Contacts of the helix formed by residues 533 - 547 (chain A) in PDB entry 2PKG
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 VAL 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A TYR* 3.5 46.2 - - + -
498A ARG* 3.9 10.1 - - - +
531A ASP* 2.9 6.6 + - - +
532A PRO* 1.3 81.7 - - + +
534A ALA* 1.3 67.9 + - - +
535A ASN* 3.8 15.9 - - + +
536A VAL* 2.8 28.6 + - + +
537A ARG* 3.5 6.2 + - - -
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Residues in contact with ALA 534 (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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532A PRO 3.6 0.8 + - - -
533A VAL* 1.3 70.8 - - - +
535A ASN* 1.3 54.6 + - - +
537A ARG* 2.8 32.5 + - - +
538A PHE* 2.7 36.7 + - - +
570A ASP* 5.1 0.2 - - - +
572A ASP* 4.0 33.2 - - + +
575A VAL* 3.9 5.3 - - + +
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Residues in contact with ASN 535 (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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495A TYR* 4.5 19.6 - - + -
499A MET* 4.5 11.5 - - - +
533A VAL* 2.8 17.8 + - + +
534A ALA* 1.3 72.8 - - - +
536A VAL* 1.3 66.2 + - - +
537A ARG 3.0 1.2 + - - -
538A PHE* 3.1 40.2 + - + -
539A ASN* 3.1 19.5 + - - -
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Residues in contact with VAL 536 (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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495A TYR* 4.1 26.7 - - + +
498A ARG* 4.2 4.5 - - + +
499A MET* 4.3 11.9 - - + -
502A LEU* 3.5 10.6 - - + +
528A MET* 3.5 33.7 - - + +
531A ASP* 3.2 39.9 - - + +
533A VAL* 2.8 26.2 + - + +
535A ASN* 1.3 73.1 - - - +
537A ARG* 1.3 57.4 + - - +
539A ASN* 3.4 1.3 + - - +
540A VAL* 2.9 22.7 + - - +
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Residues in contact with ARG 537 (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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528A MET 3.7 8.3 - - - +
529A ALA 3.9 14.4 - - - +
530A GLY* 4.0 3.5 - - - -
531A ASP* 2.6 46.6 + - + +
532A PRO* 3.4 12.5 + - - +
534A ALA* 2.8 43.8 + - - +
535A ASN 3.0 0.8 - - - -
536A VAL* 1.3 75.7 - - - +
538A PHE* 1.3 61.5 + - - +
539A ASN 2.9 5.4 - - - -
540A VAL* 2.7 27.5 - - + +
541A ALA* 3.3 7.3 + - - +
567A LEU* 5.3 4.1 - - + +
570A ASP* 3.9 30.8 + - - +
575A VAL* 4.6 8.3 - - + +
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Residues in contact with PHE 538 (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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534A ALA 2.7 13.7 + - - +
535A ASN* 3.1 50.4 + - + -
537A ARG* 1.3 73.7 - - - +
539A ASN* 1.3 80.0 + - - +
541A ALA* 4.0 2.0 - - - +
542A LYS* 2.9 34.5 + - + +
572A ASP* 6.1 0.9 - - - -
574A ASP* 4.1 16.8 - - + -
575A VAL* 3.8 33.6 - - + +
578A PHE* 3.4 34.1 - + - +
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Residues in contact with ASN 539 (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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499A MET* 3.6 28.3 - - + +
502A LEU* 4.0 8.1 - - + -
503A PHE* 3.9 27.2 - - + -
535A ASN 3.1 15.9 + - - +
536A VAL* 3.5 9.0 - - - +
537A ARG 2.9 0.4 - - - -
538A PHE* 1.3 95.2 - - - +
540A VAL* 1.3 59.8 + - - +
541A ALA 3.0 1.8 - - - -
542A LYS* 3.0 31.1 + - - +
543A SER* 2.9 32.4 + - - +
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Residues in contact with VAL 540 (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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502A LEU* 3.5 15.5 - - + -
525A VAL* 2.9 39.3 - - + +
528A MET 4.5 1.1 - - - -
529A ALA* 3.7 32.8 - - + +
536A VAL 2.9 14.3 + - - +
537A ARG* 2.7 36.1 - - + +
539A ASN* 1.3 75.6 - - - +
541A ALA* 1.3 63.7 + - + +
543A SER* 3.5 3.9 - - - -
544A LEU* 3.1 25.5 + - + +
567A LEU* 4.7 6.5 - - + -
