Contacts of the helix formed by residues 719 - 734 (chain A) 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 LYS 719 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A VAL* 4.6 4.7 - - + -
584A TYR* 3.6 46.0 + - + -
715A LEU* 3.0 26.7 + - + +
716A LEU* 3.2 7.2 - - + +
717A THR 3.3 0.2 - - - -
718A GLU* 1.3 97.1 + - + +
720A LYS* 1.3 62.2 + - - +
721A ALA 3.3 2.9 - - - +
722A ASP* 3.2 25.4 + - + +
723A VAL* 3.3 15.2 + - - +
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Residues in contact with LYS 720 (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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637A ILE* 3.7 32.4 + - + +
638A PHE* 3.6 33.1 - - + -
716A LEU 3.0 9.3 + - - +
717A THR* 3.5 18.4 - - - +
718A GLU 3.3 3.8 + - - -
719A LYS* 1.3 76.6 - - - +
721A ALA* 1.3 60.7 + - - +
723A VAL* 3.4 4.8 + - - -
724A GLU* 3.4 17.0 + - - +
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Residues in contact with ALA 721 (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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718A GLU 5.2 0.6 + - - -
719A LYS 3.3 0.6 - - - -
720A LYS* 1.3 78.2 - - - +
722A ASP* 1.3 65.3 + - - +
724A GLU* 3.5 6.9 + - - +
725A LYS* 3.2 36.8 + - - +
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Residues in contact with ASP 722 (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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580A VAL* 4.1 11.7 - - + -
584A TYR* 2.7 32.3 + - - +
719A LYS* 3.2 25.4 + - + +
721A ALA* 1.3 80.0 - - - +
723A VAL* 1.3 63.9 + - - +
725A LYS* 3.4 14.4 + - - +
726A VAL* 3.3 28.8 + - - +
745A LEU* 3.4 21.7 - - + +
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Residues in contact with VAL 723 (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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573A TYR* 4.9 0.4 - - + +
576A ALA* 4.3 17.6 - - + +
577A GLY* 4.4 3.6 - - - +
580A VAL* 3.7 25.6 - - + -
634A SER* 3.6 25.8 - - - +
637A ILE* 6.3 0.2 - - + -
638A PHE* 3.6 15.9 - - + -
716A LEU* 3.8 24.0 - - + +
719A LYS 3.3 17.0 + - - +
720A LYS 3.9 5.4 - - - +
721A ALA 3.4 0.2 - - - -
722A ASP* 1.3 76.9 - - - +
724A GLU* 1.3 63.3 + - - +
726A VAL* 3.6 1.6 + - - +
727A ALA* 3.2 24.4 + - + +
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Residues in contact with GLU 724 (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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573A TYR* 3.1 27.0 + - - -
638A PHE* 3.5 24.9 - - + -
720A LYS 3.4 11.5 + - - +
721A ALA* 3.7 11.4 - - - +
722A ASP 3.3 0.2 - - - -
723A VAL* 1.3 79.6 - - - +
725A LYS* 1.3 61.7 + - + +
727A ALA* 4.1 1.9 - - - +
728A LEU* 3.3 51.4 + - + +
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Residues in contact with LYS 725 (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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721A ALA* 3.2 24.7 + - - +
722A ASP* 3.9 20.5 + - - +
723A VAL 3.3 0.4 - - - -
724A GLU* 1.3 79.8 - - + +
726A VAL* 1.3 62.7 + - + +
727A ALA 3.4 0.2 + - - -
728A LEU* 3.8 4.0 + - - +
729A LEU* 3.4 15.1 + - - +
744A LEU* 3.4 44.0 + - + +
745A LEU* 5.1 2.0 - - + -
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Residues in contact with VAL 726 (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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576A ALA* 4.3 11.7 - - + -
579A ALA* 4.4 4.5 - - + -
580A VAL* 3.8 12.6 - - + -
722A ASP 3.3 17.8 + - - +
723A VAL 4.2 1.6 - - - +
725A LYS* 1.3 75.7 - - - +
727A ALA* 1.3 58.9 + - - +
729A LEU* 3.5 4.9 + - - +
730A LEU* 3.0 23.9 + - - +
736A LEU* 3.7 16.5 - - + +
741A MET* 3.7 27.8 - - + -
744A LEU* 3.7 14.8 - - + -
745A LEU* 3.7 31.9 - - + -
