 - - - +
422A VAL* 1.3 72.9 + - - +
438A TRP 3.1 13.2 - - - +
439A VAL* 4.3 10.5 - - + -
478A LEU* 3.2 29.6 + - + +
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Residues in contact with VAL 422 (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* 3.9 3.1 - - - -
348A PHE* 5.1 0.9 - - + -
419A LEU* 3.9 20.0 - - + -
421A ALA* 1.3 83.4 - - - +
423A LEU* 1.3 62.0 + - - +
424A THR* 3.4 20.0 - - - +
436A VAL 3.4 0.2 - - - +
438A TRP* 3.0 49.9 + - + -
446A TRP* 4.2 10.8 - - + -
462A ILE* 4.5 7.2 - - + -
465A LEU* 4.2 10.8 - - + -
474A ALA* 3.5 25.8 - - + -
476A VAL 3.4 4.0 - - - -
477A LEU* 3.9 18.2 - - + -
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Residues in contact with LEU 423 (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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117A ALA* 3.4 23.3 - - + +
118A THR* 3.2 45.1 - - - +
121A CYS* 3.8 14.7 - - - -
199A ALA* 3.7 8.7 - - + +
203A TRP* 4.1 8.5 - - + -
422A VAL* 1.3 72.7 - - - +
424A THR* 1.3 72.2 + - - +
425A HIS 4.4 0.2 - - - -
435A TYR* 3.6 26.7 - - + -
436A VAL 3.9 1.8 - - - -
437A SER* 4.6 0.4 - - - +
475A TYR* 2.9 25.8 + - + -
476A VAL* 2.9 35.9 + - + +
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Residues in contact with THR 424 (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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422A VAL* 3.4 18.4 - - - +
423A LEU* 1.3 80.6 + - - +
425A HIS* 1.3 60.2 + - - +
435A TYR* 3.2 1.9 - - - -
436A VAL* 2.6 38.0 + - + +
438A TRP* 3.2 23.1 + - - +
465A LEU* 4.2 4.8 - - + +
472A HIS* 3.2 42.0 - - + +
473A ILE 3.3 18.8 + - - +
474A ALA* 3.5 2.8 + - - -
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Residues in contact with HIS 425 (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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330A PHE* 3.4 25.2 - + + -
341A LYS* 2.9 25.8 + - - -
424A THR* 1.3 74.5 - - - +
426A GLN* 1.3 64.1 + - - +
427A GLY* 3.4 26.0 - - - -
429A SER 3.1 17.2 + - - -
432A SER 2.7 29.2 + - - -
434A HIS 3.3 13.0 - - - -
435A TYR* 3.4 44.9 - + + +
473A ILE 3.3 21.0 + - - +
475A TYR* 4.3 10.0 - - + +
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Residues in contact with GLN 426 (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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341A LYS* 3.6 2.7 - - - +
425A HIS* 1.3 77.0 - - - +
427A GLY* 1.3 60.4 + - - +
433A GLY* 3.4 1.4 - - - -
434A HIS* 2.9 38.2 + - - +
470A ASP* 3.8 21.2 - - - +
471A TRP* 4.1 11.0 - - - -
472A HIS* 3.3 57.0 + - + +
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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