Contacts of the helix formed by residues 549 - 564 (chain A) in PDB entry 2BBO
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 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A THR 4.2 0.2 + - - -
548A LEU* 1.3 75.8 - - - +
550A GLU* 1.3 65.1 + - - +
551A GLY* 3.8 5.0 + - - -
552A GLN* 2.9 43.8 + - - +
553A GLN* 2.9 11.9 + - - +
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Residues in contact with GLU 550 (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 SER* 3.6 19.3 + - - +
548A LEU 3.8 1.2 + - - -
549A SER* 1.3 72.6 - - - +
551A GLY* 1.3 55.5 + - - +
553A GLN* 3.7 12.0 - - + +
554A ALA* 3.0 28.4 + - - +
578A LEU* 3.5 33.6 - - + +
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Residues in contact with GLY 551 (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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549A SER* 3.0 6.9 + - - -
550A GLU* 1.3 75.6 - - - +
552A GLN* 1.3 61.6 + - - +
554A ALA* 3.3 5.8 + - - +
555A LYS* 3.2 28.3 + - - +
575A PHE* 4.3 2.3 - - - -
578A LEU* 4.7 2.5 - - - +
580A VAL* 3.9 28.9 - - - -
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Residues in contact with GLN 552 (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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526A LEU* 4.4 2.5 - - + +
529A ASP* 2.7 49.3 + - + +
532A LYS* 5.1 4.4 - - - +
533A PHE* 5.0 7.1 - - - -
548A LEU* 3.2 27.1 - - + +
549A SER* 2.9 36.5 + - - +
551A GLY* 1.3 74.7 - - - +
553A GLN* 1.3 58.4 + - - +
555A LYS* 3.3 13.4 + - + +
556A ILE* 3.1 33.5 + - + +
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Residues in contact with GLN 553 (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 SER* 3.8 21.9 - - - +
496A TRP* 4.7 0.2 - - - -
497A ILE* 3.5 39.8 + - + +
547A THR* 4.3 10.9 - - - +
548A LEU* 3.2 34.0 + - + +
549A SER 2.9 12.9 + - - +
550A GLU* 3.7 14.9 - - - +
552A GLN* 1.3 73.6 - - - +
554A ALA* 1.3 60.9 + - - +
556A ILE* 3.8 3.0 - - - +
557A SER* 3.1 31.7 + - - -
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Residues in contact with ALA 554 (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 SER* 3.4 15.0 + - - +
550A GLU 3.0 18.3 + - - +
551A GLY 3.5 6.7 - - - +
552A GLN 3.2 0.4 - - - -
553A GLN* 1.3 74.7 - - - +
555A LYS* 1.3 58.9 + - - +
557A SER* 3.3 4.1 + - - -
558A LEU* 3.0 30.0 + - - +
574A PRO* 3.7 19.1 - - + +
575A PHE* 3.7 23.2 - - + -
578A LEU* 3.8 8.5 - - + -
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Residues in contact with LYS 555 (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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524A CYS* 3.5 26.8 - - - +
525A GLN 3.0 18.4 + - - +
526A LEU* 3.8 14.6 - - + +
528A GLU* 6.2 0.4 - - - +
529A ASP* 2.6 31.5 + - - +
551A GLY 3.2 14.8 + - - +
552A GLN* 3.3 11.7 + - - +
554A ALA* 1.3 77.3 - - - +
556A ILE* 1.3 57.3 + - - +
558A LEU* 3.5 3.6 + - - +
559A ALA* 2.9 30.0 + - - +
575A PHE* 4.0 17.3 - - + -
580A VAL* 4.5 8.0 - - - +
582A THR* 3.4 33.2 - - - +
586A ILE* 4.2 2.7 - - + -
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Residues in contact with ILE 556 (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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497A ILE* 3.7 30.1 - - + -
502A ILE* 4.2 30.7 - - + +
505A ASN* 3.9 21.8 - - + -
506A ILE* 4.1 9.4 - - + +
526A LEU* 4.0 24.9 - - + -
541A LEU* 4.3 1.3 - - + -
548A LEU* 4.3 17.5 - - + -
552A GLN* 3.1 18.2 + - + +
553A GLN 3.8 4.5 - - - +
554A ALA 3.3 0.2 - - - -
555A LYS* 1.3 75.1 - - - +
557A SER* 1.3 55.8 + - - +
559A ALA* 3.3 2.7 + - - +
560A ARG* 2.8 38.0 + - - +
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Residues in contact with SER 557 (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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491A CYS* 3.9 13.2 - - - -
492A SER 5.6 0.7 - - - -
494A PHE 5.2 1.1 - - - -
