Contacts of the helix formed by residues 533 - 547 (chain C) in PDB entry 4RDO
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 PRO 533 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C LEU* 4.3 9.4 - - + -
516C GLU* 3.8 25.8 - - + +
517C ASN* 3.2 34.8 - - + +
531C GLU* 3.9 1.3 - - + +
532C VAL* 1.4 85.9 - - + +
534C LEU* 1.3 62.5 + - - +
535C GLU* 4.5 4.0 - - + +
536C LYS* 3.0 17.9 + - + +
537C ALA 2.8 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 534 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C MET* 4.0 30.7 - - + +
408C LYS* 3.1 41.7 - - - +
409C HIS 4.3 1.8 - - - +
410C GLY 4.4 20.6 - - - +
411C ARG* 5.9 0.4 - - - +
412C VAL* 4.8 8.5 - - + -
532C VAL 3.4 3.4 + - - -
533C PRO* 1.3 72.6 - - - +
535C GLU* 1.3 72.8 + - + +
537C ALA* 3.2 10.7 + - + +
538C LYS* 3.0 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 535 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C PRO* 3.2 3.9 - - + +
534C LEU* 1.3 86.1 - - - +
536C LYS* 1.3 68.1 + - + +
538C LYS* 3.3 33.9 + - - +
539C GLN* 3.4 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C ILE* 3.7 19.7 - - + +
514C ARG 2.9 31.2 - - - +
515C LEU* 4.2 3.1 - - + -
516C GLU* 3.2 21.9 + - - +
532C VAL* 3.8 13.5 - - + -
533C PRO* 3.0 26.1 + - + +
535C GLU* 1.3 81.6 - - + +
537C ALA* 1.3 62.5 + - - +
539C GLN* 3.5 25.5 + - - +
540C VAL* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C VAL* 3.5 42.4 - - + -
458C LEU* 5.3 0.8 - - - +
532C VAL* 3.5 10.5 - - + +
533C PRO 2.8 13.2 + - - +
534C LEU* 3.2 12.5 + - + +
536C LYS* 1.3 75.0 - - - +
538C LYS* 1.3 54.7 + - - +
540C VAL* 3.2 5.0 + - - +
541C LEU* 2.7 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C PHE* 3.6 35.9 - - + +
405C GLN* 3.7 14.3 + - - +
407C MET* 2.9 43.5 + - + -
408C LYS* 5.2 3.2 - - - +
534C LEU* 3.0 23.6 + - + +
535C GLU* 3.3 36.4 + - - +
537C ALA* 1.3 74.8 - - - +
539C GLN* 1.3 59.3 + - + +
541C LEU* 3.3 9.0 + - - +
542C LYS* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C HIS* 5.3 1.4 + - - -
513C ILE* 3.7 32.3 - - + +
535C GLU* 3.4 19.5 + - - +
536C LYS* 3.6 26.9 + - - +
537C ALA 3.2 0.2 - - - -
538C LYS* 1.3 80.1 - - + +
540C VAL* 1.3 60.0 + - - +
542C LYS* 3.8 7.0 - - - +
543C ILE* 3.3 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C LEU* 3.5 26.0 - - + -
467C PHE* 5.7 2.2 - - + -
510C LEU* 4.3 17.7 - - + +
513C ILE* 3.8 20.2 - - + -
523C VAL* 4.3 27.1 - - + -
532C VAL* 5.3 0.9 - - + -
536C LYS 3.1 16.5 + - - +
537C ALA* 3.6 7.0 - - - +
539C GLN* 1.3 71.7 - - - +
541C LEU* 1.3 66.4 + - - +
542C LYS 3.2 0.2 + - - -
543C ILE* 3.3 3.3 + - - +
544C ILE* 3.0 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C PHE* 3.9 34.6 - - + -
407C MET* 4.8 14.6 - - - -
412C VAL* 5.5 2.2 - - + -
456C TYR* 4.8 18.6 - - + -
458C LEU* 3.9 26.7 - - + -
470C VAL* 4.0 24.9 - - + -
501C PHE* 5.1 7.9 - - + -
537C ALA* 2.7 29.9 + - + +
538C LYS* 3.7 6.1 - - - +
540C VAL* 1.3 73.1 - - - +
542C LYS* 1.3 53.6 + - - +
544C ILE* 3.3 4.6 + - + +
545C ALA* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 542 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C GLU* 4.7 16.2 + - - -
401C ASN* 5.2 10.1 + - - +
404C PHE* 3.8 19.5 - - + -
405C GLN* 5.5 7.6 + - - +
538C LYS 2.9 18.1 + - - +
539C GLN* 3.8 7.4 - - - +
540C VAL 3.2 0.2 - - - -
541C LEU* 1.3 77.0 - - - +
543C ILE* 1.3 66.7 + - + +
545C ALA* 3.2 2.8 + - - +
546C SER* 2.9 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 543 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C VAL* 4.6 3.6 - - + -
509C GLN* 3.4 50.2 + - + +
510C LEU* 3.7 25.4 - - + -
512C HIS* 3.7 19.5 - - + +
513C ILE* 4.0 5.8 - - + -
539C GLN* 3.3 17.8 + - + +
540C VAL 3.3 0.4 + - - +
542C LYS* 1.3 78.9 - - + +
544C ILE* 1.3 63.8 + - - +
546C SER* 3.3 6.0 + - - -
547C TYR* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 544 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C LEU* 4.9 2.2 - - + -
467C PHE* 4.8 16.2 - - + -
469C GLY* 5.4 5.6 - - - +
470C VAL* 4.1 31.4 - - + -
501C PHE* 4.3 17.3 - - + -
503C LYS* 2.7 38.6 + - + +
505C VAL* 4.1 32.5 - - + -
510C LEU* 4.5 11.0 - - + -
540C VAL* 3.0 42.5 + - + +
541C LEU* 3.7 4.9 - - - +
543C ILE* 1.3 77.6 - - - +
545C ALA* 1.3 50.8 + - - +
546C SER 3.2 0.7 + - - -
547C TYR* 3.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C ASN* 4.3 10.3 - - - +
404C PHE* 4.1 21.5 - - + -
501C PHE* 4.2 22.7 - - + -
503C LYS* 3.6 10.8 + - - +
541C LEU 2.8 20.4 + - - +
542C LYS 3.8 3.6 - - - +
544C ILE* 1.3 74.1 - - - +
546C SER* 1.3 58.9 + - - +
547C TYR 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C LYS* 2.9 32.8 + - - +
543C ILE* 3.9 5.6 - - - -
544C ILE 3.1 0.2 - - - -
545C ALA* 1.3 78.9 - - - +
547C TYR* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 547 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C LYS* 3.4 24.7 + - + +
504C ASP 3.2 28.0 - - - -
505C VAL* 3.8 20.9 - - + -
506C PRO* 3.1 31.7 - - + +
509C GLN* 3.7 35.2 - - + -
543C ILE 3.1 14.2 + - - +
544C ILE 3.5 3.0 + - - -
545C ALA 3.6 0.4 - - - -
546C SER* 1.3 81.6 - - - +
----------------------------------------------------------
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