Contacts of the helix formed by residues 608 - 618 (chain A) in PDB entry 5FG6
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 ASP 608 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587A PHE* 3.6 9.4 - - - +
589A GLN* 3.5 22.0 - - - +
590A PRO* 3.3 29.4 - - + +
606A PRO 5.5 0.2 - - - -
607A MET* 1.3 81.8 - - - +
609A PHE* 1.3 58.3 + - - +
610A ALA* 2.8 33.1 + - - +
611A THR* 2.6 29.5 + - - -
612A MET* 3.0 27.7 + - - +
634A ILE* 3.7 12.8 - - - -
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Residues in contact with PHE 609 (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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575A LEU* 3.6 21.2 - - + +
578A LEU* 3.9 34.1 - - + -
579A GLN* 3.6 37.1 - - + +
582A ASP* 4.0 22.0 - - + -
587A PHE* 2.8 43.6 + - + +
588A ALA* 4.2 1.3 - - - -
608A ASP* 1.3 69.6 - - - +
610A ALA* 1.3 61.0 + - - +
612A MET* 3.3 7.1 + - - +
613A ARG* 2.9 28.4 + - - +
631A PHE* 4.2 11.4 - + - -
634A ILE* 3.7 17.9 - - + -
655A LEU* 3.9 20.2 - - + -
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Residues in contact with ALA 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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579A GLN* 5.4 0.2 - - - +
588A ALA 3.1 21.2 + - - +
589A GLN* 3.8 22.7 - - - +
590A PRO* 4.8 2.0 - - + -
608A ASP* 2.8 11.6 + - - +
609A PHE* 1.3 71.3 - - - +
611A THR* 1.3 59.2 + - - +
613A ARG* 3.2 9.8 + - - +
614A LYS* 3.0 41.0 + - - +
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Residues in contact with THR 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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590A PRO* 4.1 8.0 - - - +
606A PRO 5.4 1.3 - - - +
607A MET* 3.7 26.2 - - + -
608A ASP* 2.6 33.4 + - - -
610A ALA* 1.3 74.0 - - - +
612A MET* 1.3 64.3 + - - +
614A LYS* 3.3 11.3 + - + +
615A ARG* 3.1 22.7 + - + +
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Residues in contact with MET 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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575A LEU* 4.3 9.2 - - + -
578A LEU* 5.2 0.9 - - + -
607A MET* 3.7 13.7 - - - -
608A ASP 3.0 14.7 + - - +
609A PHE* 3.6 17.9 - - - +
610A ALA 3.3 0.2 - - - -
611A THR* 1.3 77.3 - - - +
613A ARG* 1.3 57.3 + - - +
615A ARG* 3.2 3.4 + - - +
616A LEU* 2.8 30.5 + - - +
621A TYR* 3.5 19.9 - - + +
627A PHE* 3.5 59.0 - - + +
630A ASP* 3.9 2.7 - - + -
631A PHE* 3.9 16.6 - - + +
634A ILE* 3.7 26.0 - - - -
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Residues in contact with ARG 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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572A ARG* 5.3 9.1 + - - +
575A LEU* 3.6 27.2 - - + +
576A ASP* 3.1 27.7 + - - -
579A GLN* 3.0 25.9 + - - -
609A PHE 2.9 13.3 + - - +
610A ALA* 3.2 11.8 + - - +
612A MET* 1.3 76.3 - - - +
614A LYS* 1.3 60.0 + - + +
616A LEU* 3.3 4.6 + - - +
617A GLU* 2.9 51.6 + - + +
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Residues in contact with LYS 614 (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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610A ALA* 3.0 25.2 + - - +
611A THR* 3.7 11.7 - - + +
612A MET 3.3 0.4 - - - -
613A ARG* 1.3 79.4 - - + +
615A ARG* 1.3 57.6 + - - +
617A GLU* 3.4 4.6 + - - +
618A ALA* 3.0 29.5 + - - +
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Residues in contact with ARG 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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607A MET* 5.9 0.6 - - - +
611A THR* 3.1 14.3 + - + +
612A MET 3.6 6.7 - - - +
614A LYS* 1.3 73.6 - - - +
616A LEU* 1.3 64.3 + - - +
618A ALA* 3.3 6.3 + - - +
619A GLN 3.1 3.8 + - - -
620A GLY* 2.9 58.9 + - - -
621A TYR* 3.5 30.3 - - + +
626A GLU* 3.2 29.1 + - - +
630A ASP* 3.0 30.6 + - - -
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Residues in contact with LEU 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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568A THR* 4.0 14.3 + - + +
571A LEU* 3.5 44.9 - - + +
572A ARG* 3.6 18.2 - - + +
575A LEU* 3.9 22.9 - - + -
612A MET 2.8 19.4 + - - +
613A ARG* 3.4 7.4 - - - +
615A ARG* 1.3 73.9 - - - +
617A GLU* 1.3 86.2 + - + +
619A GLN* 2.8 26.2 + - - +
621A TYR* 3.6 14.3 - - + -
627A PHE* 4.3 5.4 - - + -
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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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568A THR* 5.1 1.9 - - - +
572A ARG* 2.8 46.9 + - - +
613A ARG* 2.9 39.6 + - + +
614A LYS* 4.0 4.7 - - - +
616A LEU* 1.3 92.2 - - + +
618A ALA* 1.3 59.9 + - - +
619A GLN* 3.1 8.5 + - - +
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Residues in contact with ALA 618 (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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614A LYS 3.0 18.7 + - - +
615A ARG* 3.7 7.2 - - - +
616A LEU 3.2 0.4 - - - -
617A GLU* 1.3 73.1 - - - +
619A GLN* 1.3 68.8 + - - +
620A GLY* 3.3 3.2 + - - +
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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