Contacts of the helix formed by residues 549 - 564 (chain B) in PDB entry 2BBT
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547B THR 4.4 0.2 + - - -
548B LEU* 1.3 76.4 - - - +
550B GLY* 1.3 64.1 + - - +
551B GLY* 3.7 3.9 + - - -
552B GLN* 3.2 34.8 + - - +
553B ARG* 3.0 23.4 + - - +
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Residues in contact with GLY 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B SER* 4.8 1.0 + - - -
549B SER* 1.3 74.0 - - - +
551B GLY* 1.3 57.3 + - - +
553B ARG* 3.4 14.4 + - - +
554B ALA* 2.9 28.4 + - - +
577B TYR* 3.5 37.6 - - - +
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Residues in contact with GLY 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B SER* 3.2 5.6 + - - -
550B GLY* 1.3 75.6 - - - +
552B GLN* 1.3 57.9 + - - +
554B ALA* 3.4 1.6 + - - +
555B ARG* 3.0 44.0 + - - +
577B TYR* 3.5 14.4 + - - +
578B LEU* 3.8 19.5 - - - -
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Residues in contact with GLN 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B LEU* 4.5 2.3 - - + +
529B ASP* 2.7 37.8 + - + +
532B LYS* 4.2 14.3 - - - +
533B PHE* 5.1 7.9 - - - -
547B THR 4.6 1.0 - - - +
548B LEU* 3.4 31.8 - - + +
549B SER* 3.2 38.0 + - - +
551B GLY* 1.3 72.2 - - - +
553B ARG* 1.3 59.9 + - - +
555B ARG* 3.5 14.6 + - - +
556B ILE* 3.1 39.5 + - + +
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Residues in contact with ARG 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B SER* 2.8 39.2 + - - -
496B TRP* 4.2 2.2 - - - +
497B ILE* 3.7 42.3 - - + +
548B LEU* 4.2 18.4 - - + -
549B SER 3.0 21.9 + - - +
550B GLY* 3.5 12.5 - - - +
551B GLY 3.3 0.2 - - - -
552B GLN* 1.3 74.7 - - - +
554B ALA* 1.3 57.4 + - - +
556B ILE* 3.4 2.6 + - - +
557B SER* 2.9 33.4 + - - -
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Residues in contact with ALA 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B CYS* 5.3 0.5 - - - -
495B SER* 3.2 20.1 + - - +
550B GLY 2.9 18.3 + - - +
551B GLY* 3.6 5.8 - - - +
553B ARG* 1.3 75.5 - - - +
555B ARG* 1.3 56.7 + - - +
557B SER* 3.4 3.1 + - - -
558B LEU* 3.0 28.5 + - - +
574B PRO 3.9 18.2 - - - +
576B GLY* 5.1 0.9 - - - +
577B TYR* 4.9 9.0 - - + +
578B LEU* 3.8 18.2 - - + -
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Residues in contact with ARG 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B CYS* 3.4 30.4 + - + +
525B GLN* 2.7 34.6 + - - +
526B LEU* 3.4 22.0 - - + +
529B ASP* 3.2 26.8 + - - -
549B SER* 5.4 0.2 + - - -
551B GLY* 3.0 20.3 + - - +
552B GLN* 3.5 21.1 - - - +
554B ALA* 1.3 73.5 - - - +
556B ILE* 1.3 59.6 + - - +
558B LEU* 3.9 8.3 - - + -
559B ALA* 3.2 26.0 + - - +
578B LEU* 4.0 20.5 - - + +
582B THR* 4.6 4.6 + - - +
586B ILE* 3.5 23.3 - - + -
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Residues in contact with ILE 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B ILE* 3.8 19.1 - - + -
502B ILE* 3.7 35.0 - - + -
505B ASN* 4.1 10.1 - - + -
506B ILE* 4.1 14.8 - - + +
526B LEU* 4.0 17.3 - - + -
541B LEU* 4.7 0.7 - - + -
548B LEU* 3.7 29.2 - - + -
552B GLN* 3.1 25.7 + - + +
553B ARG 3.8 3.6 - - - +
555B ARG* 1.3 75.2 - - - +
557B SER* 1.3 59.3 + - - +
559B ALA* 3.3 3.1 + - - +
560B ARG* 2.9 39.6 + - - +
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Residues in contact with SER 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B CYS* 3.6 19.2 - - - +
492B SER 5.6 1.1 - - - -
495B SER* 3.4 13.0 - - - -
496B TRP* 3.2 35.4 + - - -
