Contacts of the strand formed by residues 745 - 752 (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 SER 745 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693A VAL 3.5 0.9 - - - +
694A ASP* 3.4 4.0 - - - +
695A PHE* 2.7 39.3 + - - +
740A ILE* 3.9 30.8 - - - +
741A LYS 4.8 1.9 + - - -
742A ALA 2.8 24.7 + - - -
744A PRO* 1.3 72.7 + - - +
746A VAL* 1.3 61.6 + - - +
747A LYS 4.2 0.2 - - - -
762A GLN* 4.4 16.5 + - - +
766A ARG* 3.9 5.2 + - - +
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Residues in contact with VAL 746 (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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692A VAL* 3.7 27.6 - - + -
693A VAL 3.2 8.1 - - - +
694A ASP* 4.7 4.0 - - - -
706A PHE* 3.5 38.6 - - + -
710A PHE* 4.8 4.3 - - + -
713A LEU* 5.3 0.4 - - + -
745A SER* 1.3 78.2 - - - +
747A LYS* 1.3 65.6 + - - +
762A GLN* 3.7 7.2 + - - +
763A ILE* 2.9 54.6 + - + +
765A SER 5.0 1.6 - - - +
766A ARG* 4.1 15.2 - - - +
771A ILE* 5.1 5.2 - - + -
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Residues in contact with LYS 747 (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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692A VAL* 3.3 5.2 - - - +
693A VAL 2.9 38.3 + - - -
695A PHE* 3.9 19.1 - - + -
738A ALA* 3.0 29.9 + - + +
740A ILE* 3.9 4.0 - - + -
746A VAL* 1.3 80.2 - - - +
748A LEU* 1.3 61.3 + - - +
749A TYR* 3.7 32.1 + - + +
760A GLU* 3.6 32.3 + - - +
761A GLU* 3.1 13.5 - - - +
762A GLN* 3.5 30.7 - - - +
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Residues in contact with LEU 748 (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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690A HIS* 5.6 2.0 - - + -
691A TRP 3.5 11.9 - - - +
692A VAL* 4.6 2.0 - - + +
721A VAL* 4.9 4.0 - - + -
747A LYS* 1.3 73.4 - - - +
749A TYR* 1.3 74.3 + - - +
750A GLN* 4.3 20.2 - - + +
759A TRP 3.4 3.3 - - - +
760A GLU* 3.5 1.7 - - - -
761A GLU* 2.6 44.5 + - + +
763A ILE* 3.8 23.0 - - + +
775A ILE* 3.8 45.5 - - + -
778A LYS* 4.0 32.5 - - + -
779A LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 749 (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* 3.5 21.7 - + - -
684A VAL* 3.6 23.6 - - + -
685A LEU* 3.9 11.9 - - + -
689A THR 5.0 2.0 - - - +
690A HIS* 3.1 8.6 - - - +
691A TRP* 2.7 49.4 + - + +
693A VAL* 3.7 24.5 - - + -
695A PHE* 3.6 11.8 - - - -
738A ALA* 4.5 2.4 - - - +
747A LYS* 3.7 34.2 + - + +
748A LEU* 1.3 77.4 - - - +
750A GLN* 1.3 61.9 + - - +
758A ILE* 3.6 27.6 - - + -
759A TRP 3.2 4.0 - - - -
760A GLU* 3.5 32.0 + - + -
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Residues in contact with GLN 750 (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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690A HIS* 3.7 6.1 - - + +
748A LEU* 4.3 13.6 - - + +
749A TYR* 1.3 73.9 - - - +
751A TYR* 1.3 64.4 + - - +
752A GLU 3.6 0.5 + - - -
757A SER 3.6 0.7 - - - +
758A ILE* 3.3 5.9 - - - -
759A TRP* 2.8 57.0 + - + +
761A GLU* 3.7 19.4 - - - +
778A LYS* 3.1 50.0 + - - +
779A LEU* 3.9 19.1 - - + +
781A THR 5.9 0.4 - - - -
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Residues in contact with TYR 751 (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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687A GLY 3.7 9.4 - - - -
688A LYS* 3.4 62.7 + - + +
689A THR* 3.9 8.0 + - - +
690A HIS* 3.0 26.2 + - + +
749A TYR 4.1 1.0 + - - -
750A GLN* 1.3 72.7 - - - +
752A GLU* 1.3 58.4 + - - +
753A ARG* 3.4 44.6 + - + +
756A LYS* 3.9 20.2 - - - +
757A SER 3.6 24.7 - - - -
758A ILE* 3.6 26.4 - - + +
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Residues in contact with GLU 752 (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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750A GLN 3.6 0.8 + - - -
751A TYR* 1.3 73.1 - - - +
753A ARG* 1.3 63.8 + - - +
754A ALA* 4.1 16.9 - - + +
755A LYS* 3.1 28.8 + - + +
756A LYS 3.1 17.5 + - - -
757A SER 2.9 17.6 + - - +
759A TRP* 2.7 46.1 + - + +
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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