Contacts of the helix formed by residues 564 - 576 (chain C) in PDB entry 2O1S
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 GLY 564 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C LEU 3.8 3.6 - - - -
438C SER* 3.0 14.6 + - - -
441C ARG* 2.4 30.7 + - - -
557C GLU* 3.6 3.6 - - - -
559C ASN* 3.7 3.8 - - - -
560C ALA 3.5 12.8 - - - -
561C ILE 3.2 5.6 + - - -
562C MSE 3.1 3.8 - - - -
563C GLY* 1.3 76.0 - - - +
565C ALA* 1.3 64.2 - - - -
566C GLY 3.3 2.9 - - - -
567C SER 3.1 2.3 + - - -
568C GLY 3.1 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 565 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C LEU* 4.2 6.5 + - + +
441C ARG* 4.5 1.1 - - - +
511C PHE* 3.7 41.3 - - + -
535C VAL* 3.9 24.5 - - + -
538C LEU* 4.7 2.6 - - - +
557C GLU* 2.8 20.5 + - + +
564C GLY* 1.3 71.0 - - - -
566C GLY* 1.3 61.2 + - - +
568C GLY* 3.0 11.7 + - - +
569C VAL* 3.2 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 566 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555C THR* 3.3 35.1 - - - -
557C GLU* 2.9 18.0 + - - -
565C ALA* 1.3 71.0 - - - +
567C SER* 1.3 66.1 + - - +
569C VAL* 2.9 13.5 + - - +
570C ASN* 3.0 17.2 + - - +
584C ASN* 3.4 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 567 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ARG* 3.1 19.2 + - - -
561C ILE 3.9 5.7 + - - -
563C GLY* 3.8 1.4 - - - -
564C GLY 3.1 13.7 + - - -
566C GLY* 1.3 76.3 - - - +
568C GLY* 1.3 59.7 + - - +
570C ASN* 3.0 25.8 + - - +
571C GLU* 3.1 16.6 + - - +
584C ASN* 4.1 3.0 + - - +
567D SER* 2.6 29.1 + - - -
571D GLU* 2.8 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 568 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ARG* 3.1 21.4 - - - +
538C LEU* 3.4 21.7 - - - +
565C ALA 3.0 9.8 + - - -
567C SER* 1.3 76.4 - - - +
569C VAL* 1.3 60.6 + - - +
571C GLU* 3.3 20.0 + - - +
572C VAL* 3.2 18.7 + - - +
562D MSE 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 569 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C LEU* 4.3 9.6 - - + -
511C PHE* 3.9 20.4 - - + -
538C LEU* 4.2 5.8 - - + -
543C ILE* 3.8 38.4 - - + -
553C LEU* 4.5 9.6 - - + -
555C THR* 3.9 24.0 - - + -
565C ALA 3.2 13.4 + - - +
566C GLY 2.9 8.4 + - - +
568C GLY* 1.3 75.0 - - - +
570C ASN* 1.3 65.2 + - - +
572C VAL* 3.3 3.3 + - - +
573C LEU* 3.2 25.4 + - + +
582C VAL* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 570 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C GLY 3.0 10.6 + - - +
567C SER* 3.0 14.2 + - - +
569C VAL* 1.3 75.4 - - - +
571C GLU* 1.3 58.3 + - - +
573C LEU* 3.3 3.1 + - - +
574C MSE 2.9 35.4 + - - +
582C VAL* 3.6 19.9 - - - +
584C ASN* 2.8 35.4 + - - +
570D ASN* 4.0 16.8 - - + -
571D GLU* 4.0 15.6 - - - +
574D MSE 3.7 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 571 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ARG* 2.4 36.4 + - - -
567C SER 3.1 12.5 + - - +
568C GLY* 3.3 11.2 - - - +
569C VAL 3.1 0.2 - - - -
570C ASN* 1.3 73.6 - - - +
572C VAL* 1.3 67.3 + - + +
574C MSE 3.2 2.9 + - - +
575C ALA* 2.9 26.6 + - - +
561D ILE* 3.7 7.6 - - + +
562D MSE 3.9 19.3 - - - +
563D GLY 2.8 9.9 + - - -
567D SER* 2.7 24.4 + - - +
570D ASN* 4.2 17.5 - - - +
584D ASN* 4.6 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 572 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C LEU* 3.9 16.4 - - + -
540C GLU* 3.6 43.7 - - + +
543C ILE* 4.3 21.5 - - + -
544C LEU* 4.7 2.5 - - + -
568C GLY 3.2 13.1 + - - +
569C VAL 3.3 7.4 + - - +
571C GLU* 1.3 78.3 - - + +
573C LEU* 1.3 65.3 + - - +
575C ALA* 3.2 9.6 + - - +
576C HIS* 3.1 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 573 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C ILE* 3.9 16.6 - - + -
544C LEU* 4.3 15.3 - - + -
547C ALA* 3.7 22.0 - - + -
553C LEU* 4.0 15.3 - - + -
569C VAL* 3.2 12.4 + - + +
570C ASN 3.7 6.7 - - - +
572C VAL* 1.3 79.4 - - - +
574C MSE 1.3 60.4 + - - +
576C HIS* 3.3 7.6 + - - +
578C LYS* 3.0 48.0 + - + +
579C PRO* 5.1 0.4 - - + -
580C VAL* 4.0 12.6 - - + +
582C VAL* 3.5 31.6 - - + -
574D MSE 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 574 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C ASN 2.9 25.1 + - - +
571C GLU 3.7 3.8 - - - +
573C LEU* 1.3 76.7 - - - +
575C ALA* 1.3 62.3 + - - +
577C ARG* 3.4 4.6 + - - +
578C LYS 5.1 0.7 - - - +
579C PRO* 4.4 10.1 - - - -
570D ASN* 3.6 38.8 - - + +
573D LEU* 4.5 8.5 - - + -
574D MSE 4.2 25.6 - - + -
579D PRO* 5.2 1.3 - - + -
580D VAL 3.3 21.1 - - - +
581D PRO* 4.0 6.0 - - - +
582D VAL* 3.3 51.6 - - + +
584D ASN* 4.5 3.1 - - - +
618D TRP* 3.2 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 575 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C GLU 2.9 17.1 + - - +
572C VAL* 3.2 7.1 + - - +
574C MSE 1.3 77.4 - - - +
576C HIS* 1.3 63.0 + - + +
577C ARG 3.3 0.9 - - - -
582D VAL 5.3 0.4 - - - -
583D LEU* 5.6 5.2 - - + +
584D ASN* 5.7 1.3 - - - +
618D TRP* 3.5 21.6 + - - +
621D LEU* 3.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C GLU* 3.1 23.5 + - - +
544C LEU* 3.7 40.2 - - + +
572C VAL* 3.1 38.7 + - + +
573C LEU 3.3 2.0 + - - +
574C MSE 3.3 0.2 - - - -
575C ALA* 1.3 80.8 + - + +
577C ARG* 1.3 71.5 + - - +
578C LYS* 3.0 20.8 + - + +
621D LEU* 4.4 12.4 - - - +
----------------------------------------------------------
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