553B ARG 2.9 20.2 + - - -
554B ALA 3.6 5.4 - - - -
556B ILE* 1.3 73.5 - - - +
558B LEU* 1.3 62.9 + - - +
560B ARG* 3.7 18.8 + - - +
561B ALA* 3.3 15.9 + - - +
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Residues in contact with LEU 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B CYS* 3.9 9.8 - - - -
524B CYS* 3.9 15.5 - - + -
554B ALA 3.0 17.9 + - - +
555B ARG* 4.0 7.4 - - + +
557B SER* 1.3 73.2 - - - +
559B ALA* 1.3 61.3 + - - +
561B ALA* 3.1 2.9 + - - +
562B VAL* 2.9 50.3 + - + +
571B LEU* 4.3 16.8 - - + -
574B PRO* 3.7 30.1 - - + +
575B PHE* 4.1 12.3 - - + -
578B LEU* 6.3 0.4 - - + -
586B ILE* 3.6 32.1 - - + -
590B CYS* 4.1 6.7 - - - -
591B VAL* 5.5 0.7 - - + -
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Residues in contact with ALA 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ILE* 4.0 14.8 - - + -
520B VAL* 3.5 22.6 - - + +
521B ILE* 5.3 0.2 - - + -
524B CYS* 3.9 8.7 - - + -
526B LEU* 3.8 17.7 - - + -
555B ARG 3.2 18.7 + - - +
556B ILE 3.3 5.1 + - - +
558B LEU* 1.3 79.3 - - - +
560B ARG* 1.3 52.7 + - - +
562B VAL 4.6 0.2 - - - +
563B TYR* 2.8 37.6 + - - +
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Residues in contact with ARG 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B TRP* 3.0 74.6 + - - +
497B ILE* 4.1 1.4 - - - +
498B MET* 5.4 1.8 - - - +
505B ASN* 2.6 53.1 + - - +
506B ILE* 3.7 20.1 - - - +
556B ILE* 2.9 23.7 + - - +
557B SER* 3.7 26.6 + - - +
559B ALA* 1.3 76.9 - - - +
561B ALA* 1.3 59.7 + - - +
564B LYS* 3.3 22.7 + - - +
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Residues in contact with ALA 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B SER* 2.6 29.5 + - - +
490B PHE 4.0 5.4 - - - +
491B CYS* 3.6 39.0 - - + +
557B SER 3.3 5.4 + - - +
558B LEU* 3.1 7.0 + - - +
560B ARG* 1.3 80.5 - - - +
562B VAL* 1.3 61.3 + - + +
564B LYS 3.6 2.3 + - - -
569B TYR* 3.2 17.1 - - + -
571B LEU* 4.9 5.2 - - + -
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Residues in contact with VAL 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B ARG* 3.3 15.1 + - - -
520B VAL* 4.3 6.6 - - + +
524B CYS* 5.2 0.2 - - - -
558B LEU* 2.9 32.2 + - + +
559B ALA* 4.2 4.3 - - - +
561B ALA* 1.3 76.7 - - + +
563B TYR* 1.3 65.3 + - - +
564B LYS 3.7 1.9 - - - +
569B TYR* 3.8 9.6 - - - -
571B LEU* 5.0 2.7 - - + -
590B CYS* 3.7 27.1 - - - -
594B LEU* 3.8 28.7 - - + -
595B MET* 3.7 29.2 - - + -
598B LYS* 5.0 1.4 + - - +
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Residues in contact with TYR 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ILE* 3.8 13.9 - - + -
507B ILE* 3.5 34.4 - - + +
511B SER* 2.8 30.9 + - - -
512B TYR* 3.4 1.9 - - - -
513B ASP* 2.8 26.7 + - + +
516B ARG* 2.6 48.4 + - + +
517B TYR* 3.5 40.6 - + + -
520B VAL* 3.9 12.5 - - + +
559B ALA 2.8 20.4 + - - +
560B ARG 4.1 1.6 - - - +
562B VAL* 1.3 76.4 - - - +
564B LYS* 1.3 64.1 + - - +
565B ASP* 3.2 1.4 + - - +
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Residues in contact with LYS 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B ARG* 3.8 39.6 - - - +
488B ILE 5.5 0.7 - - - +
489B SER* 3.4 31.4 - - - +
511B SER* 6.0 3.6 - - - -
516B ARG* 3.1 2.1 + - - -
560B ARG 3.3 12.4 + - - +
561B ALA 3.7 1.1 - - - +
562B VAL 3.3 0.6 - - - -
563B TYR* 1.3 79.5 - - - +
565B ASP* 1.3 59.1 + - - +
566B ALA* 3.0 3.8 + - + -
569B TYR* 2.6 33.4 + - - -
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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