Contacts of the strand formed by residues 609 - 621 (chain A) in PDB entry 4APT
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 LEU 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602A SER 5.6 1.6 - - - +
603A ALA* 3.0 25.2 - - - +
606A SER* 3.0 24.6 + - - +
607A ASN 4.8 0.7 - - - +
608A ASP* 1.3 90.6 - - + +
610A LYS* 1.3 63.3 + - - +
686A LEU* 4.1 19.5 - - + -
687A THR 3.3 16.8 - - - +
688A LEU* 4.2 9.6 - - + -
689A LYS* 4.7 2.7 - - - +
574B TYR* 3.8 48.5 - - + +
577B LYS* 4.8 15.9 - - - +
669B LEU* 5.0 4.7 - - + +
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Residues in contact with LYS 610 (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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603A ALA* 3.8 9.4 - - - -
609A LEU* 1.3 74.3 - - - +
611A ILE* 1.3 69.6 + - - +
612A ASP* 5.1 7.2 + - - -
686A LEU* 3.8 3.0 - - - -
687A THR* 2.7 49.4 + - - +
688A LEU 3.6 19.5 - - - +
689A LYS* 4.0 23.6 + - + +
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Residues in contact with ILE 611 (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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599A PHE* 3.9 30.5 - - + +
600A ILE* 5.3 14.4 - - + +
603A ALA* 3.5 14.1 - - + +
610A LYS* 1.3 86.8 - - + +
612A ASP* 1.3 65.5 + - - +
613A SER* 5.0 2.7 - - - +
684A ILE* 3.9 23.8 - - + -
685A SER 3.3 20.9 - - - +
686A LEU* 4.5 5.2 - - + -
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Residues in contact with ASP 612 (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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610A LYS* 5.1 6.0 - - - -
611A ILE* 1.3 76.8 - - - +
613A SER* 1.3 73.7 + - - +
614A SER* 4.5 3.2 + - - -
634A VAL* 4.0 20.3 - - - +
635A GLY* 3.4 20.5 - - - -
683A CYS 3.6 1.2 - - - +
684A ILE* 3.5 1.9 - - - -
685A SER* 2.9 35.9 + - - +
687A THR* 3.4 34.3 - - + +
571B LEU* 5.1 4.5 - - - +
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Residues in contact with SER 613 (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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611A ILE* 5.0 3.3 - - - +
612A ASP* 1.3 77.6 + - - +
614A SER* 1.3 62.6 + - - +
615A THR* 4.2 1.5 + - - -
633A ALA 4.1 1.0 - - - +
635A GLY* 3.1 26.2 + - - +
654A PHE* 5.2 2.1 - - - -
682A VAL* 3.5 22.2 - - - +
683A CYS 3.4 4.5 - - - -
684A ILE* 3.8 17.0 - - - +
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Residues in contact with SER 614 (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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612A ASP* 4.5 4.0 + - - -
613A SER* 1.3 75.3 + - - +
615A THR* 1.3 63.9 + - - +
616A VAL 3.7 0.5 + - - -
632A PHE* 3.7 21.0 - - - -
633A ALA 3.4 9.9 - - - -
634A VAL* 3.7 24.6 - - - +
681A ASP 3.6 1.2 - - - +
682A VAL* 4.4 0.9 - - - -
683A CYS* 2.8 39.7 + - - +
566B MET 4.9 0.7 + - - -
568B PRO* 3.9 21.0 - - - +
571B LEU* 5.9 1.6 - - - +
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Residues in contact with THR 615 (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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613A SER* 4.2 1.1 - - - -
614A SER* 1.3 72.2 - - - +
616A VAL* 1.3 65.7 + - - +
617A GLU* 3.4 15.4 + - - +
632A PHE* 3.6 1.9 - - - -
633A ALA* 2.9 35.7 + - - +
638A ARG* 3.8 18.7 + - - +
680A GLY* 3.9 26.0 - - - +
681A ASP 3.3 4.3 - - - +
682A VAL* 3.7 19.2 - - + +
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Residues in contact with VAL 616 (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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615A THR* 1.3 70.1 - - - +
617A GLU* 1.3 64.0 + - - +
618A ARG 3.9 4.9 - - - +
619A ILE* 3.6 32.1 - - + -
630A ILE* 3.7 11.7 - - + -
631A GLN 3.8 3.6 - - - -
632A PHE* 3.6 25.4 - - + -
677A LEU* 4.2 12.1 - - + -
678A SER 3.7 19.5 - - - +
679A VAL* 3.5 3.8 - - - +
680A GLY* 2.7 29.7 + - - +
681A ASP* 2.8 20.4 + - + +
683A CYS* 3.9 11.4 - - - -
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Residues in contact with GLU 617 (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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615A THR* 3.4 12.9 + - - +
616A VAL* 1.3 73.8 - - - +
618A ARG* 1.3 64.5 + - + +
631A GLN* 2.9 39.0 + - - +
633A ALA* 4.1 20.4 - - + +
638A ARG* 2.2 43.1 + - - +
679A VAL* 3.2 23.1 - - - +
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Residues in contact with ARG 618 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A VAL 3.6 0.8 - - - -
617A GLU* 1.3 81.8 - - - +
619A ILE* 1.3 68.6 + - - +
620A GLU* 3.2 49.4 + - - +
629A VAL 4.7 1.0 + - - -
630A ILE* 3.3 8.7 - - - +
631A GLN* 2.9 50.9 + - + +
679A VAL* 4.1 6.1 - - + -
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Residues in contact with ILE 619 (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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616A VAL* 3.6 19.3 - - + -
618A ARG* 1.3 87.7 + - - +
620A GLU* 1.3 68.8 + - - +
628A ALA* 5.0 3.6 - - + -
629A VAL 3.7 2.9 - - - -
630A ILE* 4.1 9.9 - - + +
661A CYS* 4.1 20.9 - - + -
677A LEU* 3.5 43.3 - - + +
678A SER* 3.9 11.0 - - - -
679A VAL* 4.2 9.4 - - + +
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Residues in contact with GLU 620 (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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618A ARG* 3.2 36.6 + - - +
619A ILE* 1.3 77.1 - - - +
621A ASP* 1.3 72.5 + - + +
628A ALA* 3.3 6.1 - - - +
629A VAL* 2.5 52.1 + - + +
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Residues in contact with ASP 621 (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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620A GLU* 1.3 93.6 - - + +
622A SER* 1.3 86.0 + - - +
624A SER 4.6 2.3 - - - +
627A VAL 3.1 10.7 - - - +
628A ALA* 4.2 6.2 - - - +
629A VAL* 4.3 2.9 - - - +
647A VAL* 5.7 1.2 - - - +
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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