Contacts of the helix formed by residues 569 - 586 (chain O) in PDB entry 5MQF
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 LYS 569 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567O HIS* 3.5 7.0 - - + +
568O LYS* 1.3 73.7 - - - +
570O PHE* 1.3 56.7 + - - +
571O THR 3.3 0.2 - - - -
572O PHE* 3.9 8.3 - - + +
573O ALA* 2.9 31.9 + - - +
602O LYS* 6.3 0.7 - - + -
603O CYS* 3.6 30.7 - - + +
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Residues in contact with PHE 570 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568O LYS* 3.0 3.2 + - + -
569O LYS* 1.3 78.4 - - - +
571O THR* 1.3 57.2 + - - +
573O ALA* 3.8 5.4 - - - +
574O LYS* 2.9 29.8 + - - +
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Residues in contact with THR 571 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530O TRP* 6.5 1.6 - - - -
561O SER 5.1 0.9 - - - -
563O GLU* 5.7 5.2 - - - -
567O HIS 5.4 0.2 - - - -
568O LYS* 2.9 19.1 + - - +
570O PHE* 1.3 77.0 - - - +
572O PHE* 1.3 60.2 + - - +
574O LYS* 3.8 4.8 - - - +
575O MET* 2.9 30.3 + - - +
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Residues in contact with PHE 572 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561O SER* 3.6 24.9 + - - +
562O LEU* 4.9 9.4 - - - +
563O GLU* 5.1 4.4 - - + +
567O HIS 5.4 0.7 - - - +
568O LYS 3.7 3.3 + - - +
569O LYS* 3.5 12.9 + - - +
571O THR* 1.3 78.9 - - - +
573O ALA* 1.3 58.8 + - - +
575O MET* 3.9 2.4 - - - +
576O TRP* 2.9 31.0 + - - +
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Residues in contact with ALA 573 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569O LYS 2.9 19.2 + - - +
570O PHE* 4.0 6.3 - - - +
572O PHE* 1.3 77.0 - - - +
574O LYS* 1.3 57.1 + - - +
576O TRP* 3.6 6.0 + - - +
577O ILE* 2.9 28.2 + - - +
599O SER* 4.9 17.5 - - - +
603O CYS* 5.6 3.4 - - + +
608O LEU* 4.5 22.7 - - + -
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Residues in contact with LYS 574 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570O PHE 2.9 20.1 + - - +
571O THR* 3.8 5.8 - - - +
572O PHE 3.3 0.2 - - - -
573O ALA* 1.3 75.4 - - - +
575O MET* 1.3 58.7 + - - +
577O ILE* 3.1 7.5 + - - +
578O LEU* 2.9 28.6 + - - +
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Residues in contact with MET 575 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537O TRP* 5.8 7.6 - - + -
558O TYR* 6.4 0.7 - - - -
561O SER* 3.7 30.1 - - - -
571O THR 2.9 18.3 + - - +
572O PHE 4.0 2.0 - - - +
574O LYS* 1.3 76.7 - - - +
576O TRP* 1.3 58.2 + - - +
578O LEU* 3.4 5.8 + - - +
579O TYR* 2.9 30.4 + - - +
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Residues in contact with TRP 576 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558O TYR* 6.2 3.8 - - + -
561O SER* 5.7 0.2 - - - -
572O PHE 2.9 19.2 + - - +
573O ALA* 3.9 7.0 - - - +
575O MET* 1.3 76.1 - - - +
577O ILE* 1.3 57.8 + - - +
579O TYR* 4.2 5.1 - - - +
580O ALA* 2.9 29.4 + - - +
595O ALA* 4.8 12.4 - - + +
599O SER* 4.4 17.4 - - - -
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Residues in contact with ILE 577 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573O ALA 2.9 19.3 + - - +
574O LYS* 3.1 8.7 + - - +
576O TRP* 1.3 76.4 - - - +
578O LEU* 1.3 59.1 + - - +
580O ALA* 3.3 7.6 + - - +
581O GLN* 2.9 27.2 + - - +
