Contacts of the helix formed by residues 543 - 565 (chain A) in PDB entry 2P8Q
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 CYS 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A TYR* 3.9 9.4 - - - -
500A SER* 3.9 17.5 - - - -
503A PHE* 3.6 47.1 - - + -
539A SER* 4.2 6.5 - - - -
540A ALA 3.1 15.0 - - - +
541A LYS 2.9 1.0 - - - -
542A ASP* 1.3 93.2 + - - +
544A TYR* 1.3 61.4 + - - +
545A PRO* 3.0 9.0 - - - -
546A ALA* 3.2 7.5 + - - +
547A VAL* 3.0 22.1 + - + +
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Residues in contact with TYR 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ALA 4.3 0.8 + - - -
541A LYS* 3.1 15.3 + - - +
543A CYS* 1.3 75.7 - - - +
545A PRO* 1.3 64.0 - - + +
547A VAL* 2.7 32.8 + - + +
548A GLN* 2.8 56.8 + - + +
594A LYS* 3.8 24.7 - - + -
595A VAL* 3.5 16.5 - - + +
596A GLN* 2.9 53.2 + - + +
599A ASP* 4.9 2.9 - - - +
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Residues in contact with PRO 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A GLU* 5.3 0.7 - - - +
541A LYS 4.6 0.2 - - - +
542A ASP* 3.9 13.0 - - - +
543A CYS* 3.0 6.7 - - - -
544A TYR* 1.3 98.5 - - + +
546A ALA* 1.3 64.5 + - + +
548A GLN* 3.7 11.6 + - + +
549A LYS* 3.4 25.9 + - - +
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PHE* 3.4 32.1 - - + -
504A GLU* 3.9 32.9 + - + +
507A VAL* 4.5 4.1 - - + +
543A CYS* 3.2 4.5 + - - +
544A TYR 3.1 0.4 - - - -
545A PRO* 1.3 81.4 - - + +
547A VAL* 1.3 63.3 + - - +
549A LYS* 3.5 5.1 + - - +
550A THR* 2.8 30.4 + - - -
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PHE* 4.1 14.6 - - + -
536A VAL* 4.4 23.7 - - + +
539A SER* 4.1 20.2 - - - +
540A ALA 5.7 0.2 - - - +
543A CYS 3.0 21.4 + - - +
544A TYR* 2.7 27.3 + - + +
546A ALA* 1.3 70.8 - - - +
548A GLN* 1.3 65.8 + - - +
550A THR* 3.5 7.0 + - - -
551A THR* 3.0 28.3 + - - +
591A VAL* 5.8 1.6 - - + +
594A LYS* 4.4 20.9 - - + +
595A VAL* 4.8 4.5 - - + -
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Residues in contact with GLN 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A TYR* 2.8 65.8 + - + +
545A PRO* 4.0 9.8 - - - +
547A VAL* 1.3 69.2 - - - +
549A LYS* 1.3 68.0 + - - +
551A THR* 3.0 9.0 + - - -
552A LEU* 2.9 31.9 + - + +
595A VAL* 5.2 5.2 - - + -
596A GLN* 5.0 3.6 + - - +
599A ASP* 4.4 13.2 - - - +
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Residues in contact with LYS 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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504A GLU* 4.3 27.4 + - - +
507A VAL* 6.5 0.2 - - + -
511A LEU* 6.2 1.6 - - + -
545A PRO 3.4 15.5 + - - +
546A ALA* 3.7 8.3 - - - +
548A GLN* 1.3 77.4 - - - +
550A THR* 1.3 64.0 + - - +
552A LEU* 3.1 17.4 + - + +
553A VAL* 3.1 32.9 + - + +
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Residues in contact with THR 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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507A VAL* 3.9 21.1 - - - +
511A LEU* 4.3 12.6 - - + +
532A LEU* 3.8 29.8 - - + -
536A VAL* 4.5 9.9 - - + -
546A ALA 2.8 17.5 + - - -
547A VAL* 3.7 7.3 - - - -
549A LYS* 1.3 79.3 - - - +
551A THR* 1.3 58.2 + - - +
553A VAL* 3.2 8.9 + - - +
554A ILE* 2.9 50.0 + - + +
591A VAL* 5.8 0.4 - - + -
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Residues in contact with THR 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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547A VAL* 3.0 20.1 + - - +
