Contacts of the strand formed by residues 455 - 463 (chain A) in PDB entry 5I4A
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 LYS 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A HIS* 3.6 2.8 - - - -
450A ASP* 3.1 32.0 + - + +
453A ALA* 4.5 9.2 - - + -
454A ARG* 1.3 91.0 + - - +
456A THR* 1.3 65.2 + - - +
457A ASN* 5.5 4.7 - - - +
477A ASN* 4.2 35.2 - - + +
478A LEU 3.1 10.1 - - - +
479A GLU* 2.7 30.6 + - - +
480A LEU* 4.1 3.6 - - - +
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Residues in contact with THR 456 (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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447A LEU* 4.7 6.7 - - + -
448A SER 3.5 4.5 - - - +
449A HIS* 2.6 35.5 + - + -
455A LYS* 1.3 71.2 - - - +
457A ASN* 1.3 77.7 + - - +
458A LEU 4.9 0.2 - - - +
477A ASN 3.6 1.0 + - - -
478A LEU* 2.5 50.7 + - + +
480A LEU* 3.3 11.6 - - - +
485A ASN* 2.8 34.4 + - + +
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Residues in contact with ASN 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ASP* 3.7 1.7 - - - +
447A LEU* 3.1 5.9 - - - +
448A SER* 2.8 55.5 + - - +
450A ASP* 5.5 10.3 + - - +
455A LYS* 5.5 4.9 + - - +
456A THR* 1.3 84.0 + - - +
458A LEU* 1.3 60.6 + - - +
475A HIS 4.0 3.8 - - - +
476A LYS* 4.2 6.7 - - - +
477A ASN* 3.4 23.5 + - - +
627A ALA* 6.2 4.5 - - + -
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Residues in contact with LEU 458 (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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445A ILE* 4.5 7.0 - - + -
446A ASP 3.4 7.2 - - - +
447A LEU* 3.8 28.0 - - + -
456A THR* 4.3 0.8 - - + -
457A ASN* 1.3 74.6 - - - +
459A CYS* 1.3 72.9 + - - +
460A ILE* 3.8 19.5 - - + -
474A LYS* 3.5 2.4 - - - +
475A HIS* 2.9 46.9 + - + +
478A LEU* 4.4 14.4 - - + -
485A ASN 5.1 1.6 - - - +
488A ILE* 3.6 31.4 - - + -
489A LEU* 4.2 20.6 - - + +
492A GLU* 4.3 7.0 - - + -
627A ALA* 5.5 1.7 - - - +
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Residues in contact with CYS 459 (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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445A ILE* 3.8 0.2 - - - -
446A ASP* 2.8 35.2 + - - +
458A LEU* 1.3 77.6 - - - +
460A ILE* 1.3 73.5 + - - +
472A ILE* 4.3 2.2 - - - -
473A GLY 3.1 15.9 - - - +
474A LYS* 4.4 4.3 - - + -
623A ALA* 3.6 25.5 - - - +
626A VAL* 3.7 30.3 - - - -
627A ALA* 3.8 23.1 - - + -
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Residues in contact with ILE 460 (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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443A ILE* 4.5 7.9 - - + -
444A GLY 3.2 9.4 - - - +
445A ILE* 3.6 21.3 - - + -
458A LEU* 3.8 18.6 - - + -
459A CYS* 1.3 81.0 - - - +
461A ALA* 1.3 68.4 + - - +
471A TYR* 3.5 36.1 - - + -
472A ILE* 3.3 6.9 - - - +
473A GLY 2.8 33.3 + - - +
489A LEU* 5.6 4.5 - - + +
492A GLU* 4.0 27.8 - - + +
493A TYR* 4.9 3.1 - - - +
496A ALA* 3.8 17.7 - - + -
623A ALA* 4.7 0.9 - - - -
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Residues in contact with ALA 461 (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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443A ILE* 3.2 2.5 - - - -
444A GLY 2.7 36.6 + - - -
460A ILE* 1.3 79.7 - - - +
462A ALA* 1.3 59.8 + - - +
469A ILE* 5.6 0.2 - - + -
471A TYR 3.4 8.1 - - - +
472A ILE* 4.4 2.7 - - + -
619A PRO* 3.5 27.5 - - + +
622A ILE* 3.7 30.5 - - + -
623A ALA* 4.1 4.9 - - + +
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Residues in contact with ALA 462 (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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441A LEU* 3.9 12.1 - - + -
442A TYR 3.2 5.2 - - - +
443A ILE* 3.8 14.6 - - + -
460A ILE* 4.7 0.4 - - - +
461A ALA* 1.3 73.0 - - - +
463A VAL* 1.3 61.7 + - - +
469A ILE* 3.6 2.1 - - - +
470A LEU* 2.7 37.3 + - + -
471A TYR 2.9 13.6 + - - +
496A ALA* 3.8 28.7 - - + +
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Residues in contact with VAL 463 (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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441A LEU* 4.1 5.7 - - - +
442A TYR* 2.8 45.9 + - + +
462A ALA* 1.3 81.4 - - - +
464A ASP* 1.3 71.4 + - - +
467A GLY* 4.5 4.9 - - - -
468A ASP 3.1 15.7 - - - +
469A ILE* 4.1 5.8 - - - -
470A LEU* 4.0 7.0 - - - +
602A LEU* 4.5 6.1 - - + -
605A VAL* 5.2 0.2 - - + -
618A TYR* 4.1 11.7 - - + -
619A PRO* 3.9 22.4 - - + -
622A ILE* 3.8 29.4 - - + -
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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