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Residues in contact with ALA 541 (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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537A ARG 3.3 6.7 + - - +
538A PHE 4.0 8.7 - - - +
539A ASN 3.0 0.4 - - - -
540A VAL* 1.3 79.5 - - - +
542A LYS* 1.3 67.7 + - - +
543A SER 2.8 3.4 + - - -
544A LEU* 2.9 21.1 + - - +
545A GLN* 2.9 12.6 + - - +
564A LEU* 5.5 1.6 - - + -
567A LEU* 4.6 8.5 - - + -
575A VAL* 4.9 1.8 - - + +
578A PHE* 4.2 2.9 - - + -
579A ALA* 3.7 38.6 - - + +
582A ALA* 4.6 5.2 - - + +
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Residues in contact with LYS 542 (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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506A ASN* 4.8 0.4 - - - -
538A PHE* 2.9 39.9 - - + +
539A ASN* 3.3 29.0 + - - +
541A ALA* 1.3 75.8 - - - +
543A SER* 1.3 57.1 + - - +
545A GLN* 3.1 20.3 - - - +
546A LYS* 2.9 25.2 + - - +
578A PHE* 3.6 35.8 - - + +
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Residues in contact with SER 543 (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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502A LEU* 3.9 16.1 - - - +
503A PHE* 5.3 0.9 - - - -
505A ILE* 6.0 0.4 - - - -
506A ASN* 3.1 33.8 + - - +
525A VAL* 4.2 13.5 - - - -
539A ASN* 2.9 19.0 + - - +
540A VAL* 3.5 8.5 - - - -
541A ALA 2.8 0.6 + - - -
542A LYS* 1.3 72.9 - - - +
544A LEU* 1.3 53.8 + - - -
545A GLN 2.8 4.3 - - - -
546A LYS* 2.7 21.1 + - - +
547A ILE* 2.8 23.0 + - - +
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Residues in contact with LEU 544 (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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522A LEU* 4.0 13.5 - - + -
525A VAL* 3.1 27.4 - - + -
526A LEU* 3.4 34.5 - - + -
529A ALA* 5.2 0.7 - - + -
540A VAL* 3.1 25.4 - - + +
541A ALA* 2.9 9.7 + - - +
543A SER* 1.3 73.2 - - - +
545A GLN* 1.3 62.3 + - - +
547A ILE* 4.0 8.2 - - + +
548A GLY* 3.5 16.8 + - - -
551A LEU* 5.7 1.4 - - - +
560A VAL* 4.8 10.5 - - + +
563A ILE 4.7 2.9 - - - +
564A LEU* 4.4 28.9 - - + -
567A LEU* 4.5 11.9 - - + -
582A ALA* 5.4 0.4 - - - -
586A LEU* 4.5 8.2 - - - +
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Residues in contact with GLN 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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541A ALA 2.9 10.0 + - - +
542A LYS* 3.1 21.1 - - - +
543A SER 2.8 0.4 - - - -
544A LEU* 1.3 79.2 - - - +
546A LYS* 1.3 65.2 + - - +
548A GLY* 3.1 12.5 + - - -
549A PRO* 3.7 7.1 - - - +
578A PHE* 5.2 6.4 - - - +
581A GLU* 4.3 15.6 + - - +
582A ALA* 4.0 30.1 + - + +
585A VAL* 3.8 29.2 - - + +
586A LEU* 4.5 8.1 - - + +
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Residues in contact with LYS 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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506A ASN* 3.1 55.2 - - + +
509A SER* 4.9 0.9 - - - +
510A GLU* 3.5 33.0 + - - +
542A LYS 2.9 11.2 + - - +
543A SER 2.7 7.3 + - - +
545A GLN* 1.3 71.2 - - - +
547A ILE* 1.3 59.8 + - + +
548A GLY 2.8 10.9 + - - -
549A PRO* 3.6 9.0 - - - +
550A ILE* 5.2 2.4 + - - +
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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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505A ILE* 4.0 17.3 - - + +
506A ASN* 4.3 4.0 - - - +
509A SER* 3.2 36.8 - - - +
517A THR* 4.3 15.7 - - + -
522A LEU* 4.4 21.8 - - + -
525A VAL* 4.0 30.3 - - + -
543A SER* 2.8 22.1 + - - +
544A LEU* 4.0 7.4 - - - +
546A LYS* 1.3 76.5 - - + +
548A GLY* 1.3 62.3 + - - +
549A PRO 3.9 0.2 - - - -
550A ILE* 4.2 11.8 - - + +
551A LEU* 3.4 20.5 + - + +
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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