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Residues in contact with ALA 727 (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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572A ALA* 4.0 6.2 - - - +
573A TYR* 3.5 34.1 - - + -
576A ALA* 3.7 19.3 - - + -
723A VAL 3.2 18.2 + - - +
724A GLU 4.1 1.3 - - - +
725A LYS 3.3 0.2 - - - -
726A VAL* 1.3 77.6 - - - +
728A LEU* 1.3 55.7 + - - +
730A LEU* 3.0 6.3 + - - +
731A LEU* 2.5 37.7 + - - +
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Residues in contact with LEU 728 (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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569A LYS* 6.5 0.2 - - - -
573A TYR* 4.5 10.1 - - + +
724A GLU* 3.3 45.8 + - + +
725A LYS* 4.4 3.6 - - - +
727A ALA* 1.3 73.2 - - + +
729A LEU* 1.3 63.4 + - - +
731A LEU* 3.9 24.5 - - + +
732A GLU* 3.1 37.2 + - + +
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Residues in contact with LEU 729 (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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725A LYS 3.4 12.5 + - - +
726A VAL 3.5 8.1 - - - +
727A ALA 3.2 0.2 - - - -
728A LEU* 1.3 79.1 - - - +
730A LEU* 1.3 55.9 + - - +
732A GLU* 5.0 7.2 - - - +
733A LYS* 3.1 55.0 + - + +
736A LEU* 3.8 22.9 - - + +
740A ASP* 4.1 22.9 - - + +
741A MET* 6.4 0.2 - - - -
744A LEU* 3.8 22.0 - - + -
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Residues in contact with LEU 730 (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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572A ALA* 3.8 24.9 - - - +
575A GLN* 4.0 11.4 - - + -
576A ALA* 4.4 6.5 - - + +
594A VAL* 3.4 48.5 - - + +
595A SER* 4.2 0.2 - - - -
596A ILE* 3.7 24.7 - - + +
726A VAL 3.0 13.8 + - - +
727A ALA 3.0 8.6 + - - +
729A LEU* 1.3 75.6 - - - +
731A LEU* 1.3 64.9 + - - +
734A GLU* 3.1 34.6 + - - +
735A VAL 5.2 0.2 - - - +
736A LEU* 3.7 19.9 - - + +
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Residues in contact with LEU 731 (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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568A LYS* 3.9 29.9 + - + +
569A LYS* 4.2 30.7 - - + +
572A ALA* 3.8 22.0 - - + -
573A TYR* 5.8 1.8 - - + -
596A ILE* 4.4 5.2 - - + -
727A ALA 2.5 19.3 + - - +
728A LEU* 3.9 27.1 - - + +
729A LEU 3.3 0.6 - - - -
730A LEU* 1.3 73.1 - - - +
732A GLU* 1.3 63.5 + - + +
734A GLU* 4.4 8.9 - - - +
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Residues in contact with GLU 732 (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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728A LEU* 3.1 22.8 + - + +
729A LEU* 4.2 6.9 - - - +
730A LEU 3.2 0.2 - - - -
731A LEU* 1.3 82.8 - - + +
733A LYS* 1.3 69.5 + - + +
734A GLU* 3.3 10.4 + - - +
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Residues in contact with LYS 733 (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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729A LEU* 3.1 38.2 + - + +
732A GLU* 1.3 82.4 - - + +
734A GLU* 1.3 62.5 + - - +
735A VAL* 3.0 29.4 + - + +
740A ASP* 3.9 25.4 + - - -
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Residues in contact with GLU 734 (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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568A LYS* 2.5 35.2 + - - +
595A SER* 2.9 22.3 + - - -
596A ILE* 3.2 26.7 + - + +
597A ILE* 3.6 21.3 - - + +
598A PRO* 5.5 2.2 - - - +
730A LEU* 3.1 28.3 + - - +
731A LEU 4.4 5.4 - - - +
732A GLU 3.8 10.6 - - - +
733A LYS* 1.3 76.9 - - - +
735A VAL* 1.3 58.2 + - + +
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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
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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