Contacts of the helix formed by residues 585 - 605 (chain A) in PDB entry 2FY2
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 SER 585 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ASP* 4.2 8.2 + - - -
428A LEU* 5.6 0.4 - - - -
560A TYR* 2.9 16.5 + - - -
577A SER* 4.2 0.2 - - - -
583A ALA 3.8 3.1 + - - -
584A THR* 1.3 76.4 - - - +
586A SER* 1.3 59.6 + - - +
587A SER* 3.7 7.1 + - - -
588A LYS* 3.3 43.9 + - - +
589A PHE* 2.9 25.5 + - - +
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Residues in contact with SER 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ASP* 2.6 43.7 + - - -
394A ILE* 3.8 15.0 - - - +
560A TYR* 4.3 0.7 - - - -
575A ILE* 3.4 27.4 + - - +
576A SER 3.6 1.6 - - - -
577A SER* 2.9 21.1 + - - -
585A SER* 1.3 72.5 + - - +
587A SER* 1.3 57.6 + - - +
589A PHE* 3.3 1.6 + - - +
590A ALA* 2.9 31.7 + - - +
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Residues in contact with SER 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ASP* 4.8 2.2 + - - -
394A ILE* 4.2 20.6 - - - +
585A SER* 3.3 6.6 + - - -
586A SER* 1.3 78.3 - - - +
588A LYS* 1.3 65.3 + - - +
590A ALA* 3.2 5.0 + - - +
591A LYS* 3.0 22.1 + - - +
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Residues in contact with LYS 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU* 3.6 29.9 - - + +
583A ALA 5.9 2.0 + - - +
585A SER* 3.3 26.2 + - - +
587A SER* 1.3 81.8 - - - +
589A PHE* 1.3 58.9 + - - +
591A LYS* 3.2 9.3 + - - +
592A ALA* 2.8 28.4 + - - +
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Residues in contact with PHE 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 4.0 28.5 - - + -
424A ALA* 4.0 8.7 - - + -
425A PHE* 3.7 39.7 - + + -
428A LEU* 3.5 12.9 - - + +
429A HIS* 5.0 0.2 - - - -
537A LEU* 4.5 15.3 - - + -
560A TYR* 3.5 32.3 - + + +
562A ALA* 4.6 11.7 - - + -
575A ILE* 3.7 26.5 - - + -
585A SER 2.9 18.9 + - - +
586A SER 3.8 3.1 - - - +
588A LYS* 1.3 76.7 - - - +
590A ALA* 1.3 63.5 + - - +
592A ALA* 3.2 2.4 + - - +
593A VAL* 2.9 39.8 + - + +
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Residues in contact with ALA 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ILE* 4.3 12.6 - - + -
396A TYR* 4.0 31.6 - - + -
575A ILE* 3.5 23.1 - - + +
586A SER 2.9 17.2 + - - +
587A SER 3.5 5.2 - - - +
589A PHE* 1.3 75.7 - - - +
591A LYS* 1.3 62.3 + - - +
593A VAL* 3.2 6.2 + - - +
594A GLU* 3.1 21.1 + - - +
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Residues in contact with LYS 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A SER 3.0 13.4 + - - +
588A LYS* 3.3 12.1 - - - +
590A ALA* 1.3 77.8 - - - +
592A ALA* 1.3 61.4 + - - +
594A GLU* 3.1 29.7 + - - +
595A GLU* 3.0 54.5 + - - +
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Residues in contact with ALA 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ALA* 3.5 28.9 - - + +
427A ARG* 3.7 12.6 - - + +
428A LEU* 4.4 8.5 - - + -
588A LYS 2.8 15.8 + - - +
589A PHE* 3.2 8.7 + - - +
591A LYS* 1.3 77.9 - - - +
593A VAL* 1.3 53.4 + - - +
595A GLU* 4.1 11.4 - - - +
596A SER* 2.6 37.6 + - - -
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Residues in contact with VAL 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A TYR* 4.9 2.5 - - + -
420A ALA* 5.5 3.4 - - + -
421A LEU* 4.0 11.4 - - + -
424A ALA* 3.7 13.5 - - + -
573A PHE* 3.7 42.2 - - + -
575A ILE* 4.5 4.3 - - + -
589A PHE* 2.9 44.6 + - + +
590A ALA* 3.4 12.1 - - - +
592A ALA* 1.3 75.0 - - - +
594A GLU* 1.3 60.2 + - - +
596A SER* 3.2 3.5 + - - -
597A LEU* 2.9 35.8 + - + +
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Residues in contact with GLU 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A TYR* 2.7 39.1 + - + +
398A PHE* 4.1 15.9 - - + -
590A ALA 3.1 11.2 + - - +
591A LYS* 3.3 38.0 + - - +
593A VAL* 1.3 76.7 - - - +
595A GLU* 1.3 58.9 + - - +
597A LEU* 3.3 2.3 + - - +
598A ILE* 3.0 42.2 + - + +
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Residues in contact with GLU 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ARG* 3.6 32.1 + - - +
591A LYS* 3.0 42.6 + - - +
592A ALA* 3.9 10.3 + - - +
594A GLU* 1.3 78.4 - - + +
596A SER* 1.3 58.0 + - - +
598A ILE* 3.7 6.3 - - - +
599A ASP* 2.8 36.1 + - - +