599O SER* 5.5 2.4 - - - -
611O VAL* 5.8 8.7 - - + -
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Residues in contact with LEU 578 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574O LYS 2.9 14.3 + - - +
575O MET* 3.8 6.5 - - - +
577O ILE* 1.3 75.6 - - - +
579O TYR* 1.3 59.5 + - - +
581O GLN* 3.0 7.6 + - - +
582O PHE* 2.9 29.9 + - - +
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Residues in contact with TYR 579 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550O ASP* 5.6 0.2 - - - +
554O THR* 5.1 17.3 - - - +
558O TYR* 5.2 9.4 - - + -
575O MET 2.9 18.7 + - - +
576O TRP* 4.2 6.5 - - - +
578O LEU* 1.3 76.5 - - - +
580O ALA* 1.3 56.6 + - - +
582O PHE* 4.5 5.6 - - - +
583O GLU* 2.9 32.1 + - - +
595O ALA* 5.8 2.2 - - + -
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Residues in contact with ALA 580 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576O TRP 2.9 22.0 + - - +
577O ILE* 3.5 9.4 - - - +
578O LEU 3.1 0.4 - - - -
579O TYR* 1.3 76.3 - - - +
581O GLN* 1.3 58.6 + - - +
583O GLU* 4.4 0.2 - - - -
584O ILE* 2.8 28.6 + - - +
592O ALA* 3.5 28.1 - - - +
595O ALA* 4.4 8.5 - - + -
596O LEU* 4.7 9.0 - - + +
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Residues in contact with GLN 581 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577O ILE 2.9 13.2 + - - +
578O LEU* 3.0 10.5 + - - +
580O ALA* 1.3 76.3 - - - +
582O PHE* 1.3 59.5 + - - +
584O ILE* 3.1 7.4 + - - +
585O ARG* 2.9 27.4 + - - +
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Residues in contact with PHE 582 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549O LYS* 5.7 0.3 - - - +
550O ASP* 4.2 16.1 - - + +
578O LEU 2.9 14.9 + - - +
579O TYR* 4.3 5.6 - - - +
581O GLN* 1.3 75.8 - - - +
583O GLU* 1.3 59.3 + - - +
585O ARG* 3.1 10.4 + - - +
586O GLN* 2.9 26.5 + - - +
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Residues in contact with GLU 583 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550O ASP* 4.2 9.3 - - + +
579O TYR 2.9 22.2 + - - +
582O PHE* 1.3 73.8 - - - +
584O ILE* 1.3 60.6 + - - +
586O GLN* 3.0 4.6 + - - -
587O LYS* 2.4 44.9 + - + +
588O ASN 2.9 5.7 + - - -
591O LEU* 5.3 1.6 - - + -
592O ALA* 3.6 19.7 - - + +
595O ALA* 6.1 1.1 - - + -
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Residues in contact with ILE 584 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580O ALA 2.8 24.5 + - - +
581O GLN* 3.1 10.7 + - - +
583O GLU* 1.3 77.9 - - - +
585O ARG* 1.3 57.4 + - - +
588O ASN* 3.4 29.2 - - - +
592O ALA* 3.4 4.2 - - + +
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Residues in contact with ARG 585 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549O LYS* 6.1 0.6 - - - +
581O GLN 2.9 12.4 + - - +
582O PHE* 3.1 11.0 + - - +
584O ILE* 1.3 75.3 - - - +
586O GLN* 1.3 56.9 + - - +
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Residues in contact with GLN 586 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549O LYS* 3.9 18.6 - - + +
550O ASP* 3.8 23.6 - - + +
582O PHE 2.9 13.8 + - - +
583O GLU* 3.0 1.9 + - - +
585O ARG* 1.3 79.5 - - - +
587O LYS* 1.3 60.6 + - + +
588O ASN* 3.3 6.1 + - - +
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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