Contacts of the helix formed by residues 533 - 549 (chain A) in PDB entry 1B3U
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 ALA 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A PRO 3.5 2.6 + - - -
532A VAL* 1.3 73.5 - - - +
534A ASN* 1.3 63.0 + - - +
536A ARG* 3.2 27.5 + - - +
537A PHE* 3.2 26.3 + - - -
571A ASP* 2.9 33.4 - - + +
574A VAL* 3.7 3.1 - - - +
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Residues in contact with ASN 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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494A TYR* 4.2 24.1 + - + -
498A MET* 3.9 8.9 - - - +
532A VAL* 3.1 16.0 - - + +
533A ALA* 1.3 80.0 - - - +
535A VAL* 1.3 63.1 + - - +
537A PHE* 3.6 24.1 - - - -
538A ASN* 3.3 37.6 + - - -
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Residues in contact with VAL 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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494A TYR* 4.7 12.3 - - + +
497A ARG* 4.1 18.4 - - + +
498A MET* 3.7 16.2 - - + -
501A LEU* 3.8 3.3 - - + +
527A MET* 3.6 25.1 - - + +
530A ASP* 3.5 43.7 - - + +
532A VAL* 3.1 12.6 + - + +
534A ASN* 1.3 77.4 - - - +
536A ARG* 1.3 62.2 + - - +
538A ASN* 3.1 5.4 + - - +
539A VAL* 3.1 26.8 + - + +
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Residues in contact with ARG 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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528A ALA 3.3 24.5 - - - +
529A GLY 4.5 1.3 - - - -
530A ASP* 3.1 40.6 + - + +
531A PRO* 3.4 19.0 + - - +
532A VAL 3.2 2.8 + - - +
533A ALA* 3.2 32.3 + - - +
535A VAL* 1.3 76.8 - - - +
537A PHE* 1.3 60.9 + - - +
539A VAL* 3.2 23.2 + - - +
540A ALA* 3.4 6.4 + - - +
566A LEU* 4.5 9.3 - - + +
569A ASP* 2.8 42.1 + - - -
570A GLN* 3.7 17.4 + - - +
571A ASP* 4.1 2.2 - - - +
574A VAL* 4.0 13.9 - - + +
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Residues in contact with PHE 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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533A ALA* 3.2 23.7 + - + -
534A ASN* 3.6 28.0 - - - -
536A ARG* 1.3 76.4 - - - +
538A ASN* 1.3 86.5 + - - +
540A ALA* 3.3 8.8 + - - +
541A LYS* 3.1 46.4 + - + +
571A ASP* 5.5 1.1 - - - -
573A ASP* 4.1 21.8 - - + -
574A VAL* 3.7 30.4 - - + +
577A PHE* 3.9 20.6 - + + +
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Residues in contact with ASN 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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498A MET* 3.2 42.0 - - + +
501A LEU* 3.7 8.0 - - + +
502A PHE* 3.8 21.7 - - + -
534A ASN* 3.3 17.0 + - - -
535A VAL 3.1 3.0 + - - +
537A PHE* 1.3 95.6 - - - +
539A VAL* 1.3 61.1 + - - +
541A LYS* 3.3 21.9 - - - +
542A SER* 2.8 31.2 + - - -
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Residues in contact with VAL 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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501A LEU* 4.0 13.2 - - + -
524A VAL* 3.5 22.0 - - + +
527A MET* 3.8 35.7 - - + +
528A ALA* 4.0 18.2 - - + +
535A VAL* 3.1 20.0 + - + +
536A ARG* 3.3 11.7 - - - +
537A PHE 3.2 0.2 - - - -
538A ASN* 1.3 78.4 - - - +
540A ALA* 1.3 56.6 + - - +
542A SER* 3.3 4.8 + - - -
543A LEU* 2.9 49.0 + - + +
562A ILE* 5.2 0.2 - - + -
566A LEU* 4.4 4.7 - - + -
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Residues in contact with ALA 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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536A ARG 3.4 5.2 + - - +
537A PHE* 3.3 12.3 + - - +
538A ASN 3.2 0.2 - - - -
539A VAL* 1.3 81.2 - - - +
541A LYS* 1.3 62.8 + - - +
543A LEU* 3.2 4.3 + - - +
544A GLN* 3.0 21.8 + - - +
563A LEU* 4.2 15.5 - - + -
566A LEU* 4.6 5.8 - - + +
574A VAL* 4.9 1.8 - - + +
577A PHE* 3.8 29.8 - - + +
578A ALA* 3.9 12.6 - - + +
581A ALA* 3.8 6.2 - - - +
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Residues in contact with LYS 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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505A ASN* 5.4 0.9 - - - -
537A PHE* 3.1 26.8 + - + +
538A ASN* 3.3 28.9 - - - +
