Contacts of the helix formed by residues 533 - 540 (chain F) in PDB entry 6X34
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 ASN 533 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472F ARG* 4.7 7.0 + - - +
475F GLN* 3.1 40.8 + - - +
476F SER* 4.0 8.9 - - - +
479F GLN* 5.4 0.8 - - - +
529F LEU 4.4 0.2 - - - +
530F ILE 3.5 10.7 + - - +
531F ARG 3.3 2.4 - - - -
532F GLY* 1.3 77.6 + - - +
534F ARG* 1.3 60.8 + - - +
535F ALA* 2.7 34.4 + - - +
536F ASN* 2.8 39.1 + - + +
537F CYS* 3.2 19.1 + - - -
570F GLU* 4.7 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 534 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532F GLY 4.7 6.1 - - - +
533F ASN* 1.3 75.9 + - - +
535F ALA* 1.3 61.3 + - - +
536F ASN 3.3 1.8 - - - -
537F CYS* 3.2 11.6 - - - -
538F ALA* 2.9 29.1 + - - +
570F GLU* 5.2 17.9 + - + +
571F SER* 5.0 9.1 - - - +
572F PRO* 6.2 1.6 - - - +
573F GLU* 5.6 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 535 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479F GLN* 5.3 8.1 - - + -
533F ASN* 2.7 15.0 + - - +
534F ARG* 1.3 72.7 - - - +
536F ASN* 1.3 61.0 + - - +
538F ALA* 3.6 7.9 - - - +
539F LEU* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 536 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F GLN* 4.7 9.1 + - - +
478F PHE* 6.1 2.2 - - - +
479F GLN* 3.4 23.0 - - - +
484F LEU* 4.1 18.1 - - + +
529F LEU* 3.2 27.4 + - - +
530F ILE* 3.7 24.6 - - + +
533F ASN* 2.8 32.2 + - + +
535F ALA* 1.3 77.7 - - - +
537F CYS* 1.3 56.8 + - - +
539F LEU* 3.3 15.8 - - - +
540F PHE* 3.3 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 537 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530F ILE* 4.5 13.8 - - + +
533F ASN 3.2 18.6 - - - +
534F ARG* 3.2 22.0 - - - -
536F ASN* 1.3 76.3 - - - +
538F ALA* 1.3 63.3 + - - +
539F LEU 3.4 0.2 - - - -
540F PHE* 3.5 14.9 + - - +
541F SER* 3.7 11.1 + - - -
566F CYS 5.4 0.4 - - - +
567F VAL* 4.2 22.5 - - + +
570F GLU* 3.7 23.8 - - + -
571F SER* 4.0 20.6 + - - +
574F VAL* 4.3 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 538 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534F ARG 2.9 20.8 + - - +
535F ALA* 3.2 9.2 + - - +
537F CYS* 1.3 79.0 - - - +
539F LEU* 1.3 60.8 + - - +
541F SER* 3.5 17.9 + - - -
542F ASN 4.9 0.3 + - - -
571F SER* 4.6 7.2 - - - +
573F GLU* 5.0 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 539 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479F GLN* 3.6 31.2 - - + +
484F LEU* 4.6 20.2 - - + -
488F LEU* 6.1 4.3 - - + -
535F ALA* 2.9 22.5 + - + +
536F ASN* 3.3 20.0 - - - +
538F ALA* 1.3 76.0 - - - +
540F PHE* 1.3 68.8 + - + +
541F SER 3.2 4.0 + - - -
542F ASN* 3.7 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 540 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488F LEU* 4.2 32.5 - - + -
526F LEU* 5.4 8.1 - - + -
530F ILE* 5.1 13.5 - - + -
536F ASN 3.3 18.3 + - - +
537F CYS* 3.8 11.9 - - - +
538F ALA 3.3 1.0 - - - -
539F LEU* 1.3 79.7 - - + +
541F SER* 1.3 55.2 + - - +
542F ASN 3.2 5.7 + - - -
543F ASN 3.2 27.1 + - - +
544F LEU* 5.0 5.1 - - + +
546F TRP* 3.9 26.9 - + - -
547F LEU* 4.0 28.9 - - + -
563F VAL* 5.2 8.3 - - + -
567F VAL* 4.1 19.3 - - + -
574F VAL* 5.3 1.5 - - - +
----------------------------------------------------------
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