Contacts of the strand formed by residues 469 - 478 (chain A) in PDB entry 5IXM
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 TRP 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A PRO* 3.8 7.4 - - - +
465A ILE* 3.5 42.3 + - + -
466A ALA* 3.5 29.6 + - + +
467A ASP 3.7 2.0 - - - +
468A ARG* 1.3 96.9 - - - +
470A ALA* 1.3 66.0 + - - +
491A LEU* 5.8 9.2 - - + -
492A GLN 3.5 6.3 - - - +
493A TYR* 3.8 26.5 - + - -
494A ASN* 5.0 1.0 + - - -
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Residues in contact with ALA 470 (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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462A SER* 6.0 2.0 - - - +
463A TRP 3.8 9.4 - - - +
464A PRO* 4.3 4.9 - - + -
465A ILE* 4.7 2.5 - - - +
469A TRP* 1.3 79.3 - - - +
471A ILE* 1.3 61.4 + - - +
472A VAL* 5.7 2.2 - - + -
491A LEU* 3.4 6.3 - - - +
492A GLN* 2.7 57.9 + - + +
494A ASN* 4.5 6.7 - - - +
541A THR* 5.4 4.0 - - + +
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Residues in contact with ILE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ALA 4.6 0.3 - - - -
462A SER* 3.4 2.4 + - - -
463A TRP* 2.9 50.6 + - + +
465A ILE* 3.7 27.4 - - + -
470A ALA* 1.3 76.0 - - - +
472A VAL* 1.3 71.2 + - - +
489A VAL* 5.1 10.3 - - + -
490A GLY 3.2 16.4 - - - +
491A LEU* 3.7 18.8 - - + -
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Residues in contact with VAL 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ALA 3.2 6.3 - - - +
462A SER* 3.4 30.5 - - - +
470A ALA* 5.7 2.2 - - + -
471A ILE* 1.3 81.4 - - - +
473A GLY* 1.3 59.3 + - - +
488A LEU* 4.4 7.6 - - + -
489A VAL* 3.7 2.8 - - - +
490A GLY* 2.8 50.5 + - - +
492A GLN* 6.0 0.7 - - + +
541A THR* 4.1 20.4 - - + +
544A MET* 3.8 27.8 - - + -
545A LEU* 3.9 13.2 - - + -
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Residues in contact with GLY 473 (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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459A THR 4.7 0.2 - - - -
460A THR* 3.3 6.0 - - - +
461A ALA* 2.9 35.2 + - - +
472A VAL* 1.3 76.0 - - - +
474A ALA* 1.3 64.6 + - - +
488A LEU* 3.2 11.4 - - - -
489A VAL* 4.6 2.2 - - - -
545A LEU* 4.4 1.3 - - - +
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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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459A THR 3.3 10.1 - - - +
460A THR* 4.2 13.9 - - + +
473A GLY* 1.3 75.8 - - - +
475A TYR* 1.3 61.1 + - - +
476A TYR* 4.3 11.0 - - + -
486A SER* 3.9 0.9 + - - +
487A GLN* 3.2 6.2 + - - +
488A LEU* 2.8 55.6 + - + -
545A LEU* 5.3 1.6 - - + -
550A LEU 5.9 2.0 - - - +
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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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457A VAL 3.9 1.1 - - - +
458A GLY* 3.4 2.4 - - - -
459A THR* 2.9 48.3 + - - +
474A ALA* 1.3 74.2 - - - +
476A TYR* 1.3 63.0 + - - +
477A TYR* 3.5 39.0 - + + -
484A PRO* 3.3 28.3 - - + +
486A SER 3.6 1.6 - - - -
487A GLN* 3.8 41.5 - - + -
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Residues in contact with TYR 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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427A GLN* 4.5 8.7 + - - -
429A ASN* 3.5 26.7 + - - -
456A GLN* 3.4 29.4 - - + -
457A VAL 3.5 1.1 - - - -
458A GLY* 3.6 13.7 - - - -
459A THR 4.4 3.6 - - - -
460A THR* 3.5 24.4 + - - -
474A ALA* 4.7 9.4 - - + -
475A TYR* 1.3 79.7 - - - +
477A TYR* 1.3 61.1 + - - +
484A PRO* 3.6 4.3 - - - +
485A ALA* 2.9 27.6 + - + -
486A SER* 2.8 29.2 + - - +
550A LEU* 3.4 48.5 + - + -
551A PRO 5.3 1.9 + - - -
552A TYR* 5.8 2.3 - - - -
67B VAL 5.0 1.8 - - - -
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Residues in contact with TYR 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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456A GLN* 3.4 7.5 - - - +
457A VAL* 2.8 42.3 + - + +
475A TYR* 3.5 39.3 - + + -
476A TYR* 1.3 74.2 - - - +
478A ASP* 1.3 85.6 + - - +
479A THR* 3.6 14.9 + - + +
482A LYS* 3.0 29.6 + - + +
483A GLN* 3.5 24.9 - - - -
484A PRO* 3.8 4.3 - - + -
485A ALA* 4.9 0.7 - - - -
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Residues in contact with ASP 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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455A SER 3.5 15.0 + - - +
456A GLN* 4.8 2.9 - - + +
477A TYR* 1.3 73.6 - - - +
479A THR* 1.3 62.8 + - - +
480A LYS* 3.3 15.2 + - - +
481A ALA* 3.2 27.7 + - + +
482A LYS* 2.9 21.1 + - - -
483A GLN* 2.9 32.2 + - + +
485A ALA* 4.5 11.6 - - + +
508A ILE* 6.1 1.1 - - + -
70B PHE 5.9 0.5 - - - -
71B ARG* 4.3 13.2 + - - +
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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