Contacts of the helix formed by residues 579 - 586 (chain f) in PDB entry 5T0J
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 579 (chain f).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544f ARG* 2.5 46.7 + - - +
548f LEU* 3.9 5.7 - - - +
577f THR 5.0 0.2 - - - +
578f ASN* 1.3 94.3 + - - +
580f ALA* 1.3 67.4 + - - +
581f ARG* 3.4 28.7 - - - +
582f LEU* 3.9 19.5 + - + +
583f ALA* 3.6 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 580 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579f ASN* 1.3 77.7 + - - +
581f ARG* 1.3 59.7 + - - +
582f LEU 3.4 0.7 - - - -
583f ALA* 3.5 6.1 + - - +
584f ALA* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 581 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548f LEU* 4.1 31.0 - - + +
552f SER* 4.4 16.4 + - - -
556f HIS* 6.1 2.0 - - - -
579f ASN* 3.4 19.0 - - - +
580f ALA* 1.3 76.9 - - - +
582f LEU* 1.3 59.6 + - + +
584f ALA* 4.5 11.3 - - - +
585f MET* 3.0 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 582 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544f ARG* 5.4 1.8 - - - +
548f LEU* 4.0 25.4 - - + -
570f MET* 4.1 19.1 - - + -
574f GLY 3.7 17.7 - - - +
577f THR 4.5 6.5 - - - +
578f ASN* 4.9 3.6 - - - +
579f ASN* 3.9 25.9 + - + +
580f ALA 3.4 0.4 - - - -
581f ARG* 1.3 77.0 - - - +
583f ALA* 1.3 60.8 + - - +
585f MET* 3.8 12.6 + - + +
586f LEU* 3.2 27.6 + - - +
606f ALA* 5.4 2.9 - - + +
609f LEU* 3.7 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 583 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578f ASN* 5.2 2.7 - - - +
579f ASN 3.6 14.3 + - - +
580f ALA* 3.5 7.3 + - - +
581f ARG 3.2 0.6 - - - -
582f LEU* 1.3 79.4 - - - +
584f ALA* 1.3 63.3 + - - +
586f LEU* 3.3 29.9 + - + +
587f ARG 4.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 584 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580f ALA 2.9 18.3 + - - +
581f ARG* 4.2 13.7 - - - +
583f ALA* 1.3 74.3 - - - +
585f MET* 1.3 64.3 + - - +
586f LEU 3.4 0.5 + - - -
587f ARG* 3.5 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 585 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548f LEU* 6.4 1.3 - - - -
552f SER* 6.1 3.6 - - - -
555f SER* 4.9 9.2 - - - -
556f HIS* 5.7 8.7 - - + +
567f ILE* 5.2 2.5 - - + -
570f MET* 4.7 24.9 - - + -
581f ARG* 3.0 32.3 + - - +
582f LEU* 4.0 15.3 - - + +
583f ALA 3.3 0.4 - - - -
584f ALA* 1.3 72.0 - - - +
586f LEU* 1.3 60.1 + - + +
587f ARG 2.8 21.3 - - - +
589f LEU* 3.2 22.4 - - + +
602f MET* 4.2 24.7 - - + -
606f ALA* 5.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582f LEU 3.2 20.6 - - - +
583f ALA* 3.4 20.4 - - + +
584f ALA 3.2 0.8 - - - -
585f MET* 1.3 79.1 - - + +
587f ARG* 1.3 60.3 + - - +
588f GLN 3.8 0.3 + - - -
589f LEU* 3.6 22.7 + - + +
590f ALA* 4.1 6.4 + - - +
603f VAL* 4.4 8.2 - - + +
606f ALA* 3.9 33.4 - - + +
607f GLN* 3.3 38.8 - - - +
628f LEU* 4.8 9.0 - - + -
----------------------------------------------------------
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