Contacts of the strand formed by residues 722 - 727 (chain A) in PDB entry 3APO
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 ARG 722 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A ILE* 3.9 31.1 - - - +
683A LYS* 4.4 13.7 - - - +
689A THR* 4.5 15.5 - - + +
690A HIS 3.1 10.2 + - - +
691A TRP* 3.2 52.6 - - + -
692A VAL* 2.9 25.1 + - - +
718A LYS* 6.3 2.7 - - - +
721A VAL* 1.3 76.7 - - - +
723A ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 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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671A ALA 4.6 3.0 + - - +
672A SER* 3.1 11.0 - - - +
673A ILE* 2.9 24.8 + - - +
691A TRP* 3.9 8.5 - - - -
692A VAL* 3.3 20.0 - - + +
710A PHE* 4.1 6.1 - - + -
714A ALA* 3.6 34.1 - - + -
717A ILE* 5.0 1.1 - - + -
721A VAL 4.3 0.4 + - - +
722A ARG* 1.3 76.6 - - - +
724A GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 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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673A ILE 3.3 9.0 - - - -
675A LEU* 3.8 17.0 - - - -
691A TRP* 4.0 6.0 - - - -
692A VAL 2.8 9.4 + - - -
693A VAL* 3.9 7.6 - - - -
694A ASP 3.0 21.7 + - - -
710A PHE* 3.2 10.9 - - - -
723A ALA* 1.3 74.6 - - - +
725A LYS* 1.3 64.5 + - - -
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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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670A GLN* 4.6 2.7 - - - +
672A SER* 3.4 24.7 - - - +
673A ILE 3.1 5.8 + - - +
674A ASP* 3.8 20.5 + - - +
675A LEU* 2.9 27.3 + - - +
694A ASP* 3.2 21.8 - - + -
696A TYR* 3.7 32.6 + - + -
707A ALA* 4.1 23.0 + - - +
710A PHE* 3.7 11.7 - - + -
711A GLU* 3.7 12.1 + - - +
724A GLY* 1.3 80.1 - - - +
726A VAL* 1.3 64.7 + - - +
727A ASP 4.1 1.1 + - - -
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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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675A LEU* 4.1 15.3 - - + +
676A THR 5.7 1.1 - - - +
680A PHE* 4.0 18.6 - - + -
693A VAL* 3.7 19.3 - - + -
694A ASP 2.9 6.9 + - - -
695A PHE* 3.5 20.3 - - + -
696A TYR* 2.9 30.0 + - - -
725A LYS* 1.3 78.7 - - - +
727A ASP* 1.3 65.4 + - - +
728A CYS 3.3 2.9 + - - -
731A TYR* 4.5 10.3 - - + -
734A THR* 4.0 18.2 - - + -
735A CYS* 3.7 22.4 - - - -
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Residues in contact with ASP 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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675A LEU 4.9 0.4 + - - -
696A TYR* 3.6 26.9 + - - +
698A PRO* 3.4 25.3 - - - +
725A LYS 4.1 0.8 + - - -
726A VAL* 1.3 73.2 - - - +
728A CYS* 1.3 56.5 + - - +
729A GLN* 2.9 23.4 + - - +
730A ALA* 3.0 21.0 + - + +
731A TYR* 2.9 39.1 + - + +
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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