Contacts of the helix formed by residues 560 - 572 (chain C) in PDB entry 3KSA
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 THR 560 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG* 5.4 12.6 - - - -
542C LEU* 5.1 2.0 - - - -
543C TYR* 4.8 5.8 - - - -
558C ALA* 3.8 1.4 - - - +
559C TRP* 1.3 83.3 - - - +
561C ASP* 1.3 63.7 + - - +
562C GLY 2.5 20.2 + - - -
563C GLU* 2.7 18.9 + - - +
564C LEU 4.5 1.6 - - - -
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Residues in contact with ASP 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542C LEU* 5.4 1.6 - - - +
543C TYR* 4.1 21.7 + - - -
560C THR* 1.3 75.9 - - - +
562C GLY* 1.3 65.2 + - - +
563C GLU 3.2 0.2 - - - -
564C LEU* 2.8 26.8 + - - +
565C GLU* 3.2 6.6 + - - +
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Residues in contact with GLY 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560C THR 2.5 7.2 + - - -
561C ASP* 1.3 76.1 - - - +
563C GLU* 1.3 61.6 + - - +
565C GLU* 3.1 19.0 + - - +
566C GLU* 3.5 9.7 + - - +
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Residues in contact with GLU 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C TYR 5.4 0.9 - - - +
558C ALA* 3.8 20.6 - - + -
559C TRP* 3.9 12.1 - - + +
560C THR 2.7 17.1 + - - +
562C GLY* 1.3 70.1 - - - -
564C LEU* 1.3 60.9 + - - +
566C GLU* 3.4 8.0 + - - +
567C LEU* 3.0 23.7 + - - +
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Residues in contact with LEU 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE 5.4 0.4 - - - +
147A ASP* 5.1 6.3 - - - +
543C TYR* 3.2 53.6 - - + +
545C MET* 4.1 24.5 - - + -
558C ALA* 3.9 5.9 - - + +
560C THR 3.8 0.6 + - - -
561C ASP* 2.8 22.1 + - - +
563C GLU* 1.3 79.0 - - - +
565C GLU* 1.3 54.5 + - - +
567C LEU* 3.2 5.0 + - + -
568C ARG* 2.8 29.8 + - + +
577C LEU* 3.9 26.0 - - + -
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Residues in contact with GLU 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561C ASP 3.2 4.7 + - - +
562C GLY* 3.1 12.5 + - - +
564C LEU* 1.3 78.1 - - - +
566C GLU* 1.3 57.1 + - - +
568C ARG* 3.2 8.6 + - - +
569C LYS* 2.9 27.9 + - - +
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Residues in contact with GLU 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C GLY 3.5 6.5 + - - +
563C GLU* 3.4 10.4 + - - +
564C LEU 3.3 0.4 - - - -
565C GLU* 1.3 75.5 - - - +
567C LEU* 1.3 66.1 + - - +
569C LYS* 3.3 8.3 + - - +
570C GLN* 3.0 22.3 + - - +
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Residues in contact with LEU 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C MET* 4.0 17.7 - - + -
556C ALA* 5.1 8.3 - - + -
557C TYR 5.7 3.1 - - - +
558C ALA* 5.1 7.6 - - + -
563C GLU 3.0 14.9 + - - +
564C LEU* 3.5 13.0 - - + +
566C GLU* 1.3 76.3 - - - +
568C ARG* 1.3 55.8 + - - +
570C GLN* 3.2 6.6 + - - +
571C PHE* 3.0 43.5 + - + -
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Residues in contact with ARG 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASP* 5.4 4.9 - - - +
545C MET* 3.8 26.5 - - + +
564C LEU* 2.8 18.6 + - + +
565C GLU* 3.4 12.6 - - - +
567C LEU* 1.3 70.4 - - - +
569C LYS* 1.3 65.0 + - - +
571C PHE* 3.6 1.6 + - - +
572C GLY* 3.3 22.5 + - - +
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Residues in contact with LYS 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565C GLU 2.9 14.3 + - - +
566C GLU* 3.3 12.3 + - - +
568C ARG* 1.3 75.9 - - - +
570C GLN* 1.3 65.4 + - - +
572C GLY* 3.3 8.4 + - - -
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Residues in contact with GLN 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566C GLU 3.0 13.0 + - - +
567C LEU* 3.2 11.4 + - - +
569C LYS* 1.3 78.2 - - - +
571C PHE* 1.3 66.8 + - + +
572C GLY 2.9 6.8 + - - -
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Residues in contact with PHE 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C MET* 3.3 33.9 - - + -
546C SER* 3.8 4.5 - - - -
547C LYS* 3.4 32.2 - - + +
554C GLU* 3.0 33.0 - - + -
555C VAL* 3.9 2.0 - - - -
556C ALA* 3.4 34.1 - - + -
567C LEU* 3.0 28.9 + - + +
568C ARG 4.3 2.2 - - - +
570C GLN* 1.3 84.9 - - + +
572C GLY* 1.3 66.8 + - - +
573C LYS 3.0 9.2 - - - +
575C ALA* 3.6 18.7 - - + +
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Residues in contact with GLY 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C MET* 5.9 0.2 - - - +
568C ARG 3.3 14.6 + - - +
569C LYS 3.3 6.5 + - - -
570C GLN 2.9 8.7 + - - -
571C PHE* 1.3 87.9 - - - +
573C LYS* 1.3 63.2 + - - +
575C ALA* 3.8 10.9 + - - +
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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