Contacts of the helix formed by residues 593 - 609 (chain C) in PDB entry 3S9L
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 LYS 593 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387C ASP* 4.2 12.1 - - + +
589C THR* 4.0 11.7 - - - +
590C ARG* 3.4 29.0 + - - +
592C ASP* 1.3 79.6 + - - +
594C GLU* 1.3 59.3 + - - +
595C ALA 3.4 2.0 - - - -
596C CYS* 4.3 10.1 - - + +
597C VAL* 2.9 32.8 + - + +
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Residues in contact with GLU 594 (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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405C VAL* 5.2 5.6 - - + -
407C VAL* 3.9 21.9 - - + +
589C THR* 4.0 9.9 - - + -
590C ARG 3.2 9.6 + - - +
591C LYS* 3.3 17.7 - - - +
592C ASP 3.1 2.0 - - - -
593C LYS* 1.3 76.1 - - - +
595C ALA* 1.3 65.3 + - - +
597C VAL* 4.1 1.1 - - - +
598C HIS* 3.1 26.3 + - - +
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Residues in contact with ALA 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ASP* 5.2 8.5 - - - +
339C CYS* 5.3 0.2 - - - -
592C ASP 4.2 7.5 + - - +
593C LYS 3.4 0.2 - - - -
594C GLU* 1.3 80.1 - - - +
596C CYS* 1.3 67.9 + - - +
598C HIS* 3.4 8.1 - - - +
599C LYS* 3.2 20.1 + - - +
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Residues in contact with CYS 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ASP* 5.4 2.2 - - - -
339C CYS* 2.0 59.0 - - + -
340C LYS 4.6 3.8 - - - +
342C VAL* 4.6 6.3 - - + -
592C ASP 5.9 0.9 - - - -
593C LYS* 3.9 11.4 + - + +
594C GLU 3.5 0.2 - - - -
595C ALA* 1.3 79.6 - - - +
597C VAL* 1.3 57.5 + - - +
598C HIS 3.0 1.8 - - - -
599C LYS* 2.7 6.0 + - - +
600C ILE* 2.5 43.7 + - + +
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Residues in contact with VAL 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C VAL* 3.9 24.9 - - + -
387C ASP* 5.1 1.1 - - + +
388C ALA* 4.3 13.9 - - + -
407C VAL* 3.8 22.4 - - + -
408C LEU* 4.3 2.9 - - + +
587C VAL* 4.6 3.4 - - + -
589C THR* 3.4 17.0 - - - +
593C LYS* 2.9 30.4 + - + +
594C GLU 4.1 3.1 - - - +
596C CYS* 1.3 77.2 - - - +
598C HIS* 1.3 62.1 - - - +
599C LYS 3.3 0.7 + - - -
601C LEU* 3.4 49.1 + - + +
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Residues in contact with HIS 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C VAL* 3.1 45.0 + - + +
408C LEU* 4.7 9.9 - - + +
594C GLU 3.1 15.3 + - - +
595C ALA* 3.4 8.5 - - - +
596C CYS 3.0 0.4 - - - -
597C VAL* 1.3 83.2 - - - +
599C LYS* 1.3 54.9 + - - +
602C ARG* 3.4 20.6 + - - +
640C LYS* 3.2 28.9 - - + +
641C LEU 3.7 16.8 + - - -
642C HIS* 5.1 2.0 + - - -
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Residues in contact with LYS 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C CYS* 5.3 4.5 - - - -
595C ALA 3.2 13.1 + - - +
596C CYS* 2.7 11.1 + - - +
598C HIS* 1.3 78.3 - - - +
600C ILE* 1.3 68.3 + - + +
601C LEU 3.5 0.4 - - - -
602C ARG* 3.4 6.1 + - - +
603C GLN* 3.2 30.1 + - - +
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Residues in contact with ILE 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C CYS* 4.8 16.2 - - + -
340C LYS 5.1 3.1 - - - +
342C VAL* 3.9 22.7 - - + -
365C LYS* 3.8 34.3 - - + +
366C ILE* 3.6 30.7 - - + -
596C CYS* 2.5 28.4 + - + +
599C LYS* 1.3 70.0 - - + +
601C LEU* 1.3 58.6 + - + +
602C ARG 3.0 4.3 - - - -
603C GLN* 3.0 38.0 + - + +
604C GLN* 3.4 13.1 + - - +
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Residues in contact with LEU 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C VAL* 4.4 11.9 - - + -
344C TRP* 3.3 39.7 - - + -
358C TRP* 4.8 9.9 - - + -
366C ILE* 5.4 3.4 - - + -
408C LEU* 3.6 28.7 - - + -
587C VAL* 4.3 6.5 - - + -
597C VAL* 3.4 33.1 + - + +
600C ILE* 1.3 88.6 - - + +
602C ARG* 1.3 58.9 + - - +
