Contacts of the helix formed by residues 533 - 548 (chain j) in PDB entry 5JPQ
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 533 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525j THR* 3.1 18.7 - - - +
528j SER 2.7 21.1 - - - -
529j PHE* 3.2 6.3 - - - -
530j HIS 3.2 31.6 + - - -
532j VAL* 1.3 69.3 - - - +
534j GLU* 1.3 69.7 + - - +
535j LYS* 3.0 10.8 + - - +
536j PHE* 3.4 13.0 + - - +
537j LEU* 3.8 6.6 + - - +
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Residues in contact with GLU 534 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525j THR 3.7 0.4 + - - -
526j LEU* 3.9 19.5 - - - +
528j SER 3.3 5.0 + - - +
529j PHE* 5.7 4.5 - - + -
533j SER* 1.3 80.2 - - - +
535j LYS* 1.3 54.9 + - - +
536j PHE 3.4 0.2 + - - -
537j LEU* 3.5 4.7 + - - +
538j GLN* 2.8 31.2 + - + +
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Residues in contact with LYS 535 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533j SER* 3.0 7.9 - - - +
534j GLU* 1.3 76.6 - - - +
536j PHE* 1.4 60.4 + - - +
538j GLN* 3.1 7.4 + - - +
539j GLN* 2.8 31.6 + - - +
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Residues in contact with PHE 536 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525j THR* 5.4 4.9 - - - -
532j VAL* 4.5 10.3 - - + -
533j SER 3.4 19.1 + - - +
535j LYS* 1.4 77.6 - - - +
537j LEU* 1.3 63.2 + - - +
539j GLN* 3.2 8.6 + - - +
540j MET* 3.0 21.1 + - - +
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Residues in contact with LEU 537 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523j ARG 6.1 0.2 - - - +
525j THR* 5.2 7.3 - - - -
526j LEU* 5.2 12.1 - - + +
533j SER 3.8 6.5 + - - +
534j GLU* 3.5 7.8 + - - +
536j PHE* 1.3 75.7 - - - +
538j GLN* 1.3 68.1 + - - +
540j MET* 3.1 8.8 + - - +
541j VAL* 2.8 23.8 + - - +
559j MET* 6.6 0.2 - - + -
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Residues in contact with GLN 538 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534j GLU* 2.8 20.9 + - + +
535j LYS* 3.1 9.4 + - - +
537j LEU* 1.3 76.3 - - - +
539j GLN* 1.4 56.9 + - - +
541j VAL* 3.1 9.6 + - - +
542j ALA* 2.9 28.3 + - - +
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Residues in contact with GLN 539 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500j LEU* 5.7 1.6 - - - +
535j LYS 2.8 13.7 + - - +
536j PHE* 3.2 10.3 + - - +
538j GLN* 1.4 72.1 - - - +
540j MET* 1.3 66.5 + - - +
542j ALA* 3.2 8.3 + - - +
543j LEU* 3.1 22.0 + - - +
582j PRO* 5.6 12.1 - - + +
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Residues in contact with MET 540 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536j PHE 3.0 12.0 + - - +
537j LEU* 3.4 12.3 - - - +
539j GLN* 1.3 76.0 - - - +
541j VAL* 1.3 63.7 + - - +
543j LEU* 3.2 6.9 + - - +
544j TYR* 2.9 23.2 + - - +
567j LEU* 5.7 9.4 - - + -
569j VAL* 5.9 6.5 - - + -
585j VAL* 4.5 18.1 - - + +
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Residues in contact with VAL 541 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495j CYS* 6.0 6.5 - - + -
537j LEU 2.8 12.1 + - - +
538j GLN* 3.3 12.1 - - - +
540j MET* 1.3 73.6 - - - +
542j ALA* 1.3 66.8 + - - +
544j TYR* 3.3 2.6 + - - +
545j VAL* 2.8 31.0 + - + +
556j LEU* 6.2 5.4 - - + -
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Residues in contact with ALA 542 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497j ASP 4.5 15.7 - - - +
498j ALA* 5.8 3.1 - - - -
500j LEU* 4.9 16.8 - - + +
538j GLN 2.9 13.0 + - - +
539j GLN* 3.2 11.0 + - - +
541j VAL* 1.3 74.6 - - - +
543j LEU* 1.3 58.7 + - - +
545j VAL* 3.8 4.1 - - - +
546j ALA* 2.8 33.4 + - - +
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Residues in contact with LEU 543 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500j LEU* 5.5 7.6 - - + +
539j GLN 3.1 12.4 + - - +
540j MET* 3.2 9.2 + - - +
542j ALA* 1.3 74.7 - - - +
544j TYR* 1.4 69.6 + - - +
546j ALA* 3.2 5.4 + - - +
547j SER* 3.2 21.0 + - - -
582j PRO* 5.6 11.2 - - + +
583j LEU 6.5 0.4 - - - -
584j CYS* 5.8 4.9 - - - +
585j VAL* 5.1 8.7 - - + -
639j ALA* 4.4 6.7 - - + +
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Residues in contact with TYR 544 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540j MET 2.9 14.9 + - - +
541j VAL* 4.4 2.7 - - - +
543j LEU* 1.4 76.3 - - - +
545j VAL* 1.3 65.4 + - - +
547j SER* 3.1 14.4 + - - -
548j HIS* 3.3 11.8 + - - +
585j VAL* 5.2 9.4 - - + +
587j GLN* 5.9 3.4 - - + -
637j ARG* 4.2 26.0 - - + -
639j ALA* 4.3 15.2 - - + +
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Residues in contact with VAL 545 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421j GLY* 3.9 5.4 - - - -
541j VAL* 2.8 20.4 + - + +
542j ALA* 3.8 4.7 - - - +
544j TYR* 1.3 76.5 - - - +
546j ALA* 1.3 63.9 + - - +
548j HIS* 3.1 21.7 + - - +
550j LYS 4.8 2.4 - - - +
551j ASN* 4.8 16.3 - - + +
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Residues in contact with ALA 546 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421j GLY* 3.1 19.8 - - - -
422j ARG* 4.5 3.6 - - + +
423j SER* 2.9 37.5 + - - +
424j LEU 3.3 0.2 + - - -
498j ALA* 5.2 15.0 - - + +
500j LEU* 6.5 0.9 - - + -
501j PRO* 5.3 7.2 - - + -
542j ALA 2.8 20.4 + - - +
543j LEU* 3.6 6.5 - - - +
545j VAL* 1.3 78.9 - - - +
547j SER* 1.3 57.1 + - - +
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Residues in contact with SER 547 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423j SER* 3.4 14.4 - - - -
424j LEU* 3.9 11.8 - - - +
543j LEU 3.2 5.9 + - - -
544j TYR 3.1 9.8 + - - -
546j ALA* 1.3 74.5 - - - +
548j HIS* 1.3 61.2 + - - +
549j TYR 3.9 0.5 + - - -
638j ILE 5.6 0.2 - - - -
639j ALA* 3.8 26.0 - - - -
640j THR 5.9 1.6 - - - -
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Residues in contact with HIS 548 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421j GLY* 3.1 22.7 + - - -
424j LEU* 3.9 3.8 - - - +
544j TYR 3.3 8.3 + - - +
545j VAL* 3.1 13.1 + - - +
546j ALA 3.9 0.2 - - - +
547j SER* 1.3 80.0 - - - +
549j TYR* 1.3 65.5 + - - +
550j LYS 3.4 18.4 - - - +
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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