Contacts of the strand formed by residues 691 - 696 (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 TRP 691 (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* 4.4 10.3 - - + -
675A LEU* 4.4 17.3 - - + -
683A LYS* 2.8 40.1 + - + -
684A VAL* 3.5 38.6 - - + -
689A THR* 3.3 35.8 + - - -
690A HIS* 1.3 73.2 - - - +
692A VAL* 1.3 59.6 + - - +
693A VAL* 4.2 3.4 - - + -
721A VAL* 3.9 5.2 - - - -
722A ARG* 3.2 70.9 - - + -
723A ALA 3.9 21.5 - - - -
724A GLY* 4.0 9.4 - - - -
748A LEU* 3.5 4.5 - - - +
749A TYR* 2.7 42.6 + - + +
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Residues in contact with VAL 692 (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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691A TRP* 1.3 73.6 - - - +
693A VAL* 1.3 61.0 + - - +
710A PHE* 3.8 17.2 - - + -
713A LEU* 4.0 11.7 - - + -
717A ILE* 3.9 19.1 - - + -
721A VAL* 3.9 3.8 - - + +
722A ARG 2.9 7.2 + - - +
723A ALA* 3.3 16.9 - - + -
724A GLY 2.8 24.8 + - - +
746A VAL* 3.7 28.3 - - + -
747A LYS 3.3 7.6 - - - +
748A LEU* 4.7 3.1 - - - -
763A ILE* 4.9 1.3 - - + -
771A ILE* 4.7 1.1 - - + -
775A ILE* 4.0 25.4 - - + -
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Residues in contact with VAL 693 (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* 4.3 6.7 - - + -
680A PHE* 4.4 2.7 - - + -
684A VAL* 4.3 14.8 - - + -
691A TRP* 4.2 10.1 - - + -
692A VAL* 1.3 79.4 - - - +
694A ASP* 1.3 62.6 - - - +
695A PHE* 3.6 28.2 - - + -
710A PHE* 4.2 2.5 - - - -
724A GLY* 3.4 14.6 - - - +
726A VAL* 3.7 26.2 - - + -
745A SER 3.5 1.6 - - - +
746A VAL* 3.2 5.9 - - - -
747A LYS 2.9 36.9 + - - -
749A TYR* 3.7 24.5 - - + -
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Residues in contact with ASP 694 (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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693A VAL* 1.3 69.4 - - - +
695A PHE* 1.3 62.9 + - - +
696A TYR* 3.7 15.2 + - - +
703A SER 5.3 1.9 - - - +
706A PHE* 3.9 17.2 - - + -
707A ALA* 4.8 4.0 - - - +
710A PHE* 3.5 45.2 - - + +
724A GLY 3.0 7.3 + - - +
725A LYS* 3.2 15.8 - - + -
726A VAL 2.9 25.4 + - - +
744A PRO* 3.5 23.2 - - - +
745A SER 3.4 5.4 - - - +
746A VAL* 4.6 1.1 - - - +
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Residues in contact with PHE 695 (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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680A PHE* 3.7 20.6 - + - -
693A VAL* 3.6 27.6 - - + -
694A ASP* 1.3 71.6 - - - +
696A TYR* 1.3 59.0 + - - +
726A VAL* 3.5 32.1 - - + -
728A CYS* 3.8 8.5 - - - -
734A THR* 4.8 3.6 - - + -
735A CYS* 3.7 10.8 - - - -
738A ALA* 3.9 16.8 - - + -
740A ILE* 3.5 36.1 - - + -
743A TYR* 3.9 5.1 - - - -
744A PRO* 3.4 3.1 - - - +
745A SER 2.7 37.4 + - - +
747A LYS* 3.9 16.2 - - + -
749A TYR* 3.6 24.0 - - - -
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Residues in contact with TYR 696 (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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674A ASP* 4.3 9.9 + - - -
694A ASP* 3.7 21.8 - - - +
695A PHE* 1.3 75.0 - - - +
697A ALA* 1.3 70.1 + - - +
698A PRO* 3.9 23.3 - - + -
703A SER* 3.6 22.7 - - - +
725A LYS* 3.7 38.7 + - + -
726A VAL 2.9 28.1 + - - -
727A ASP* 3.6 19.8 + - + +
728A CYS* 2.8 29.5 + - - +
743A TYR* 4.1 7.0 - - - -
744A PRO* 4.5 1.8 - - + -
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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