Contacts of the helix formed by residues 564 - 582 (chain F) in PDB entry 6NYY
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 GLN 564 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A GLU* 4.1 30.8 + - - +
613A GLN* 5.6 3.4 - - + -
563F LEU* 1.3 94.2 - - + +
565F PRO* 1.3 74.3 - - + +
566F GLU* 4.2 8.1 - - + +
567F GLU* 3.2 12.6 + - + +
568F LYS* 3.0 25.8 + - - +
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Residues in contact with PRO 565 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563F LEU 4.2 4.0 - - - +
564F GLN* 1.3 95.3 - - + +
566F GLU* 1.3 61.5 + - - +
568F LYS* 3.9 12.0 - - + +
569F LYS* 3.5 18.7 + - - +
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Residues in contact with GLU 566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564F GLN* 3.2 5.5 - - + +
565F PRO* 1.3 79.4 - - - +
567F GLU* 1.3 64.0 + - + +
569F LYS* 3.7 12.6 + - - +
570F THR* 3.1 25.1 + - - +
639F PHE* 5.2 9.0 - - - -
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Residues in contact with GLU 567 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A GLN* 3.3 37.6 - - + +
614A TYR* 3.4 17.5 + - - +
615A LEU* 3.5 26.6 + - + +
563F LEU* 2.4 48.0 - - + +
564F GLN* 3.2 9.4 + - + -
566F GLU* 1.3 81.8 - - + +
568F LYS* 1.3 52.5 + - - +
569F LYS 3.2 2.0 - - - -
570F THR* 2.9 8.3 + - - +
571F VAL* 2.6 41.1 + - + +
603F LEU* 5.6 0.7 - - - +
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Residues in contact with LYS 568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562F VAL* 4.9 8.2 - - - +
563F LEU* 3.5 45.1 + - + +
564F GLN 3.0 19.7 + - - +
565F PRO* 4.2 9.9 - - + +
566F GLU 3.4 0.4 - - - -
567F GLU* 1.3 77.1 - - - +
569F LYS* 1.3 58.0 + - - +
571F VAL* 4.4 4.0 - - - +
572F ALA* 3.1 30.5 + - - +
596F ILE* 4.7 17.0 - - + +
731F LEU* 3.6 17.6 - - + +
734F GLU* 4.2 17.4 + - - +
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Residues in contact with LYS 569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565F PRO 3.5 10.9 + - - +
566F GLU* 3.9 17.5 - - - +
567F GLU 3.2 0.6 - - - -
568F LYS* 1.3 78.0 - - - +
570F THR* 1.3 60.6 + - - +
572F ALA* 4.2 1.1 - - - -
573F TYR* 3.3 58.2 + - + -
639F PHE* 4.0 17.7 - - + -
731F LEU* 4.4 15.4 - - + +
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Residues in contact with THR 570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A LEU* 4.9 9.9 - - + -
566F GLU* 3.1 17.8 + - - +
567F GLU* 2.9 14.1 + - - +
569F LYS* 1.3 77.2 - - - +
571F VAL* 1.3 59.8 + - - +
573F TYR* 3.5 2.3 + - - +
574F HIS* 3.0 26.5 + - - +
635F GLU* 3.7 20.2 - - - +
639F PHE* 3.9 26.6 - - + -
641F ARG* 6.5 0.2 - - + -
643F THR* 4.1 19.3 - - + -
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Residues in contact with VAL 571 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LEU* 4.1 25.1 - - + -
563F LEU* 4.1 14.8 - - + -
567F GLU 2.6 23.0 + - - +
568F LYS* 4.4 4.5 - - - +
570F THR* 1.3 72.9 - - - +
572F ALA* 1.3 53.7 + - - +
574F HIS* 3.0 9.0 + - + +
575F GLN* 2.7 40.4 + - + +
596F ILE* 3.8 33.9 - - + +
603F LEU* 4.4 25.4 - - + +
604F GLY* 5.2 1.1 - - - +
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Residues in contact with ALA 572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568F LYS 3.1 20.2 + - - +
569F LYS* 4.6 1.8 - - - +
571F VAL* 1.3 77.5 - - - +
573F TYR* 1.3 59.9 + - + +
575F GLN 4.1 0.7 - - - -
576F ALA* 3.3 26.9 - - - +
596F ILE* 3.9 17.0 - - + -
727F ALA* 3.3 18.1 - - + +
730F LEU* 3.6 18.3 - - + +
731F LEU* 4.2 13.2 - - + +
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Residues in contact with TYR 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569F LYS* 3.3 51.5 + - + +
570F THR 4.0 3.1 - - - +
571F VAL 3.2 0.6 - - - -
572F ALA* 1.3 77.9 - - + +
574F HIS* 1.3 63.8 + - - +
576F ALA* 4.1 0.8 - - - -
577F GLY 3.5 5.5 + - - -
634F SER* 2.6 30.7 + - - +
635F GLU* 4.9 1.6 - - + -
638F PHE* 3.4 44.2 - + + -
639F PHE* 3.4 24.9 - + + -
723F VAL* 4.8 0.6 - - - +
724F GLU* 4.2 22.6 + - + +
727F ALA* 3.5 27.8 - - + -
728F LEU* 4.8 11.6 - - + +
731F LEU* 6.6 0.2 - - + -
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Residues in contact with HIS 574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570F THR 3.0 10.0 + - - +
571F VAL* 3.0 12.8 + - + +
