Contacts of the helix formed by residues 719 - 729 (chain A) in PDB entry 4ZGA
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 VAL 719 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A TYR* 3.0 53.7 + - + +
718A ARG* 1.3 83.8 - - + +
720A LEU* 1.3 70.2 + - + +
721A VAL 3.3 2.5 + - - -
722A LYS* 3.5 6.9 + - - +
723A LYS* 3.3 23.3 + - + +
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Residues in contact with LEU 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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715A TYR* 3.0 44.4 + - + +
716A PHE* 3.7 14.4 - - + +
719A VAL* 1.3 81.1 - - + +
721A VAL* 1.3 56.9 + - - +
723A LYS* 3.4 16.4 - - + +
724A TYR* 2.8 48.2 + - + +
816A VAL* 4.4 1.6 - - + -
817A GLU* 3.2 39.9 - - + +
820A MET* 3.4 33.7 - - + -
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Residues in contact with VAL 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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634A TYR* 4.4 10.5 - - + +
636A VAL* 3.7 33.0 - - + -
686A LEU* 3.9 10.5 - - + -
716A PHE* 3.0 48.7 + - + +
717A GLN* 3.9 14.8 + - - +
719A VAL 3.3 0.8 + - - -
720A LEU* 1.3 76.7 - - - +
722A LYS* 1.3 58.2 + - - +
724A TYR* 3.1 10.7 + - + +
725A ALA* 2.9 26.2 + - - +
731A VAL* 4.6 3.8 - - + +
733A VAL* 4.6 14.1 - - + -
772A ILE* 5.7 0.2 - - + -
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Residues in contact with LYS 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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636A VAL* 4.7 6.3 - - + -
638A LYS 5.1 0.7 - - - +
640A ALA* 5.5 11.4 - - + -
685A TYR* 5.9 2.9 - - + +
686A LEU* 5.2 12.9 - - + +
717A GLN 5.2 1.2 + - - -
718A ARG 5.3 4.9 - - - +
719A VAL 3.5 8.3 + - - +
721A VAL* 1.3 79.2 - - - +
723A LYS* 1.3 56.9 + - - +
725A ALA* 3.1 10.0 + - - +
726A SER* 2.8 31.8 + - - -
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Residues in contact with LYS 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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719A VAL* 3.3 17.6 + - + +
720A LEU* 3.4 22.6 - - + +
722A LYS* 1.3 72.8 - - - +
724A TYR* 1.3 70.0 + - + +
726A SER* 3.2 7.2 + - - +
727A GLU* 3.1 50.5 + - + +
817A GLU* 2.7 31.9 + - - -
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Residues in contact with TYR 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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716A PHE* 4.2 10.5 - + - -
720A LEU* 2.8 44.5 + - + +
721A VAL* 3.1 9.8 + - + +
723A LYS* 1.3 82.4 - - + +
725A ALA* 1.3 61.0 + - - +
727A GLU* 3.4 18.4 + - - -
728A ARG* 3.3 31.3 + - - +
731A VAL* 3.5 23.6 - - + +
772A ILE* 3.9 33.0 - - + -
792A SER* 5.9 1.3 - - - -
817A GLU* 2.6 30.3 + - - +
820A MET* 4.2 11.9 - - + +
859A TYR* 5.2 6.6 + - - -
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Residues in contact with ALA 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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636A VAL* 3.6 39.5 - - + +
637A SER 3.9 8.3 - - - +
638A LYS* 3.2 12.1 - - - +
721A VAL 2.9 12.5 + - - +
722A LYS* 3.3 9.4 - - - +
723A LYS 3.1 0.4 - - - -
724A TYR* 1.3 76.2 - - - +
726A SER* 1.3 61.2 + - - +
729A ASN 3.4 2.8 + - - -
730A GLY* 3.0 26.3 + - - +
731A VAL* 4.1 7.4 - - + +
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Residues in contact with SER 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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638A LYS* 3.7 42.8 + - - -
722A LYS 2.8 17.6 + - - -
723A LYS* 3.2 8.3 + - - -
725A ALA* 1.3 77.9 - - - +
727A GLU* 1.3 62.7 + - - +
728A ARG 3.6 0.3 + - - -
729A ASN 4.3 0.7 + - - -
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Residues in contact with GLU 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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723A LYS* 3.1 44.3 + - + +
724A TYR* 3.4 18.8 + - - +
725A ALA 3.3 0.2 - - - -
726A SER* 1.3 80.2 - - - +
728A ARG* 1.3 67.7 + - + +
778A PHE* 5.4 3.8 - - - +
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Residues in contact with ARG 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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724A TYR* 3.3 25.8 + - - +
727A GLU* 1.3 88.2 - - + +
729A ASN* 1.3 75.0 + - - +
730A GLY 3.7 7.2 - - - +
731A VAL* 4.4 2.5 - - - -
772A ILE* 3.1 39.9 + - - +
774A SER* 2.9 36.0 + - - +
775A CYS 4.8 1.4 + - - +
778A PHE* 4.2 18.7 - - + +
780A GLN 4.8 1.6 - - - +
790A SER* 3.0 39.8 + - - -
791A VAL* 4.0 2.4 - - - +
792A SER* 3.3 17.1 + - - +
857A HIS* 6.0 1.8 + - - -
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Residues in contact with ASN 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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638A LYS* 4.2 32.7 - - + +
725A ALA 3.4 7.0 + - - -
726A SER 4.3 1.6 + - - -
727A GLU 3.8 1.0 - - - -
728A ARG* 1.3 79.1 - - - +
730A GLY* 1.3 63.2 + - - +
778A PHE* 2.9 26.2 + - + +
779A THR* 3.8 8.1 + - - +
780A GLN 3.6 3.5 - - - +
781A PRO* 3.6 31.2 - - - +
782A ALA 2.9 24.4 + - - -
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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