Contacts of the helix formed by residues 567 - 585 (chain C) 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 GLU 567 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563C LEU* 3.7 18.4 - - + +
564C GLN* 3.0 18.9 + - + +
566C GLU* 1.3 84.8 - - + +
568C LYS* 1.3 59.1 + - - +
569C LYS 3.4 0.4 - - - +
570C THR* 3.9 8.1 - - - +
571C VAL* 3.3 25.5 + - - +
612D GLU 5.0 0.3 - - - +
613D GLN* 3.0 48.3 - - - +
614D TYR 3.5 11.7 + - - -
615D LEU* 3.7 28.9 + - + +
620D GLN* 4.8 3.3 + - - +
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Residues in contact with LYS 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C GLN* 3.4 40.7 - - - +
563C LEU* 4.0 32.5 + - + +
564C GLN 2.7 20.8 + - - +
565C PRO* 4.5 4.7 - - + -
567C GLU* 1.3 71.0 - - - +
569C LYS* 1.3 59.6 + - - +
570C THR 3.2 0.2 - - - -
571C VAL* 3.4 2.8 + - + +
572C ALA* 2.9 27.9 + - - +
596C ILE* 3.7 29.6 - - + +
731C LEU* 4.2 15.0 - - + +
734C GLU* 4.0 11.3 + - + +
762D GLY 5.6 1.0 + - - -
763D THR* 5.0 8.7 + - - +
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Residues in contact with LYS 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C PRO 3.3 21.4 + - - +
566C GLU* 4.4 22.1 + - - +
567C GLU 3.4 0.2 - - - -
568C LYS* 1.3 79.9 - - - +
570C THR* 1.3 56.5 + - - +
572C ALA* 3.7 5.9 - - - +
573C TYR* 3.1 63.9 + - + -
639C PHE* 4.4 12.6 - - + -
728C LEU* 6.3 0.9 - - - -
731C LEU* 4.4 20.8 - - + +
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Residues in contact with THR 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C GLU 3.1 19.1 + - - -
567C GLU* 3.9 3.5 - - - +
568C LYS 3.2 0.4 - - - -
569C LYS* 1.3 76.1 - - - +
571C VAL* 1.3 58.7 + - - +
573C TYR* 3.5 2.8 + - - +
574C HIS* 2.9 27.4 + - - +
635C GLU* 4.0 18.4 - - - +
639C PHE* 3.2 31.1 - - + -
643C THR* 4.2 16.6 - - + -
615D LEU* 3.7 26.5 - - + -
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Residues in contact with VAL 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LEU* 4.1 10.5 - - + -
567C GLU 3.3 16.4 - - - +
568C LYS* 3.4 7.3 + - + +
570C THR* 1.3 75.4 - - - +
572C ALA* 1.3 58.4 + - - +
574C HIS* 3.2 6.5 + - - +
575C GLN* 2.8 41.1 + - + +
596C ILE* 4.3 12.3 - - + +
603C LEU* 3.4 45.8 - - + +
604C GLY* 4.5 0.4 - - - +
615D LEU* 3.7 18.8 - - + -
6I ALA* 4.7 8.7 - - + -
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Residues in contact with ALA 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568C LYS 2.9 17.5 + - - +
569C LYS* 3.7 4.9 - - - +
570C THR 3.2 0.2 - - - -
571C VAL* 1.3 78.3 - - - +
573C TYR* 1.3 59.3 + - + +
575C GLN 3.5 0.2 + - - -
576C ALA* 3.1 23.0 + - - +
596C ILE* 3.8 18.3 - - + +
727C ALA* 3.3 28.5 - - + +
730C LEU* 3.7 5.9 - - + +
731C LEU* 3.8 23.8 - - + -
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Residues in contact with TYR 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C LYS* 3.1 37.4 + - + +
570C THR 4.0 3.6 - - - +
572C ALA* 1.3 77.6 - - + +
574C HIS* 1.3 61.7 + - - +
576C ALA* 3.8 2.0 + - - +
577C GLY 3.4 6.2 + - - -
634C SER* 2.8 31.5 + - - +
