Contacts of the helix formed by residues 568 - 580 (chain C) in PDB entry 4UQJ
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 THR 568 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C ASN* 1.3 67.5 + - - +
570C GLU* 3.4 4.9 - - - +
571C PHE* 3.5 17.1 + - - +
572C GLY* 3.4 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 569 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C THR* 1.3 78.7 - - - +
570C GLU* 1.3 63.8 + - - +
572C GLY* 3.3 9.9 + - - -
573C ILE* 3.4 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 570 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C THR 3.4 2.8 - - - +
569C ASN* 1.3 75.1 - - - +
571C PHE* 1.3 60.8 + - - +
572C GLY 3.0 1.8 - - - -
573C ILE* 2.9 24.2 + - + +
574C PHE* 2.9 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 571 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C THR* 3.6 21.2 - - - +
569C ASN 3.3 0.4 - - - -
570C GLU* 1.3 78.6 - - - +
572C GLY* 1.3 58.5 + - - +
574C PHE* 4.0 5.9 + - - +
575C ASN* 3.4 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 572 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C PHE* 2.9 40.6 - - - -
568C THR 3.4 6.8 + - - -
569C ASN 3.3 9.2 + - - -
570C GLU 3.0 0.4 - - - -
571C PHE* 1.3 80.2 - - - +
573C ILE* 1.3 58.4 + - - +
575C ASN* 3.9 0.9 - - - -
576C SER* 3.0 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 573 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C ASN 3.4 10.1 + - - +
570C GLU* 2.9 14.0 + - + +
572C GLY* 1.3 76.6 - - - +
574C PHE* 1.3 59.5 + - - +
576C SER* 3.3 5.9 + - - -
577C LEU* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 574 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B ARG* 5.6 1.7 - - - +
570C GLU 2.9 13.7 + - - +
571C PHE* 4.3 6.3 - - - +
573C ILE* 1.3 76.5 - - - +
575C ASN* 1.3 58.3 + - - +
577C LEU* 3.5 6.7 + - - +
578C TRP* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 575 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C PHE* 4.2 11.9 - - + -
544C SER* 4.1 22.2 - - - +
571C PHE 3.4 17.5 + - - +
572C GLY* 4.0 3.6 - - - +
573C ILE 3.2 0.6 - - - -
574C PHE* 1.3 75.8 - - - +
576C SER* 1.3 59.6 + - - +
577C LEU 3.1 1.8 - - - -
578C TRP* 2.9 8.7 + - - +
579C PHE* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C SER* 5.4 2.6 - - - +
541C PHE* 3.8 18.5 - - - -
572C GLY 3.0 20.4 + - - -
573C ILE* 3.3 7.2 + - - -
575C ASN* 1.3 77.1 - - - +
577C LEU* 1.3 57.7 + - - +
579C PHE* 4.1 4.6 - - - +
580C SER* 3.2 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B ARG* 5.1 4.3 - - - +
596B LEU* 4.0 36.9 - - + +
573C ILE 3.0 16.3 + - - +
574C PHE* 3.8 7.6 - - - +
575C ASN 3.1 0.2 - - - -
576C SER* 1.3 75.4 - - - +
578C TRP* 1.3 60.2 + - - +
580C SER* 3.8 8.3 - - - -
581C LEU* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 578 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B ARG* 4.3 17.9 - - + -
574C PHE 3.1 13.3 + - - +
575C ASN* 2.9 12.1 + - - +
577C LEU* 1.3 77.9 - - - +
579C PHE* 1.3 59.3 + - - +
580C SER 3.2 0.4 - - - -
581C LEU* 3.2 8.1 + - - +
582C GLY* 2.9 22.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
537C SER* 3.5 33.6 - - - +
540C LEU* 4.4 19.9 - - + +
541C PHE* 4.5 6.7 - - - +
575C ASN 2.8 15.0 + - - +
576C SER* 4.3 4.5 - - - +
578C TRP* 1.3 75.4 - - - +
580C SER* 1.3 57.4 + - - +
581C LEU 3.2 0.2 - - - -
582C GLY* 3.4 5.0 + - - +
583C ALA* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 580 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU* 5.3 6.5 - - - -
533C TYR* 3.3 9.2 + - - -
537C SER* 4.5 6.3 - - - -
576C SER 3.2 20.1 + - - -
577C LEU* 3.8 9.9 - - - -
578C TRP 3.2 0.4 - - - -
579C PHE* 1.3 76.6 - - - +
581C LEU* 1.3 59.3 + - - +
583C ALA* 3.3 8.6 - - - +
584C PHE* 2.8 25.3 + - - +
----------------------------------------------------------
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