495A SER* 3.6 6.2 - - - -
496A TRP* 3.1 34.3 + - - -
553A GLN 3.1 19.4 + - - -
554A ALA* 3.3 8.0 + - - -
556A ILE* 1.3 74.1 - - - +
558A LEU* 1.3 63.9 + - - +
560A ARG* 3.3 18.2 + - - +
561A ALA* 3.2 22.2 + - - +
574A PRO* 4.7 3.6 - - - -
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Residues in contact with LEU 558 (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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491A CYS* 3.9 16.5 - - - -
524A CYS* 3.9 12.8 - - + -
554A ALA 3.0 16.2 + - - +
555A LYS* 3.9 3.1 - - - +
557A SER* 1.3 72.3 - - - +
559A ALA* 1.3 60.3 + - - +
561A ALA* 3.1 3.5 + - - +
562A VAL* 2.8 46.8 + - + +
571A LEU* 3.8 34.8 - - + -
573A SER* 5.4 6.5 - - - +
574A PRO* 5.2 0.9 - - + -
575A PHE* 4.1 15.9 - - + -
586A ILE* 3.5 32.3 - - + -
590A CYS* 4.4 7.0 - - - -
591A VAL* 5.2 6.1 - - + -
602A LEU* 6.2 0.7 - - + -
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Residues in contact with ALA 559 (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 ILE* 3.9 24.9 - - + -
520A VAL* 3.8 20.0 - - + +
521A ILE* 5.3 0.4 - - + -
524A CYS* 3.8 15.4 - - + -
526A LEU* 4.2 5.4 - - + -
555A LYS 2.9 18.1 + - - +
556A ILE* 3.3 6.0 + - - +
558A LEU* 1.3 76.0 - - - +
560A ARG* 1.3 52.8 + - - +
562A VAL* 3.1 1.4 + - - +
563A TYR* 2.7 37.9 + - - +
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Residues in contact with ARG 560 (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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496A TRP* 2.9 75.3 + - - +
505A ASN* 2.7 49.4 + - - +
506A ILE* 3.6 20.1 - - - +
508A PHE* 3.9 18.2 - - + -
556A ILE* 2.8 29.7 + - - +
557A SER* 3.3 30.4 + - - +
559A ALA* 1.3 74.9 - - - +
561A ALA* 1.3 62.1 + - - +
563A TYR 3.6 0.2 + - - -
564A LYS* 3.3 26.2 + - - +
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Residues in contact with ALA 561 (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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489A SER* 2.6 28.4 + - - +
490A PHE 3.9 13.9 - - - +
491A CYS* 3.6 33.4 - - + +
557A SER 3.2 5.2 + - - +
558A LEU 3.1 7.2 + - - +
560A ARG* 1.3 80.5 - - - +
562A VAL* 1.3 61.6 + - - +
564A LYS* 3.5 7.6 - - - +
569A TYR* 3.4 10.5 - - - -
571A LEU* 4.9 5.8 - - + -
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Residues in contact with VAL 562 (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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516A ARG* 3.9 6.2 + - - -
520A VAL* 4.1 18.4 - - + +
558A LEU* 2.8 42.7 + - + +
559A ALA* 3.9 5.2 - - - +
561A ALA* 1.3 77.0 - - - +
563A TYR* 1.3 63.8 + - - +
564A LYS 3.2 7.7 - - - +
569A TYR* 3.7 13.5 + - + -
571A LEU* 4.8 3.6 - - + -
590A CYS* 4.1 14.1 - - - -
594A LEU* 4.5 4.9 - - + -
595A MET* 3.9 42.6 - - + -
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Residues in contact with TYR 563 (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 ILE* 3.9 28.9 - - + +
507A ILE* 3.6 30.0 - - + +
510A VAL* 3.9 19.0 - - + +
511A SER 2.7 29.5 + - - -
512A TYR* 3.3 3.3 - - - -
513A ASP* 2.8 22.7 + - - +
516A ARG* 2.7 50.2 + - + +
517A TYR* 3.5 40.8 - - + -
520A VAL* 4.2 9.1 - - + +
559A ALA 2.7 21.6 + - - +
560A ARG 4.0 0.2 - - - +
562A VAL* 1.3 73.5 - - - +
564A LYS* 1.3 61.0 + - - +
565A ASP 3.4 1.0 + - - -
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Residues in contact with LYS 564 (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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488A ILE 4.8 5.9 + - - +
489A SER* 3.5 27.8 + - - +
490A PHE 4.8 9.5 + - - +
508A PHE* 6.2 1.6 - - - -
510A VAL* 4.3 25.4 - - + -
560A ARG* 3.3 20.1 + - - +
561A ALA* 3.7 7.7 - - - +
562A VAL 3.2 1.2 - - - +
563A TYR* 1.3 80.6 - - - +
565A ASP* 1.3 70.4 + - - +
569A TYR* 2.9 27.8 + - - -
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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