635C GLU* 5.1 2.2 - - - +
638C PHE* 3.4 41.5 - + + -
639C PHE* 3.4 39.9 - + + -
723C VAL 5.1 0.9 - - - -
724C GLU* 3.5 27.7 + - - -
727C ALA* 3.5 23.1 - - + -
728C LEU* 4.4 14.5 - - + +
731C LEU* 5.8 1.8 - - + -
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Residues in contact with HIS 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C THR 2.9 18.6 + - - +
571C VAL* 3.5 8.1 - - - +
572C ALA 3.2 0.2 - - - -
573C TYR* 1.3 77.7 - - - +
575C GLN* 1.3 60.3 + - - +
577C GLY 3.0 15.1 + - - -
578C HIS* 3.2 14.7 + + - -
631C GLY* 3.2 43.6 + - - -
632C ARG 3.6 3.4 - - - -
635C GLU* 3.1 24.2 + - - +
645C GLY 4.7 1.6 + - - -
646C ALA* 4.0 17.3 - - + -
649C ASP* 3.3 13.0 - - - -
802C ZN 2.3 32.2 - - - -
5I ALA 3.9 0.4 + - - -
6I ALA* 3.6 23.5 - - + +
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Residues in contact with GLN 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C VAL* 2.8 27.5 + - + +
572C ALA 4.2 2.5 - - - +
574C HIS* 1.3 78.7 - - - +
576C ALA* 1.3 59.9 + - - +
578C HIS* 3.4 13.0 + - - +
579C ALA* 3.1 24.6 + - - +
594C VAL* 3.9 22.4 - - + +
595C SER 4.5 4.9 - - - +
596C ILE* 4.2 12.3 - - + -
604C GLY* 3.6 17.0 - - - -
605C TYR 2.9 31.5 - - - +
606C ALA* 4.0 7.4 + - - +
730C LEU* 4.4 0.7 - - + -
4I ALA 4.9 0.7 - - - +
5I ALA* 3.9 4.9 - - - +
6I ALA* 3.6 29.7 - - - +
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Residues in contact with ALA 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C ALA 3.1 17.7 + - - +
573C TYR 4.0 2.0 - - - +
574C HIS 3.2 0.2 - - - -
575C GLN* 1.3 76.7 - - - +
577C GLY* 1.3 59.0 + - - +
579C ALA* 4.0 7.6 - - - -
580C VAL* 2.9 33.6 + - - +
723C VAL* 3.8 24.2 - - + +
726C VAL* 4.0 15.0 - - + -
727C ALA* 3.7 19.7 - - + -
730C LEU* 4.3 1.0 - - + +
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Residues in contact with GLY 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C TYR 3.4 5.1 + - - -
574C HIS 3.0 9.0 + - - -
576C ALA* 1.3 77.0 - - - +
578C HIS* 1.3 62.3 + - - +
580C VAL* 5.2 0.4 - - - -
581C ALA* 3.3 27.4 + - - +
630C GLY* 3.3 27.4 - - - +
634C SER* 3.8 13.0 - - - -
716C LEU* 4.3 6.1 - - - +
723C VAL* 4.8 1.3 - - - -
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Residues in contact with HIS 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C HIS* 3.2 31.6 + + - -
575C GLN* 3.8 16.8 - - - +
576C ALA 3.3 0.2 - - - -
577C GLY* 1.3 75.7 - - - +
579C ALA* 1.3 62.9 + - - +
582C GLY 3.3 10.2 + - - -
606C ALA* 4.5 13.5 - - + -
608C TYR* 2.2 32.0 + - + +
627C MET* 3.6 18.3 + - - +
628C THR* 3.6 15.6 - - - -
631C GLY* 3.9 6.2 - - - -
649C ASP* 3.0 20.2 + - - -
802C ZN 2.2 36.3 - - - -
4I ALA* 3.8 19.4 - - + +
5I ALA 5.4 0.2 - - - -
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Residues in contact with ALA 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C GLN 3.1 17.3 + - - +
576C ALA* 3.2 9.8 + - - +
578C HIS* 1.3 79.3 - - - +
580C VAL* 1.3 59.3 + - + +
582C GLY* 3.8 1.2 - - - -
583C TRP* 3.0 28.0 + - - +
591C LEU* 4.1 19.4 - - + +