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Residues in contact with SER 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ALA* 3.5 22.9 - - - -
423A LEU* 3.4 12.0 - - - +
424A ALA* 3.1 20.1 + - - -
427A ARG* 3.3 16.5 + - - +
592A ALA 2.6 21.9 + - - -
593A VAL* 3.5 5.4 - - - -
595A GLU* 1.3 77.6 - - - +
597A LEU* 1.3 56.9 + - - +
599A ASP* 3.4 1.7 + - - +
600A MET* 3.0 36.5 + - - +
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Residues in contact with LEU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PHE* 3.5 45.5 - - + -
401A TYR* 2.6 34.1 + - + +
416A PHE* 4.1 14.4 - - + -
417A ILE* 5.0 2.5 - - + -
420A ALA* 3.5 26.9 - - + -
571A ILE* 4.6 10.8 - - + -
573A PHE* 3.7 25.8 - - + -
593A VAL* 2.9 24.1 + - + +
594A GLU 3.8 1.6 - - - +
596A SER* 1.3 72.8 - - - +
598A ILE* 1.3 61.3 + - - +
600A MET* 3.4 2.5 + - - +
601A ARG* 3.0 19.1 + - - +
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Residues in contact with ILE 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PHE* 4.0 18.8 - - + -
400A ASN* 4.0 13.5 - - + +
594A GLU* 3.0 30.9 + - + +
595A GLU* 3.7 6.5 - - - +
597A LEU* 1.3 74.9 - - - +
599A ASP* 1.3 69.1 + - - +
601A ARG* 3.0 41.7 + - - +
602A ASP* 3.0 30.4 + - - +
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Residues in contact with ASP 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 4.5 6.5 - - + -
427A ARG* 2.7 36.4 + - - +
466A VAL* 4.2 14.2 - - + +
595A GLU* 2.8 20.5 + - - +
596A SER* 3.6 6.5 - - - +
598A ILE* 1.3 80.3 - - - +
600A MET* 1.3 57.5 + - + +
602A ASP* 3.4 10.7 + - - +
603A LEU* 3.0 37.6 + - + +
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Residues in contact with MET 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A PHE* 3.4 53.8 - - + +
419A VAL* 3.6 23.3 - - + -
420A ALA* 3.6 28.7 - - - -
423A LEU* 4.5 3.8 - - + -
462A PHE* 4.2 15.0 - - + -
482A LEU* 4.0 26.9 - - + +
486A ILE* 4.6 1.1 - - + -
596A SER 3.0 21.8 + - - +
597A LEU 3.8 4.3 - - - +
598A ILE 3.2 0.2 - - - -
599A ASP* 1.3 73.4 - - - +
601A ARG* 1.3 65.2 + - - +
603A LEU* 3.3 2.4 + - - +
604A CYS* 3.0 29.1 + - - -
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Residues in contact with ARG 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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400A ASN* 3.1 41.4 + - - +
401A TYR* 3.7 12.0 + - + -
405A PHE* 3.7 32.5 - - + -
597A LEU 3.0 14.1 + - - +
598A ILE* 3.3 31.4 + - - +
600A MET* 1.3 75.5 - - - +
602A ASP* 1.3 89.0 + - - +
604A CYS* 3.0 13.9 + - - +
605A SER* 3.0 20.5 + - - +
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Residues in contact with ASP 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ILE* 3.0 18.8 + - - +
599A ASP* 3.7 12.2 - - - +
601A ARG* 1.3 107.8 + - - +
603A LEU* 1.3 62.9 + - + +
605A SER* 3.1 18.2 + - - +
606A LEU* 3.3 21.0 - - + +
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Residues in contact with LEU 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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462A PHE* 3.8 24.2 - - + -
466A VAL* 4.6 6.3 - - + -
475A ALA* 3.8 23.3 - - + +
478A LYS* 3.8 33.7 - - + +
479A LEU* 3.4 22.3 - - + +
482A LEU* 3.6 25.1 - - + -
599A ASP* 3.0 28.2 + - + +
600A MET* 3.5 7.9 - - - +
601A ARG 3.1 0.2 - - - -
602A ASP* 1.3 78.0 - - + +
604A CYS* 1.3 57.7 + - - +
605A SER 3.1 3.6 + - - -
606A LEU* 3.4 19.1 + - + +
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Residues in contact with CYS 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 4.2 4.2 - - + -
409A GLN* 3.5 42.8 + - + +
416A PHE* 4.3 13.0 - - - -
479A LEU* 4.1 8.7 - - - +
482A LEU* 4.3 12.8 - - - -
483A LYS* 3.9 27.1 - - - +
600A MET 3.0 15.7 + - - +
601A ARG 3.0 9.2 + - - +
603A LEU* 1.3 75.4 - - - +
605A SER* 1.3 58.9 + - - +
606A LEU 3.5 1.1 + - - -
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Residues in contact with SER 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 4.1 15.9 - - - -
601A ARG* 3.0 19.8 + - - +
602A ASP* 3.1 12.3 + - - +
603A LEU 3.0 1.8 - - - -
604A CYS* 1.3 80.8 - - - +
606A LEU* 1.3 65.3 + - - +
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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
------------------------------------------------------------
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