548A GLN* 3.0 13.0 + - - -
550A THR* 1.3 73.2 - - - +
552A LEU* 1.3 68.8 + - + +
554A ILE* 3.8 8.0 - - + +
555A MET* 2.9 43.4 + - + +
591A VAL* 3.8 31.6 - - + +
595A VAL* 4.6 14.7 - - + +
603A ILE* 4.9 10.3 - - + -
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Residues in contact with LEU 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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548A GLN* 2.9 23.6 + - + +
549A LYS* 3.4 15.5 - - + +
551A THR* 1.3 77.6 - - + +
553A VAL* 1.3 58.1 + - + +
555A MET* 4.1 19.9 - - + +
556A GLU* 3.1 27.9 + - - +
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Residues in contact with VAL 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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511A LEU* 4.1 29.4 - - + -
549A LYS* 3.1 26.6 + - + +
550A THR 3.4 6.5 - - - +
552A LEU* 1.3 77.4 - - + +
554A ILE* 1.3 60.4 + - - +
556A GLU* 3.3 15.2 - - - +
557A ARG* 3.0 51.3 + - + +
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Residues in contact with ILE 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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511A LEU* 5.0 5.2 - - + -
529A TYR* 5.7 2.0 - - + -
532A LEU* 4.5 12.1 - - + -
536A VAL* 5.7 1.3 - - + -
550A THR* 2.9 39.4 + - + +
551A THR* 3.2 5.4 + - + +
553A VAL* 1.3 74.7 - - - +
555A MET* 1.3 62.0 + - + +
557A ARG* 3.1 9.3 + - - +
558A LEU* 2.8 28.8 + - + +
584A LEU* 3.9 28.6 - - + +
587A THR* 3.4 33.4 - - + -
588A LEU* 4.8 14.4 - - + +
591A VAL* 3.8 18.4 - - + -
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Residues in contact with MET 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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551A THR* 2.9 29.1 + - + +
552A LEU* 4.1 20.0 - - + +
554A ILE* 1.3 75.9 - - - +
556A GLU* 1.3 56.1 + - - +
558A LEU* 2.9 8.3 + - - +
559A GLN* 2.6 46.5 + - + +
588A LEU* 4.8 7.6 - - + -
603A ILE* 3.3 56.8 - - + +
606A VAL* 5.1 12.1 - - + -
607A VAL* 4.5 13.9 - - + -
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Residues in contact with GLU 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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552A LEU 3.1 17.6 + - - +
553A VAL* 3.3 18.2 - - - +
555A MET* 1.3 79.6 - - - +
557A ARG* 1.3 69.2 + - - +
559A GLN* 3.7 6.9 - - - +
560A GLN* 3.1 25.1 + - + +
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Residues in contact with ARG 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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511A LEU* 3.0 38.9 + - - +
514A THR* 2.7 24.4 + - - +
515A ASP* 2.5 30.4 + - - -
529A TYR* 2.8 29.5 + - - -
553A VAL* 3.0 32.7 + - + +
554A ILE* 3.1 7.8 + - - +
556A GLU* 1.3 80.9 + - - +
558A LEU* 1.3 62.1 + - - +
560A GLN* 3.2 13.3 + - - +
561A VAL* 2.9 27.7 + - - +
580A LEU* 5.8 2.9 - - + -
584A LEU* 3.7 18.8 - - + -
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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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554A ILE* 2.8 22.0 + - + +
555A MET* 3.5 6.1 - - - +
557A ARG* 1.3 70.3 - - - +
559A GLN* 1.3 67.0 + - + +
561A VAL* 3.3 4.6 + - + +
562A LEU* 3.0 43.4 + - + +
581A GLN* 4.6 7.9 - - + +
584A LEU* 3.6 29.1 - - + +
585A CYS* 4.2 22.0 - - - -
588A LEU* 3.9 37.5 - - + -
607A VAL* 4.0 19.5 - - + -
611A LEU* 6.2 0.4 - - + -
