Contacts of the helix formed by residues 587 - 606 (chain C) in PDB entry 1RR8
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 587 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A T 3.6 23.8 + - - +
10A T 3.3 30.1 + - - +
116B T 3.5 32.1 - - - +
117B C 2.7 33.9 + - - +
443C LYS* 3.8 20.6 - - - +
487C LEU 6.0 0.7 - - - -
488C ARG* 6.4 1.3 - - - +
489C ALA* 5.1 2.6 - - + +
585C THR* 4.0 6.3 - - - +
586C ALA* 1.3 68.0 - - - +
588C VAL* 1.3 69.3 + - + +
589C PHE 3.2 2.2 - - - -
590C ARG* 3.2 23.8 + - + +
591C THR* 3.3 17.1 + - - -
723C PTR 5.2 3.1 - - + -
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Residues in contact with VAL 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C LYS* 5.2 3.4 - - + +
446C THR* 3.9 28.5 - - + +
447C ALA* 3.8 27.6 - - + +
450C LEU* 3.9 13.0 - - + -
583C GLY 4.5 1.3 - - - +
584C LEU* 3.8 7.9 - - + -
585C THR* 3.4 38.6 - - - +
586C ALA 3.2 0.6 - - - -
587C LYS* 1.3 82.4 - - + +
589C PHE* 1.3 58.4 + - - +
591C THR* 3.4 6.2 + - - -
592C TYR* 2.8 27.9 + - - +
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Residues in contact with PHE 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C LEU* 3.9 31.9 - - + -
454C VAL* 4.5 10.1 - - + -
457C ILE* 4.3 15.0 - - + -
461C TYR* 5.5 1.6 - + - -
479C LEU* 3.9 15.9 - - + -
482C ILE* 3.8 24.9 - - + +
483C ASP* 3.7 36.8 - - + -
577C LEU* 3.9 27.8 - - + -
584C LEU* 4.0 12.8 - - + -
585C THR 4.1 6.5 - - - -
586C ALA* 3.4 18.1 + - - +
587C LYS 3.2 0.4 - - - -
588C VAL* 1.3 78.8 - - - +
590C ARG* 1.3 55.0 + - - +
592C TYR* 3.5 4.5 + + - +
593C ASN* 2.9 38.7 + - - +
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Residues in contact with ARG 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ILE* 5.1 0.8 + - - +
486C ALA* 2.8 40.6 + - + +
487C LEU* 4.2 8.1 - - - +
488C ARG* 3.6 38.7 - - - +
586C ALA 4.3 1.0 + - - +
587C LYS* 3.2 18.2 + - - +
589C PHE* 1.3 76.4 - - - +
591C THR* 1.3 59.7 + - - +
593C ASN* 4.0 1.0 - - - +
594C ALA* 3.1 31.5 + - - +
629C LEU 5.0 0.4 + - - -
630C CYS* 2.8 49.9 + - - +
631C ASN* 5.1 1.6 - - - +
632C HIS* 3.7 0.6 + - - -
723C PTR 2.5 58.0 + - + -
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Residues in contact with THR 591 (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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10A T 4.3 10.6 + - - -
443C LYS* 4.5 17.7 - - - +
444C TYR* 3.7 36.3 - - + -
447C ALA* 3.9 15.3 - - + -
587C LYS* 3.3 13.0 + - - -
588C VAL* 3.4 10.4 + - - -
590C ARG* 1.3 75.5 - - - +
592C TYR* 1.3 64.6 + - - +
594C ALA* 4.0 1.5 - - - +
595C SER* 3.0 25.7 + - - +
722C ASN 5.0 1.1 + - - +
723C PTR 4.1 19.0 - - + +
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Residues in contact with TYR 592 (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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447C ALA* 3.8 24.8 - - + +
450C LEU* 3.9 19.5 - - + -
451C LYS* 3.7 32.4 - - + +
454C VAL* 3.5 29.1 - - + +
458C ARG* 3.8 27.2 + - - -
483C ASP* 4.6 3.6 - - - -
588C VAL 2.8 19.4 + - - +
589C PHE* 3.7 5.2 - + - +
590C ARG 3.3 0.2 - - - -
591C THR* 1.3 76.8 - - - +
593C ASN* 1.3 74.5 + - - +
595C SER* 4.0 0.9 - - - -
596C ILE* 3.0 51.5 + - + +
765C PHE* 4.0 10.2 - + - -