604C GLN* 3.7 10.8 + - - +
605C GLN* 3.2 27.5 + - - +
621C LEU* 5.7 0.5 - - - +
631C PHE* 4.5 1.3 - - + -
638C LEU* 4.1 15.3 - - + +
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Residues in contact with ARG 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C LEU* 5.6 3.3 - - + +
598C HIS 3.4 21.6 + - - +
599C LYS* 3.4 8.6 + - - +
600C ILE 3.0 1.0 - - - -
601C LEU* 1.3 79.7 - - - +
603C GLN* 1.3 61.8 + - + +
604C GLN 3.4 0.2 - - - -
605C GLN* 3.4 21.6 - - - +
606C HIS* 4.1 4.7 + - - +
638C LEU 6.1 0.9 - - - -
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Residues in contact with GLN 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LYS* 5.2 3.8 - - - +
599C LYS* 3.2 14.7 - - - +
600C ILE* 3.0 34.0 + - + +
602C ARG* 1.3 77.6 - - + +
604C GLN* 1.3 65.2 + - + +
605C GLN 3.3 0.4 - - - -
606C HIS* 3.6 12.1 + - - +
607C LEU* 3.6 21.9 + - + +
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Residues in contact with GLN 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C TRP* 3.2 27.5 - - + +
362C SER* 3.3 15.0 - - - +
365C LYS* 4.0 7.3 - - - +
366C ILE* 3.2 23.1 - - + +
600C ILE* 3.4 14.9 - - - +
601C LEU* 4.0 9.0 - - - +
602C ARG 3.4 0.6 - - - -
603C GLN* 1.3 75.3 - - - +
605C GLN* 1.3 57.1 + - - +
606C HIS 3.1 2.0 - - - -
607C LEU* 2.7 11.9 + - - +
608C PHE* 2.5 69.9 + - + -
609C GLY 4.5 0.2 - - - -
621C LEU* 4.3 17.7 - - + -
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Residues in contact with GLN 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C LEU 3.2 16.7 - - - +
602C ARG* 3.4 15.0 - - - +
604C GLN* 1.3 78.7 - - - +
606C HIS* 1.3 56.6 + - - +
608C PHE 4.9 0.2 - - - -
609C GLY* 3.1 27.7 + - - +
610C SER 4.1 4.0 + - - +
621C LEU* 4.8 4.2 - - - +
622C PHE* 3.3 20.8 - - - -
636C VAL 4.4 1.0 + - - -
637C CYS* 3.7 26.3 - - - +
638C LEU* 3.1 48.1 - - + +
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Residues in contact with HIS 606 (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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602C ARG 4.1 3.1 + - - +
603C GLN* 3.6 11.5 + - - +
604C GLN 3.1 0.8 - - - -
605C GLN* 1.3 77.8 - - - +
607C LEU* 1.3 65.6 + - + +
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Residues in contact with LEU 607 (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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361C ASN 6.0 0.7 - - - +
362C SER* 6.5 0.7 - - - -
603C GLN* 3.6 20.0 - - + +
604C GLN* 2.7 11.1 + - - +
606C HIS* 1.3 87.3 - - + +
608C PHE* 1.3 93.6 + - + +
609C GLY 3.8 0.4 - - - -
611C ASP* 4.8 9.6 - - - +
619C PHE 5.0 0.3 - - - +
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Residues in contact with PHE 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C TRP* 4.2 6.1 - - - -
361C ASN* 3.6 50.9 - - + -
362C SER* 4.8 0.2 - - - -
604C GLN* 2.5 47.2 + - - +
607C LEU* 1.3 103.5 - - + +
609C GLY* 1.3 63.3 + - - +
611C ASP* 5.3 5.8 - - - -
618C ASN* 6.3 0.4 - - + -
619C PHE* 3.4 33.0 - + + +
620C CYS* 4.3 1.7 - - - -
621C LEU* 3.2 46.8 + - + +
622C PHE* 4.1 1.9 - - - -
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Residues in contact with GLY 609 (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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604C GLN 3.6 0.8 + - - -
605C GLN* 3.1 25.5 + - - -
606C HIS 4.9 0.2 - - - -
607C LEU 3.8 0.6 - - - -
608C PHE* 1.3 83.0 - - - +
610C SER* 1.3 61.3 + - - -
611C ASP* 3.0 12.4 + - - +
620C CYS* 5.9 2.1 - - - +
622C PHE* 3.5 29.0 - - - -
636C VAL 5.1 0.4 - - - -
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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
------------------------------------------------------------
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