Contacts of the helix formed by residues 581 - 596 (chain C) in PDB entry 3QHE
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 581 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C GLU* 2.8 31.3 + - + +
539C ASP* 3.0 29.2 + - - +
579C VAL* 3.4 6.9 - - - +
580C LYS* 1.3 80.7 - - + +
582C GLU* 1.3 65.7 + - - +
583C SER* 4.0 15.9 + - - +
584C THR* 3.1 16.9 + - - +
585C LEU* 3.2 11.6 + - - +
622C TYR* 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 582 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C LYS 3.9 2.0 + - - -
581C LYS* 1.3 70.9 - - - +
583C SER* 1.3 64.1 + - - +
585C LEU* 3.3 5.7 + - - +
586C LYS* 3.0 25.7 + - + +
622C TYR* 3.4 36.5 + - + +
624C SER* 3.0 23.4 + - - -
625C GLN* 3.3 36.9 + - + +
626C THR* 3.8 15.6 + - - -
628C THR* 5.2 2.9 + - - -
631C ILE* 4.2 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 583 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C ASP* 5.3 1.4 + - - -
542C GLN* 3.4 22.6 + - - +
581C LYS* 4.0 21.7 + - - +
582C GLU* 1.3 79.8 - - - +
584C THR* 1.3 64.5 + - - +
586C LYS* 3.6 10.7 + - - +
587C SER* 3.6 13.5 + - - -
389D GLN* 4.8 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 584 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C GLU* 3.1 49.3 + - - +
539C ASP* 5.2 0.7 + - - -
541C GLN* 3.9 19.1 - - + +
542C GLN* 3.9 13.6 - - - +
579C VAL* 3.6 19.7 - - + -
581C LYS* 3.1 15.1 + - - +
583C SER* 1.3 78.5 + - - +
585C LEU* 1.3 65.1 + - - +
587C SER* 3.2 5.7 + - - -
588C VAL* 3.0 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 585 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C ALA* 3.9 17.7 - - + +
579C VAL* 3.5 16.0 - - + +
581C LYS 3.2 5.5 + - - +
582C GLU 3.7 7.2 - - - +
584C THR* 1.3 78.4 - - - +
586C LYS* 1.3 57.3 + - - +
588C VAL* 4.3 4.9 - - + -
589C LEU* 2.8 60.9 + - + +
615C PHE* 3.7 33.7 - - + -
619C THR* 5.1 1.3 - - + -
622C TYR* 4.0 30.5 - - + +
631C ILE* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 586 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A HIS 5.9 1.3 + - - -
714A LYS* 6.4 0.2 - - - +
549C ARG* 6.3 0.7 - - - +
582C GLU* 3.0 18.6 + - + +
583C SER* 3.7 11.0 - - - +
584C THR 3.2 0.2 - - - -
585C LEU* 1.3 76.7 - - - +
587C SER* 1.3 59.0 + - - +
589C LEU* 4.1 1.3 - - - +
590C SER* 3.0 31.7 + - - -
628C THR* 5.5 5.5 - - - +
630C ALA* 4.0 26.9 - - + +
631C ILE* 3.5 15.6 - - + +
634C SER* 4.5 3.6 + - - +
383D TYR* 3.8 22.0 - - - +
388D SER* 5.1 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 587 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C GLN* 3.3 45.0 + - - -
545C ALA* 3.5 16.7 - - - +
546C SER* 3.5 12.0 + - - +
549C ARG* 5.0 8.2 + - - +
583C SER 3.6 5.4 + - - -
584C THR 3.2 6.5 + - - -
586C LYS* 1.3 76.4 - - - +
588C VAL* 1.3 66.3 + - - +
590C SER* 3.4 8.0 - - - -
591C ALA* 3.2 19.8 + - - +
383D TYR* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 588 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C LEU* 5.2 0.2 - - + -
541C GLN 4.7 1.8 - - - +
545C ALA* 3.7 19.1 - - + -
572C LEU* 3.3 39.5 - - + +
575C CYS* 3.8 22.4 - - - -
576C ALA* 3.7 21.5 - - + +
579C VAL* 4.6 2.0 - - + -
584C THR* 3.0 29.5 + - + +
585C LEU* 3.9 7.0 - - + +
587C SER* 1.3 78.4 - - - +
589C LEU* 1.3 62.6 + - + +
591C ALA* 3.4 3.8 + - - +
592C LEU* 3.1 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 589 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C ALA* 4.2 15.5 - - + -
585C LEU* 2.8 54.0 + - + +
586C LYS* 4.2 1.3 - - - +
588C VAL* 1.3 69.6 - - - +