573F TYR* 1.3 77.1 - - - +
575F GLN* 1.3 70.9 + - - +
577F GLY 3.1 10.6 + - - -
578F HIS* 3.4 4.8 - + - -
631F GLY* 3.2 55.7 + - - -
632F ARG 3.8 3.3 + - - -
635F GLU* 3.3 26.8 + - - +
645F GLY* 4.8 7.3 + - - -
646F ALA* 4.2 19.1 - - + -
649F ASP* 2.8 14.5 + - - -
801F ZN 2.2 33.3 - - - -
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Residues in contact with GLN 575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571F VAL* 2.7 24.4 + - + +
574F HIS* 1.3 82.7 - - + +
576F ALA* 1.3 56.8 + - - +
577F GLY 3.2 2.5 + - - -
578F HIS* 3.5 26.5 + - - +
579F ALA* 3.5 9.9 + - - +
594F VAL* 3.7 19.0 - - + +
595F SER 3.4 19.2 + - - +
596F ILE* 4.2 4.9 - - + -
604F GLY* 2.9 35.8 + - - +
605F TYR 4.2 4.0 - - - -
606F ALA* 3.4 19.6 - - - +
730F LEU* 4.1 9.0 - - + -
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Residues in contact with ALA 576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572F ALA 3.3 20.6 + - - +
573F TYR 4.1 2.9 - - - +
574F HIS 3.3 0.4 - - - -
575F GLN* 1.3 74.8 - - - +
577F GLY* 1.3 58.7 + - - +
578F HIS 3.5 0.2 - - - -
579F ALA* 3.8 11.0 - - + -
580F VAL* 3.4 23.0 - - - +
594F VAL* 5.0 0.2 - - - -
723F VAL* 3.5 9.1 - - + +
726F VAL* 3.8 15.3 - - + -
727F ALA* 3.8 20.9 - - + +
730F LEU* 3.8 14.1 - - + +
736F LEU* 5.3 0.2 - - + -
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Residues in contact with GLY 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573F TYR 3.5 2.8 + - - -
574F HIS 3.1 10.3 + - - -
576F ALA* 1.3 77.3 - - - +
578F HIS* 1.3 61.3 + - - +
579F ALA 3.3 0.4 - - - -
580F VAL* 4.0 1.9 - - - +
581F ALA* 3.1 31.5 + - - +
630F GLY 3.7 20.3 - - - +
634F SER* 3.8 14.6 - - - -
716F LEU* 4.4 4.4 - - - +
723F VAL* 4.4 3.8 - - - -
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Residues in contact with HIS 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574F HIS* 3.2 26.9 + + - -
575F GLN* 3.5 22.1 + - - +
577F GLY* 1.3 79.2 - - - +
579F ALA* 1.3 56.4 + - - +
581F ALA* 4.9 0.2 - - - -
582F GLY* 2.9 29.0 + - - +
591F LEU* 5.2 1.9 - - - +
606F ALA* 5.8 0.7 - - + -
608F TYR* 4.1 19.8 + - + +
627F MET* 2.9 29.7 + - - +
628F THR* 3.1 28.6 - - - -
631F GLY* 3.3 11.9 + - - -
649F ASP* 3.1 12.4 + - - -
801F ZN 2.5 31.8 - - - -
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Residues in contact with ALA 579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575F GLN 3.5 1.8 + - - +
576F ALA* 4.0 16.8 - - - -
577F GLY 3.3 1.2 - - - -
578F HIS* 1.3 78.6 - - - +
580F VAL* 1.3 59.1 + - - +
582F GLY 4.3 0.7 - - - -
583F TRP* 3.3 18.6 + - - +
591F LEU* 3.7 29.2 - - + +
594F VAL* 3.8 17.9 - - + -
726F VAL* 4.3 7.4 - - + -
741F MET* 3.5 22.4 - - + +
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Residues in contact with VAL 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576F ALA 3.4 20.4 + - - +
577F GLY 3.6 3.0 + - - +
578F HIS 3.2 0.2 - - - -
579F ALA* 1.3 80.2 - - - +
581F ALA* 1.3 60.7 + - - +
582F GLY 3.2 1.1 - - - -
583F TRP* 3.0 4.3 + - - +
584F TYR* 3.0 55.3 + - + +
715F LEU* 5.1 0.4 - - - +
716F LEU* 4.2 7.0 - - + -
719F LYS* 4.7 2.2 - - + -
722F ASP* 4.1 7.2 - - + +
723F VAL* 3.9 29.8 - - + -
726F VAL* 3.8 27.8 - - + -
745F LEU* 4.5 5.4 - - + -
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Residues in contact with ALA 581 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577F GLY 3.1 19.1 + - - +
578F HIS* 4.5 0.7 - - - +
580F VAL* 1.3 78.0 - - - +
582F GLY* 1.3 57.4 + - - +
583F TRP 3.1 3.0 + - - -
585F LEU* 3.3 32.8 + - + +
626F CYS 4.0 20.6 - - - +
627F MET* 4.6 3.8 - - - -
630F GLY* 4.2 9.0 - - - -
712F THR* 4.6 3.4 - - + -
715F LEU* 4.1 20.0 - - + -
716F LEU* 4.3 10.2 - - + +
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Residues in contact with GLY 582 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578F HIS 2.9 21.0 + - - -
579F ALA* 4.5 2.0 - - - -
581F ALA* 1.3 75.1 - - - +
583F TRP* 1.3 59.0 + - - +
585F LEU 4.7 0.2 - - - -
588F ALA* 3.6 21.9 - - - +
589F ASP 3.7 13.0 - - - +
591F LEU* 5.2 6.3 - - - +
627F MET* 3.8 20.0 - - - +
748F ARG* 4.1 5.5 + - - -
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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
------------------------------------------------------------
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