Contacts of the helix formed by residues 578 - 587 (chain C) in PDB entry 7ATU
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 578 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C PRO 3.7 0.8 + - - -
577C PRO* 1.3 80.0 + - - +
579C PHE* 1.3 58.6 + - - -
580C PHE 2.7 3.9 + - - -
581C PRO* 2.8 15.4 - - - +
582C ILE* 2.7 39.0 + - - +
607C LEU* 3.4 10.2 - - - +
621C LEU* 3.2 51.5 - - - +
624C LEU* 5.7 1.3 - - - -
625C ASP* 2.8 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 579 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C TRP* 3.8 26.5 - + - -
437C ARG* 4.1 4.9 - - + -
438C VAL* 3.6 26.0 - - + -
441C ALA* 3.8 15.7 - - + -
539C LEU* 3.4 33.4 - - + +
542C ILE* 4.3 8.3 - - + -
543C ILE* 3.3 27.3 - - + +
575C CYS* 5.4 1.6 - - + -
576C PRO* 3.7 20.6 + - + +
577C PRO 2.9 5.6 + - - +
578C SER* 1.3 77.0 + - - +
580C PHE* 1.3 51.5 + - - +
582C ILE* 3.9 6.6 + - + +
583C THR* 2.7 30.5 + - - -
604C LEU* 4.0 10.8 - - + -
607C LEU* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 580 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C CYS* 4.5 0.4 - - - -
543C ILE* 3.8 13.9 - - + +
561C LEU* 4.2 13.5 - - + -
563C VAL* 4.3 9.6 - - + -
566C PHE* 3.2 43.5 - + + -
567C LEU* 4.4 13.2 - - + -
571C CYS* 4.1 21.1 - - + -
575C CYS* 5.8 2.5 - - + -
576C PRO 4.4 4.2 + - - +
578C SER 2.7 4.0 + - - -
579C PHE* 1.3 76.4 - - - +
581C PRO* 1.3 65.9 - - + +
582C ILE 3.3 1.1 - - - -
583C THR* 3.1 18.1 + - + -
584C VAL* 2.8 50.4 + - + +
628C PHE* 4.2 21.8 - + - -
629C TRP* 6.2 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 581 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C PRO 5.5 0.7 - - - +
578C SER* 2.8 31.6 - - - +
580C PHE* 1.3 86.0 - - + +
582C ILE* 1.4 62.5 + - - +
584C VAL* 3.0 3.1 + - - +
585C ARG* 2.9 24.7 + - - +
624C LEU* 3.4 28.3 - - + +
625C ASP* 3.9 11.9 - - - +
628C PHE* 3.8 42.3 - - + -
629C TRP* 5.3 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 582 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C LEU* 4.4 11.4 - - + -
578C SER* 2.7 57.5 + - - +
579C PHE* 3.8 9.0 - - - +
581C PRO* 1.4 71.2 - - - +
583C THR* 1.3 58.4 + - - +
585C ARG* 3.1 7.3 + - - +
586C CYS* 2.8 33.1 + - - -
600C LEU* 3.4 31.0 - - + -
603C TRP* 3.4 29.4 - - + -
604C LEU* 4.7 11.9 - - + -
607C LEU* 4.8 6.3 - - + -
621C LEU* 3.8 12.6 - - + -
624C LEU* 5.7 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 583 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C GLY 3.5 24.0 - - - +
539C LEU* 3.4 23.3 - - + +
540C CYS* 3.5 23.6 - - - +
543C ILE* 3.2 9.8 - - + +
561C LEU* 4.9 0.4 - - + -
579C PHE 2.7 21.6 + - - -
580C PHE* 3.1 21.8 + - + -
582C ILE* 1.3 78.4 - - - +
584C VAL* 1.3 61.5 + - - +
586C CYS* 3.7 6.8 - - - +
587C CYS* 3.3 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 584 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C LEU* 4.2 3.8 - - + -
563C VAL* 4.0 25.1 - - + -
580C PHE* 2.8 44.9 + - + +
581C PRO 3.0 4.5 + - - +
583C THR* 1.3 74.1 - - - +
585C ARG* 1.3 65.8 + - + +
587C CYS* 3.2 15.0 + - - +
588C ASP* 3.5 11.6 + - - +
628C PHE* 3.8 29.8 - - + -
632C TYR* 4.3 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 585 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C PRO 2.9 15.9 + - - +
582C ILE* 3.7 6.1 - - - +
584C VAL* 1.3 76.1 - - + +
586C CYS* 1.3 65.3 + - - +
587C CYS 3.4 0.3 + - - -
588C ASP* 3.4 21.9 + - - +
593C LYS* 3.9 18.9 - - - +
594C ARG* 3.6 9.1 - - - +
595C PRO* 3.6 19.6 - - + +
603C TRP* 4.8 16.2 - - + -
624C LEU* 6.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 586 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C VAL* 3.6 18.9 - - - +
533C PHE* 3.8 7.8 - - - -
535C PHE* 3.8 13.5 - - - -
536C GLY* 3.8 9.0 - - - -
539C LEU* 4.9 0.7 - - - -
582C ILE* 2.8 22.4 + - - +
583C THR* 3.7 8.1 - - - +
585C ARG* 1.3 78.0 - - - +
587C CYS* 1.3 57.1 + - - +
588C ASP 3.2 0.2 - - - -
594C ARG* 3.1 27.5 + - - -
595C PRO* 3.8 8.4 - - - +
600C LEU* 3.6 42.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 587 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C PHE* 3.2 22.7 - - + +
536C GLY* 3.5 31.9 - - - -
537C ILE* 3.8 18.4 - - - -
540C CYS* 4.5 0.9 - - - -
560C GLY* 4.5 2.4 - - - -
561C LEU* 4.1 37.0 + - + -
583C THR 3.3 17.1 + - - +
584C VAL 3.2 8.3 + - - +
585C ARG 3.2 1.4 - - - -
586C CYS* 1.3 75.6 - - - +
588C ASP* 1.3 67.3 + - - +
589C LEU* 3.8 0.5 + - - +
----------------------------------------------------------
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