594C VAL* 3.7 21.5 - - + -
608C TYR* 4.4 0.9 - - - -
726C VAL* 4.3 7.4 - - + -
741C MET* 4.1 13.0 - - + -
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Residues in contact with VAL 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C ALA 2.9 19.3 + - - +
579C ALA* 1.3 74.6 - - + +
581C ALA* 1.3 61.5 + - - +
583C TRP* 3.0 20.3 + - - +
584C TYR* 3.0 40.4 + - + +
715C LEU* 5.7 0.2 - - - -
716C LEU* 3.8 18.4 - - + -
719C LYS* 4.4 6.1 - - + -
722C ASP* 3.9 19.5 - - + +
723C VAL* 3.8 24.5 - - + -
726C VAL* 4.0 14.8 - - + -
745C LEU* 4.8 7.4 - - + -
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Residues in contact with ALA 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577C GLY 3.3 19.6 + - - +
580C VAL* 1.3 79.1 - - - +
582C GLY* 1.3 60.2 + - - +
583C TRP 3.3 0.9 + - - -
584C TYR 4.1 0.2 - - - -
585C LEU* 3.3 31.1 + - - +
626C CYS 3.9 21.3 - - - +
627C MET* 4.2 10.3 - - - +
630C GLY* 4.4 6.1 - - - -
712C THR* 4.8 0.2 - - + -
715C LEU* 4.3 18.6 - - + -
716C LEU* 4.3 9.5 - - + +
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Residues in contact with GLY 582 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C HIS 3.3 15.2 + - - -
579C ALA 3.8 1.8 - - - -
581C ALA* 1.3 78.0 - - - +
583C TRP* 1.3 57.0 + - - +
584C TYR 3.5 0.2 - - - -
585C LEU 4.1 0.3 - - - +
588C ALA* 3.7 14.9 - - - +
589C ASP 3.9 5.6 - - - +
591C LEU* 5.9 3.0 - - - +
608C TYR* 4.1 9.0 - - - -
627C MET* 3.7 18.7 - - - +
748C ARG* 3.4 24.4 + - - -
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Residues in contact with TRP 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579C ALA 3.0 16.7 + - - +
580C VAL* 3.0 11.0 + - - +
582C GLY* 1.3 79.6 - - - +
584C TYR* 1.3 86.0 + + - +
585C LEU 3.6 0.9 - - - -
591C LEU* 4.5 17.5 - - + -
738C LYS* 4.7 19.5 - - + -
741C MET* 3.7 39.3 - - + -
742C VAL* 4.2 14.6 - - + -
745C LEU* 3.8 29.3 - - + +
746C GLY 3.2 25.2 + - - -
747C PRO 4.5 1.6 + - - -
748C ARG* 3.6 59.4 + - + +
749C PRO* 4.3 2.7 - - - +
750C PHE* 4.6 1.0 - - - -
752C GLU* 5.4 0.7 - - - -
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Residues in contact with TYR 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580C VAL* 3.0 30.1 + - + +
581C ALA 3.5 0.9 + - - +
583C TRP* 1.3 105.4 - + - +
585C LEU* 1.3 66.9 + - - +
715C LEU* 4.4 20.3 - - + +
719C LYS* 3.6 49.5 + - + -
722C ASP* 3.2 22.1 + - + -
745C LEU* 4.3 16.7 + - + +
749C PRO* 4.4 19.7 - - + -
750C PHE* 3.2 19.6 - - - -
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Residues in contact with LEU 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C ALA 3.3 19.8 + - - +
582C GLY 4.4 0.2 + - - -
583C TRP 3.6 0.6 - - - -
584C TYR* 1.3 81.4 - - - +
586C GLU* 1.3 69.5 + - - +
588C ALA* 3.4 12.7 - - + +
623C ASP* 3.7 29.8 - - - +
626C CYS* 3.7 37.5 - - + +
627C MET* 4.2 1.3 - - + +
711C ARG* 3.9 22.4 - - + +
715C LEU* 3.8 25.8 - - + -
748C ARG* 3.2 21.1 + - - -
750C PHE* 3.5 3.4 - - - -
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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