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Residues in contact with ASN 593 (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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458C ARG* 4.6 4.4 - - - +
482C ILE 4.1 3.3 - - - +
483C ASP* 2.7 35.7 + - - +
484C LYS 5.6 0.2 - - - -
486C ALA* 4.2 9.5 - - + +
589C PHE 2.9 23.6 + - - +
590C ARG 4.1 2.7 - - - +
592C TYR* 1.3 91.9 - - - +
594C ALA* 1.3 62.8 + - - +
596C ILE* 3.6 7.1 - - - +
597C THR* 2.7 34.1 + - - -
629C LEU* 4.2 21.4 - - + +
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Residues in contact with ALA 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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590C ARG 3.1 19.3 + - - +
591C THR 4.0 0.9 - - - +
593C ASN* 1.3 78.2 - - - +
595C SER* 1.3 62.7 + - - +
597C THR 3.4 0.2 + - - -
598C LEU 3.2 17.5 + - - -
626C VAL* 3.6 27.3 - - + +
629C LEU* 4.0 5.3 - - - +
630C CYS* 4.0 9.2 - - - -
723C PTR 3.7 25.1 - - + -
724C LEU* 3.3 11.3 - - + +
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Residues in contact with SER 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C TYR* 4.0 4.7 - - - -
591C THR 3.0 16.8 + - - -
594C ALA* 1.3 75.6 - - - +
596C ILE* 1.3 62.2 + - - +
598C LEU* 3.4 2.9 + - - +
599C GLN* 3.2 17.2 + - - +
723C PTR 3.3 10.4 + - - -
724C LEU* 3.8 7.6 - - - +
725C ASP* 3.2 23.9 + - - +
728C ILE* 3.3 21.8 - - - +
765C PHE* 3.7 27.8 - - - -
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Residues in contact with ILE 596 (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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451C LYS* 4.3 15.0 - - + -
592C TYR* 3.0 45.4 + - + +
593C ASN* 3.6 14.4 - - - +
595C SER* 1.3 73.4 - - - +
597C THR* 1.3 64.3 + - - +
599C GLN* 3.5 26.0 + - + +
600C GLN* 3.0 37.0 + - + +
603C LYS* 6.2 0.4 - - - +
765C PHE* 4.1 18.3 - - + +
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Residues in contact with THR 597 (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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593C ASN* 2.7 25.4 + - - -
594C ALA* 3.8 4.3 - - - -
596C ILE* 1.3 76.0 - - - +
598C LEU* 1.3 60.8 + - - +
600C GLN* 4.1 16.9 + - - +
601C GLN* 2.8 45.0 + - + +
625C ALA* 4.5 15.3 - - + +
626C VAL* 4.3 13.9 - - + -
629C LEU* 4.3 17.2 - - + +
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Residues in contact with LEU 598 (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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594C ALA 3.2 13.3 + - - +
595C SER 3.7 7.4 - - - +
596C ILE 3.3 0.2 - - - -
597C THR* 1.3 76.1 - - - +
599C GLN* 1.3 57.0 + - - +
601C GLN* 3.8 1.0 - - - +
602C LEU* 2.9 49.6 + - + +
619C TYR* 4.1 13.5 - - + +
622C ALA* 4.0 22.4 - - + -
623C ASN* 4.1 17.7 - - - +
626C VAL* 3.8 9.5 - - + +
724C LEU* 3.8 35.2 - - + -
728C ILE* 4.0 17.9 - - + -
729C THR* 4.0 19.1 - - - +
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Residues in contact with GLN 599 (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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595C SER 3.2 11.4 + - - +
596C ILE* 3.5 29.3 - - + +
598C LEU* 1.3 79.9 - - - +
600C GLN* 1.3 61.1 + - - +
602C LEU* 3.7 3.4 - - - +
603C LYS* 3.2 49.1 + - + +