590C SER* 1.3 54.8 + - - +
592C LEU* 3.2 8.0 + - + -
593C TRP* 2.6 36.4 + - - +
615C PHE* 4.4 7.6 - - + -
616C LEU* 4.7 4.9 - - + -
619C THR* 4.1 12.6 - - + -
631C ILE* 3.9 31.4 - - + +
634C SER* 3.6 15.9 - - - -
635C GLY* 4.2 4.3 - - - +
638C ILE* 3.4 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 590 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C ARG* 3.8 22.9 - - - -
586C LYS 3.0 19.2 + - - -
587C SER* 3.4 8.3 - - - -
589C LEU* 1.3 77.0 - - - +
591C ALA* 1.3 60.7 + - - -
593C TRP* 3.2 9.6 + - - +
594C ASN* 3.1 26.9 + - - +
634C SER* 4.0 6.0 + - - -
382D GLY* 5.3 0.2 - - - -
383D TYR* 2.7 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 591 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C ALA 3.8 4.3 - - - +
548C LEU* 4.1 4.5 - - + +
549C ARG* 3.7 31.6 - - - +
552C SER* 3.6 2.6 + - - -
572C LEU* 3.7 22.7 - - + -
587C SER 3.2 14.1 + - - +
588C VAL 3.7 4.7 - - - +
590C SER* 1.3 78.7 - - - +
592C LEU* 1.3 58.6 + - - +
594C ASN 3.3 1.4 + - - -
595C LEU* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 592 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C VAL* 3.7 27.6 - - + +
572C LEU* 3.7 21.8 - - + -
573C MET* 3.5 41.5 - - + +
576C ALA* 5.2 1.1 - - + -
588C VAL 3.1 12.5 + - - +
589C LEU* 3.4 15.9 - - + +
591C ALA* 1.3 73.5 - - - +
593C TRP* 1.3 67.3 + - - +
595C LEU* 4.4 4.7 - - + -
596C SER* 2.9 29.1 + - - -
606C ILE* 4.3 16.6 - - + -
616C LEU* 4.7 0.2 - - + -
638C ILE* 3.6 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 593 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A HIS* 4.3 15.5 - + - -
589C LEU 2.6 21.2 + - - +
590C SER* 3.2 8.7 + - - +
592C LEU* 1.3 72.9 - - - +
594C ASN* 1.3 59.7 + - - +
596C SER* 2.9 15.8 + - - -
633C GLU* 3.9 14.8 - - + -
634C SER* 3.5 31.2 - - - +
637C GLY* 3.3 29.4 + - - -
638C ILE* 3.5 11.4 - - + +
640C ARG* 5.9 1.2 - - - +
641C ASN* 3.3 7.5 + - - -
675C THR* 3.7 24.9 - - + -
679C ASN* 4.1 13.8 + - - -
380D TYR* 3.3 22.6 + - + +
381D GLU 3.8 4.6 + - - -
382D GLY* 3.4 28.0 - - - +
383D TYR* 4.2 17.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 594 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C ARG* 2.8 33.9 + - - +
552C SER* 3.1 24.3 + - - +
553C TRP* 3.7 9.1 - - - +
590C SER 3.1 8.5 + - - +
591C ALA 3.7 0.9 - - - +
592C LEU 3.3 0.2 - - - -
593C TRP* 1.3 74.0 - - - +
595C LEU* 1.3 63.9 + - - +
597C ALA* 3.1 15.9 + - - +
598C HIS* 3.1 16.9 + - - -
381D GLU* 3.6 11.4 - - + +
382D GLY* 2.6 32.4 + - - -
383D TYR 2.9 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 595 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C LEU* 5.3 4.0 - - + +
552C SER* 3.7 22.2 - - - +
563C LEU* 3.9 24.7 - - + -
568C SER* 3.9 16.8 - - - -
569C VAL* 4.2 18.6 - - + -
572C LEU* 3.4 33.0 - - + -
591C ALA* 2.9 19.3 + - + +
592C LEU* 4.0 5.2 - - + +
594C ASN* 1.3 76.8 - - - +
596C SER* 1.3 58.5 + - - +
597C ALA 3.1 0.2 - - - -
598C HIS* 3.0 30.1 + - + +
602C ASN* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 596 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592C LEU 2.9 16.4 + - - -
593C TRP 2.9 20.4 + - - -
595C LEU* 1.3 76.5 - - - +
597C ALA* 1.3 56.5 + - - +
598C HIS 3.4 0.2 - - - -
599C CYS 4.6 1.0 - - - +
602C ASN* 4.6 4.9 - - - -
603C LYS* 3.3 30.6 - - - +
606C ILE* 3.4 27.1 - - - +
638C ILE* 3.7 10.5 - - - -
641C ASN* 3.1 23.8 + - - +
642C VAL* 4.2 7.0 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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