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Residues in contact with GLN 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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555A MET* 2.6 33.4 + - + +
556A GLU* 3.7 6.7 - - - +
558A LEU* 1.3 74.3 - - - +
560A GLN* 1.3 62.0 + - - +
562A LEU* 3.6 8.4 + - - +
563A GLN* 3.3 23.8 + - - +
606A VAL* 3.6 30.8 + - + +
607A VAL* 4.0 18.0 - - - +
610A SER* 2.6 30.1 + - - -
613A ARG* 4.8 3.1 + - - -
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Residues in contact with GLN 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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556A GLU* 3.1 16.1 + - + +
557A ARG* 3.3 14.9 - - - +
558A LEU 3.1 0.4 - - - -
559A GLN* 1.3 74.9 - - - +
561A VAL* 1.3 65.6 + - - +
563A GLN* 3.4 9.3 + - + +
564A MET* 3.0 53.4 + - + +
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Residues in contact with VAL 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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557A ARG 2.9 18.5 + - - +
558A LEU* 3.7 9.9 - - + +
560A GLN* 1.3 73.8 - - - +
562A LEU* 1.3 62.5 + - - +
564A MET* 3.0 24.8 + - + +
565A GLU* 3.1 22.2 + - - +
577A PHE* 3.2 44.2 - - + +
580A LEU* 4.2 17.5 - - + -
581A GLN* 4.1 10.8 - - + +
584A LEU* 3.5 23.6 - - + -
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Residues in contact with LEU 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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558A LEU* 3.0 39.6 + - + +
559A GLN* 3.7 5.8 - - - +
561A VAL* 1.3 79.6 - - - +
563A GLN* 1.3 59.7 + - - +
565A GLU* 3.3 18.9 + - - +
566A SER* 3.9 3.8 + - - -
581A GLN* 3.8 18.4 - - + +
607A VAL* 4.5 2.5 - - + +
610A SER* 3.5 40.4 - - - +
611A LEU* 3.8 26.5 - - + +
614A MET* 3.7 40.0 + - + +
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Residues in contact with GLN 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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559A GLN 3.3 11.7 + - - +
560A GLN* 3.5 13.6 - - + +
562A LEU* 1.3 74.8 - - - +
564A MET* 1.3 85.5 + - - +
565A GLU 3.0 6.1 - - - -
566A SER* 3.0 25.4 + - - +
567A HIS* 3.3 25.1 + - - -
613A ARG* 6.1 5.4 - - - +
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Residues in contact with MET 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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560A GLN* 3.0 58.8 + - + +
561A VAL* 3.0 23.3 + - + +
563A GLN* 1.3 90.8 + - - +
565A GLU* 1.3 56.0 + - - +
566A SER 3.3 0.2 - - - -
567A HIS* 3.4 21.7 + - - +
577A PHE* 3.4 48.7 - - + -
580A LEU* 5.5 6.5 - - + -
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Residues in contact with GLU 565 (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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561A VAL* 3.2 22.8 - - - +
562A LEU* 3.5 13.6 - - - +
563A GLN 3.0 1.2 - - - -
564A MET* 1.3 75.8 - - - +
566A SER* 1.3 57.4 + - - +
567A HIS 3.2 5.2 - - - -
568A ILE* 3.6 27.5 + - + +
577A PHE* 3.7 25.4 - - + -
578A ASN* 2.7 30.4 + - - -
581A GLN* 2.5 32.3 - - - +
614A MET* 4.0 15.1 - - + +
617A SER* 5.1 0.7 - - - -
618A THR* 4.4 17.6 + - - -
625A GLN* 3.6 5.2 + - - -
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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
------------------------------------------------------------
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