Contacts of the strand formed by residues 543 - 549 (chain A) in PDB entry 1JSC
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 LEU 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A ALA* 4.4 11.4 - - + -
487A THR* 4.3 11.9 - - + +
489A ARG* 3.6 31.3 - - + +
490A HIS 2.8 12.0 + - - +
491A VAL* 3.3 22.4 - - + +
492A ILE 2.9 25.3 + - - +
536A GLN* 5.1 0.2 - - - +
541A GLU 3.9 1.0 + - - -
542A SER* 1.3 72.2 - - - +
544A VAL* 1.3 58.0 + - - +
545A ILE* 4.4 11.9 - - + -
569A PRO 5.5 0.4 - - - +
571A LYS* 3.7 37.0 - - + -
633A VAL* 3.8 30.1 - - + +
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Residues in contact with VAL 544 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A ILE* 3.4 22.4 - - + +
494A THR* 4.7 1.6 - - + -
532A ALA* 3.7 37.9 - - + +
535A ALA* 4.4 9.2 - - + -
536A GLN* 3.5 49.1 - - - +
542A SER* 3.5 9.1 + - - +
543A LEU* 1.3 77.8 - - - +
545A ILE* 1.3 65.6 + - - +
569A PRO 5.4 0.2 + - - -
570A VAL* 3.7 4.0 - - + +
571A LYS* 2.9 28.6 + - - +
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Residues in contact with ILE 545 (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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480A LEU* 4.1 29.6 - - + -
484A ALA* 4.3 12.1 - - + -
491A VAL* 4.4 5.8 - - + -
492A ILE 2.8 12.5 + - - +
493A VAL* 3.2 9.4 - - + +
494A THR* 2.8 26.7 + - - +
508A TRP* 3.9 24.2 - - + -
543A LEU* 4.4 15.7 - - + -
544A VAL* 1.3 80.6 - - - +
546A ASP* 1.3 71.0 + - - +
547A ILE* 3.9 15.9 + - + -
571A LYS* 3.4 20.2 - - + +
573A LEU* 4.7 1.1 - - + -
632A PHE* 4.6 6.1 - - + -
633A VAL* 4.7 3.6 - - + -
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Residues in contact with ASP 546 (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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494A THR* 3.3 17.0 + - - +
495A THR* 3.7 1.2 - - - -
528A GLY* 3.4 27.2 - - - +
529A LEU* 3.4 10.2 + - - -
532A ALA* 4.1 4.9 - - + +
544A VAL 4.3 0.4 + - - -
545A ILE* 1.3 72.3 - - - +
547A ILE* 1.3 67.2 + - - +
548A ASP* 2.8 29.9 - - - +
571A LYS 2.9 8.9 + - - -
572A ILE* 3.7 30.3 - - + +
573A LEU* 2.8 31.4 + - - +
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Residues in contact with ILE 547 (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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477A ILE* 4.5 12.8 - - + -
480A LEU* 4.8 2.9 - - + -
493A VAL* 3.9 20.4 - - + -
494A THR 2.9 11.5 + - - +
495A THR* 3.1 24.7 - - + -
500A HIS* 3.1 17.1 - - + +
504A ALA* 4.0 24.0 - - + -
508A TRP* 4.0 27.6 - - + -
545A ILE* 4.0 15.0 - - + -
546A ASP* 1.3 70.1 - - - +
548A ASP* 1.3 59.4 + - - +
573A LEU* 3.9 16.8 - - + -
575A LEU* 4.1 25.4 - - + -
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Residues in contact with ASP 548 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A GLY* 3.4 20.6 - - - -
500A HIS* 3.4 8.4 - - - -
526A GLY* 5.5 1.8 + - - -
528A GLY* 4.1 1.8 + - - -
529A LEU* 3.9 9.0 + - - +
546A ASP* 2.8 30.5 - - - +
547A ILE* 1.3 72.6 - - - +
549A GLY* 1.3 72.7 + - - +
552A SER* 3.4 11.1 - - - -
553A PHE* 3.6 28.5 - - + -
573A LEU 2.8 18.0 + - - +
574A ILE* 4.4 2.0 - - + -
575A LEU* 3.0 31.4 + - - +
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Residues in contact with GLY 549 (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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500A HIS* 3.1 27.4 + - - -
548A ASP* 1.3 80.4 + - - +
550A ASP* 1.3 61.3 + - - -
551A ALA 3.4 2.0 - - - -
553A PHE* 2.9 29.9 + - - +
574A ILE* 4.4 2.5 - - - -
575A LEU 4.1 7.2 - - - -
700A TPP 3.7 10.5 - - - -
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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