539A VAL 3.3 0.2 - - - -
540A ALA* 1.3 75.4 - - - +
542A SER* 1.3 57.8 + - - +
544A GLN* 3.2 11.8 + - - +
545A LYS* 3.0 27.2 + - - +
577A PHE* 3.7 47.1 - - + -
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Residues in contact with SER 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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501A LEU* 4.2 13.4 + - - +
504A ILE* 4.5 3.5 - - - +
505A ASN* 2.7 35.2 + - - +
524A VAL* 4.0 20.2 - - - +
538A ASN 2.8 19.0 + - - -
539A VAL* 3.6 7.4 - - - -
540A ALA 3.2 0.2 - - - -
541A LYS* 1.3 78.3 - - - +
543A LEU* 1.3 57.1 + - - +
545A LYS* 3.1 2.8 + - - +
546A ILE* 2.9 32.7 + - - +
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Residues in contact with LEU 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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521A LEU* 4.0 24.0 - - + -
524A VAL* 3.7 20.9 - - + -
525A LEU* 4.0 10.5 - - + -
539A VAL* 2.9 30.7 + - + +
540A ALA 3.7 4.3 - - - +
542A SER* 1.3 75.5 - - - +
544A GLN* 1.3 58.2 + - - +
546A ILE* 4.3 7.0 - - + -
547A GLY* 3.0 27.5 + - - -
550A LEU* 5.9 0.2 - - + -
559A VAL* 4.3 17.8 - - + +
562A ILE* 4.1 22.7 - - + -
563A LEU* 3.7 31.4 - - + -
566A LEU* 5.0 0.2 - - + -
585A LEU* 3.8 7.2 - - - +
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Residues in contact with GLN 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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540A ALA 3.0 12.6 + - - +
541A LYS* 3.4 12.9 - - - +
542A SER 3.1 0.2 - - - -
543A LEU* 1.3 78.2 - - - +
545A LYS* 1.3 60.4 + - - +
548A PRO* 3.5 17.8 - - - +
577A PHE* 4.7 1.7 - - - +
580A GLU* 3.7 19.2 + - - +
581A ALA* 3.2 30.9 + - + +
584A VAL* 3.9 38.7 - - + +
585A LEU* 3.8 14.7 - - + +
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Residues in contact with LYS 545 (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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505A ASN* 3.4 34.2 + - + +
508A SER* 4.2 3.2 + - - -
509A GLU* 3.0 42.4 + - - +
541A LYS 3.0 13.1 + - - +
542A SER* 3.1 11.0 + - - +
544A GLN* 1.3 81.0 - - - +
546A ILE* 1.3 61.4 + - + +
548A PRO* 3.7 8.5 - - - +
549A ILE* 5.0 4.5 - - - +
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Residues in contact with ILE 546 (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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504A ILE* 4.2 24.5 - - + +
505A ASN* 4.2 13.9 - - - +
508A SER* 3.4 33.7 - - - +
516A THR* 4.4 16.2 - - + -
521A LEU* 4.5 24.5 - - + +
524A VAL* 4.6 10.1 - - + -
542A SER* 2.9 20.0 + - - +
543A LEU* 4.3 9.2 - - + +
545A LYS* 1.3 75.0 - - + +
547A GLY* 1.3 70.1 + - - +
548A PRO* 3.3 3.8 - - - -
549A ILE* 3.0 22.7 + - - +
550A LEU* 3.6 12.4 - - + +
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Residues in contact with GLY 547 (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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543A LEU 3.0 19.9 + - - -
546A ILE* 1.3 77.3 - - - +
548A PRO* 1.3 61.9 - - - +
550A LEU* 2.9 34.6 + - - +
555A LEU* 3.7 27.9 - - - +
559A VAL* 5.8 0.7 - - - -
585A LEU* 4.2 6.3 - - - -
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Residues in contact with PRO 548 (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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544A GLN 3.5 17.0 - - - +
545A LYS 3.7 8.1 - - - +
546A ILE 3.4 4.3 - - - -
547A GLY* 1.3 89.4 - - - +
549A ILE* 1.3 61.2 + - + +
550A LEU 3.3 4.6 + - - +
555A LEU* 5.6 1.8 - - + -
584A VAL* 6.5 0.7 - - + -
585A LEU* 4.1 11.6 - - + -
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Residues in contact with ILE 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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508A SER* 2.9 59.0 - - - +
509A GLU* 3.9 8.3 - - + +
512A GLY* 4.4 0.9 - - - -
513A GLN* 3.0 49.4 + - + +
516A THR* 4.4 13.5 - - + +
545A LYS* 5.0 4.0 - - - +
546A ILE* 3.0 15.3 + - - +
548A PRO* 1.3 81.4 - - + +
550A LEU* 1.3 59.3 + - - +
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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