728C ILE* 3.9 27.0 - - + +
763C TYR 4.0 7.1 + - - -
764C GLU* 3.6 12.6 - - - +
765C PHE* 2.8 41.0 + - - +
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Residues in contact with GLN 600 (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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596C ILE* 3.0 22.4 + - + +
597C THR* 3.7 19.4 + - - +
599C GLN* 1.3 75.9 - - - +
601C GLN* 1.3 79.4 + - - +
603C LYS* 3.3 19.3 + - - +
604C GLU* 3.1 49.8 + - - +
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Residues in contact with GLN 601 (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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597C THR* 2.8 33.3 + - + +
600C GLN* 1.3 85.9 + - - +
602C LEU* 1.3 58.8 + - - +
604C GLU* 3.8 20.0 + - - +
605C LEU* 2.8 53.4 + - + +
621C ARG 5.1 0.5 - - - +
622C ALA* 3.8 21.3 - - + +
625C ALA* 3.3 23.0 - - + +
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Residues in contact with LEU 602 (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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598C LEU* 2.9 40.5 + - + +
599C GLN 3.7 3.8 - - - +
601C GLN* 1.3 72.5 - - - +
603C LYS* 1.3 65.4 + - + +
605C LEU* 4.6 0.9 - - - +
606C THR* 2.6 34.0 + - - +
618C SER 4.4 1.1 - - - +
619C TYR* 3.7 43.1 - - + -
622C ALA* 3.9 11.2 - - + -
728C ILE* 4.1 15.0 - - + +
732C TRP* 3.7 48.2 + - + +
736C TRP* 5.3 1.0 + - - -
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Residues in contact with LYS 603 (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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596C ILE* 6.2 0.2 - - - +
599C GLN* 3.2 40.3 + - + +
600C GLN* 3.5 16.0 - - - +
602C LEU* 1.3 80.4 - - - +
604C GLU* 1.3 61.3 + - + +
605C LEU 3.7 0.3 + - - -
606C THR 3.9 12.1 - - - +
735C LYS* 5.5 9.0 - - - +
736C TRP* 5.9 3.1 - - - -
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Residues in contact with GLU 604 (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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600C GLN* 3.1 41.2 + - - +
601C GLN* 3.8 21.9 + - - +
602C LEU 3.3 0.2 - - - -
603C LYS* 1.3 80.1 - - + +
605C LEU* 1.3 63.4 + - + +
606C THR 3.7 1.0 - - - +
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Residues in contact with LEU 605 (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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601C GLN* 2.8 40.9 + - - +
602C LEU* 5.2 0.2 - - - -
604C GLU* 1.3 80.5 - - + +
606C THR* 1.3 61.6 + - - +
607C ALA* 3.9 3.5 + - - +
618C SER* 3.2 27.8 + - - +
621C ARG* 3.4 71.8 - - + +
622C ALA* 3.9 7.9 - - - +
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Residues in contact with THR 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 LEU* 2.6 26.8 + - - +
603C LYS 3.9 11.1 - - - +
604C GLU 5.0 0.9 - - - +
605C LEU* 1.3 78.4 - - - +
607C ALA* 1.3 62.1 + - - +
608C PRO* 4.4 1.6 - - - +
615C LYS* 4.1 14.8 - - + -
618C SER* 4.3 9.3 - - - -
732C TRP* 2.9 39.5 + - + +
736C TRP* 3.7 39.1 - - + -
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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
------------------------------------------------------------
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