Contacts of the strand formed by residues 446 - 455 (chain A) in PDB entry 1D0N
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 SER 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A ARG* 3.9 1.0 - - - -
425A VAL* 3.1 31.4 + - - +
445A ASP* 1.3 72.7 + - - +
447A TYR* 1.3 64.2 + - - +
466A TRP 3.2 13.6 + - - -
467A GLN* 4.1 5.0 - - - -
471A SER* 2.7 27.9 + - - -
475A GLU* 4.2 6.4 + - - -
476A VAL* 3.8 13.9 - - - +
479A SER* 3.7 24.9 + - - -
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Residues in contact with TYR 447 (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 ILE* 4.5 4.7 - - + -
423A TRP 3.1 17.3 - - - +
424A ARG* 3.9 27.1 - - + -
425A VAL* 5.2 1.1 - - - -
433A VAL* 4.1 16.4 - - + -
440A GLN 4.8 3.1 + - - -
441A PHE* 3.5 35.2 - + + -
442A TYR* 2.8 32.6 + - - +
445A ASP* 2.8 25.3 + - + -
446A SER* 1.3 74.2 - - - +
448A ILE* 1.3 63.3 + - - +
449A ILE* 5.0 2.2 - - + -
464A TYR 4.3 0.2 - - - -
465A ASN* 3.3 9.4 + - - -
466A TRP* 2.9 70.6 + + + -
525A SER* 3.7 7.1 + - - -
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Residues in contact with ILE 448 (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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423A TRP* 3.0 53.7 + - + +
425A VAL* 4.5 14.8 - - + -
430A LYS* 4.2 18.8 - - + -
447A TYR* 1.3 77.0 - - - +
449A ILE* 1.3 68.0 + - - +
463A ILE* 3.8 18.8 - - + -
464A TYR 3.1 5.6 - - - +
465A ASN* 5.0 1.3 - - - +
479A SER* 5.4 1.6 - - - +
482A LEU* 4.3 4.0 - - + +
483A THR* 4.0 27.4 - - - +
486A LEU* 3.4 34.3 - - + -
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Residues in contact with ILE 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LYS* 4.6 7.4 - - + -
421A GLN 3.4 10.1 - - - +
422A ILE* 3.9 25.8 - - + -
441A PHE* 3.9 27.6 - - + -
447A TYR* 5.2 2.9 - - + -
448A ILE* 1.3 84.9 - - - +
450A LEU* 1.3 69.1 + - - +
451A TYR* 4.7 1.6 - - + +
462A ILE 3.3 2.4 - - - +
463A ILE* 3.1 6.7 - - - -
464A TYR* 2.7 50.8 + - + +
466A TRP* 5.3 7.6 - - + -
508A LEU* 3.9 25.4 - - + -
511A LEU* 4.5 18.2 - - + -
512A PHE* 5.1 1.8 - - + -
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Residues in contact with LEU 450 (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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419A GLN 4.0 0.5 - - - +
420A LYS* 3.1 6.6 - - - +
421A GLN* 3.0 50.2 + - + +
423A TRP* 3.9 24.8 - - + -
448A ILE 4.3 0.2 - - - -
449A ILE* 1.3 74.3 - - - +
451A TYR* 1.3 64.4 + - - +
452A ASN* 5.0 5.5 + - - +
461A GLN* 4.0 24.9 - - + +
462A ILE 4.0 2.2 - - - +
463A ILE* 3.8 26.0 - - + +
486A LEU* 4.6 9.6 - - + -
490A LEU* 3.8 30.3 - - + -
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Residues in contact with TYR 451 (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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414A ASP* 2.6 42.8 + - - -
416A GLY* 3.0 8.7 - - - -
417A THR 3.1 0.3 + - - -
418A GLY* 2.8 43.8 + - - -
419A GLN 3.6 11.0 - - - -
420A LYS* 3.9 10.1 - - + -
449A ILE* 3.9 2.4 + - + -
450A LEU* 1.3 75.8 - - - +
452A ASN* 1.3 66.5 + - - +
453A TYR* 3.5 15.8 + - + -
461A GLN* 3.1 5.5 - - - +
462A ILE* 2.8 52.5 + - + +
464A TYR* 5.1 2.9 - - + -
507A HIS* 3.5 17.5 - + - -
511A LEU* 3.4 35.2 - - + -
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Residues in contact with ASN 452 (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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418A GLY* 3.6 3.6 - - - -
419A GLN* 3.0 31.3 + - + +
420A LYS* 5.2 0.2 - - - +
421A GLN* 5.9 3.0 - - - +
450A LEU* 5.0 7.2 + - - +
451A TYR* 1.3 88.1 - - - +
453A TYR* 1.3 59.8 - - - +
454A ARG* 3.2 29.6 + - - +
460A GLY 3.4 5.8 - - - +
461A GLN* 2.8 38.5 + - - +
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Residues in contact with TYR 453 (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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413A ASP* 4.3 16.4 - - + -
414A ASP* 3.1 21.5 - - + +
451A TYR* 3.5 13.1 + - + -
452A ASN* 1.3 74.3 - - - +
454A ARG* 1.3 65.6 + - - +
455A HIS 4.4 0.2 - - - -
458A ARG* 3.7 20.5 - - - +
459A GLN* 3.4 12.0 + - - +
460A GLY* 2.9 64.5 + - - +
461A GLN* 3.7 4.9 - - - -
462A ILE* 3.6 30.7 - - + -
495A VAL* 5.0 3.1 - - + +
724A PHE 4.7 5.7 + - - -
725A GLU 4.4 2.3 + - - -
726A PRO* 3.9 15.1 - - + +
727A PRO* 3.7 29.0 - - + +
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Residues in contact with ARG 454 (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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401A HIS* 4.9 5.5 - - - +
414A ASP* 3.1 23.3 + - - +
415A ASP* 5.6 1.0 - - - +
417A THR* 4.0 5.9 + - - -
418A GLY* 3.1 26.4 - - - -
419A GLN* 3.5 25.6 - - - +
452A ASN* 3.2 25.5 + - - +
453A TYR* 1.3 79.0 - - - +
455A HIS* 1.3 60.7 + - - +
456A GLY 4.0 1.8 - - - +
458A ARG 4.1 2.0 - - - -
459A GLN* 4.2 23.8 - - + +
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Residues in contact with HIS 455 (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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400A LEU* 2.9 32.3 + - + -
401A HIS* 3.6 24.7 - - - -
402A THR 4.7 1.1 - - - -
403A SER 3.5 9.7 + - - -
404A THR* 3.8 25.6 - - + -
407A ALA* 4.4 3.6 - - + +
413A ASP 3.2 31.2 - - - +
414A ASP* 4.8 1.1 - - - -
453A TYR* 4.6 1.6 - - + -
454A ARG* 1.3 72.1 - - - +
456A GLY* 1.3 52.4 + - - +
457A SER* 2.3 39.8 + - - -
458A ARG 2.8 21.3 + - - +
459A GLN* 4.8 0.6 - - - +
727A PRO* 3.8 16.5 - - + +
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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