Contacts of the helix formed by residues 597 - 612 (chain A) in PDB entry 5N6R
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 ASN 597 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A THR* 4.7 12.8 - - + +
548A PHE* 5.9 4.0 - - - -
593A ALA 3.8 8.4 + - - +
594A PHE* 3.1 9.1 + - - +
595A VAL 3.1 0.4 - - - -
596A ASP* 1.3 86.2 + - - +
598A TYR* 1.3 65.3 + - - +
599A GLY 3.3 2.9 - - - -
600A VAL* 3.2 31.3 + - + +
601A ALA* 2.9 23.8 + - - +
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Residues in contact with TYR 598 (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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594A PHE* 3.2 39.4 + + - -
595A VAL* 3.1 34.6 + - + +
596A ASP 3.8 0.2 - - - -
597A ASN* 1.3 76.9 - - - +
599A GLY* 1.3 63.0 + - - +
601A ALA* 3.4 6.2 + - - +
602A MET* 3.2 21.5 + - + +
640A GLU* 4.2 20.6 - - + -
643A LEU* 3.0 23.4 + - + +
644A TYR* 3.0 40.4 + + + +
647A VAL* 4.0 9.1 - - + +
692A ILE* 5.4 9.4 - - + -
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Residues in contact with GLY 599 (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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597A ASN 3.3 0.4 - - - -
598A TYR* 1.3 77.5 - - - +
600A VAL* 1.3 56.5 + - - +
602A MET* 3.1 8.4 + - - +
603A GLU* 2.9 45.0 + - - +
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Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A THR* 4.2 14.1 - - + -
596A ASP 5.5 0.2 - - - +
597A ASN* 3.2 35.6 + - + +
599A GLY* 1.3 73.7 - - - +
601A ALA* 1.3 61.2 + - - +
603A GLU* 3.4 15.7 + - - +
604A MET* 3.2 31.1 + - + +
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Residues in contact with ALA 601 (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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545A THR* 3.9 26.0 - - + +
546A ILE* 3.8 14.7 - - + +
594A PHE* 6.2 3.4 - - + -
597A ASN 2.9 17.0 + - - +
598A TYR* 3.6 7.2 - - - +
599A GLY 3.2 0.2 - - - -
600A VAL* 1.3 74.5 - - - +
602A MET* 1.3 63.6 + - - +
604A MET* 3.0 26.9 - - - +
605A ALA* 3.0 11.7 + - - +
639A LEU* 6.2 0.2 - - - -
643A LEU* 4.9 12.6 - - + -
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Residues in contact with MET 602 (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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598A TYR* 3.2 10.5 + - + +
599A GLY* 3.1 10.1 + - - +
601A ALA* 1.3 77.0 - - - +
603A GLU* 1.3 72.1 + - + +
605A ALA* 4.2 4.7 - - - -
606A GLU* 2.9 53.1 + - + +
638A SER* 5.0 5.2 - - - -
639A LEU* 4.8 7.6 - - + +
640A GLU* 3.6 57.7 - - + +
643A LEU* 5.7 3.3 - - + +
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Residues in contact with GLU 603 (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 GLY* 2.9 30.3 + - - +
600A VAL* 3.6 15.1 + - - +
601A ALA 3.3 0.2 - - - -
602A MET* 1.3 90.7 - - + +
604A MET* 1.3 59.1 + - - +
606A GLU* 3.4 7.0 - - - +
607A LYS* 3.3 38.8 + - - +
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Residues in contact with MET 604 (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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541A GLN 3.8 8.3 - - - +
542A GLN* 3.1 52.7 - - + +
545A THR* 3.6 39.9 - - + +
546A ILE* 4.0 7.4 - - + -
600A VAL* 3.2 19.5 + - + +
601A ALA 3.0 21.3 - - - +
603A GLU* 1.3 74.7 - - - +
605A ALA* 1.3 61.2 + - - +
607A LYS* 3.0 10.8 + - - +
608A CYS* 2.8 33.4 + - - -
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Residues in contact with ALA 605 (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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546A ILE* 3.8 13.2 - - + -
601A ALA 3.0 18.7 + - - +
602A MET* 3.6 2.9 - - - +
604A MET* 1.3 76.7 - - - +
606A GLU* 1.3 62.9 + - - +
608A CYS* 3.2 4.3 + - - +
609A CYS* 3.1 30.3 + - - -
615A PHE* 3.5 8.9 - - + -
639A LEU* 3.5 41.1 - - + -
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Residues in contact with GLU 606 (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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602A MET* 2.9 36.6 + - + +
603A GLU* 3.4 19.0 - - - +
605A ALA* 1.3 74.3 - - - +
607A LYS* 1.3 90.5 + - - +
609A CYS* 3.7 14.9 + - - +
610A GLN* 3.8 19.4 + - - +
638A SER* 5.7 9.0 - - - +
639A LEU* 5.4 1.5 - - - +
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Residues in contact with LYS 607 (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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542A GLN* 5.8 3.6 - - - +
603A GLU* 3.3 28.5 + - - +
604A MET* 3.0 9.3 + - - +
606A GLU* 1.3 92.7 - - - +
608A CYS* 1.3 62.2 + - - +
609A CYS 3.2 0.2 - - - -
610A GLN* 3.2 9.1 + - - +
611A ALA* 2.9 31.2 + - + +
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Residues in contact with CYS 608 (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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538A LEU* 3.5 32.1 - - + -
542A GLN* 3.9 29.8 - - - -
546A ILE* 5.6 0.9 - - - -
604A MET* 2.8 29.0 + - - -
605A ALA* 3.2 6.3 + - - +
607A LYS* 1.3 75.6 - - - +
609A CYS* 1.3 57.6 + - - +
611A ALA* 3.6 6.6 - - - -
612A ASN* 2.9 34.7 + - - +
615A PHE* 3.5 24.7 - - + +
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Residues in contact with CYS 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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605A ALA 3.1 18.5 + - - -
606A GLU* 3.8 9.6 - - - +
607A LYS 3.2 0.4 - - - -
608A CYS* 1.3 74.7 - - - +
610A GLN* 1.3 64.7 + - + +
612A ASN 3.2 16.5 + - - +
615A PHE* 3.5 11.2 - - - -
616A ALA* 3.4 26.4 - - + +
619A SER* 3.2 34.3 - - - -
636A LYS* 4.7 16.2 - - - +
639A LEU* 5.4 3.6 - - - -
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Residues in contact with GLN 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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606A GLU* 3.8 15.0 + - - +
607A LYS* 3.2 8.5 + - - +
609A CYS* 1.3 78.7 - - + +
611A ALA* 1.3 60.9 + - - +
612A ASN 3.5 1.2 + - - -
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Residues in contact with ALA 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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538A LEU* 5.7 3.6 - - + -
607A LYS* 2.9 20.2 + - + +
608A CYS* 3.8 6.1 - - - +
610A GLN* 1.3 78.0 - - - +
612A ASN* 1.3 60.4 + - + +
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Residues in contact with ASN 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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537A VAL* 3.5 44.4 + - - +
538A LEU* 4.7 4.7 - - + -
608A CYS 2.9 12.0 + - - +
609A CYS 3.2 7.3 - - - +
610A GLN 3.4 2.1 - - - -
611A ALA* 1.3 80.6 + - + +
613A ALA* 1.3 59.9 + - - +
614A GLN* 2.8 31.8 + - - +
615A PHE* 3.0 20.6 + - + +
616A ALA 2.9 23.2 + - - -
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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