Contacts of the helix formed by residues 599 - 609 (chain E) in PDB entry 4YJL
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 CYS 599 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560E LYS* 6.2 0.2 - - + -
564E ARG* 4.4 7.4 - - - -
596E SER 4.1 0.3 - - - +
597E ALA 3.4 2.7 - - - -
598E HIS* 1.3 83.9 - - - +
600E THR* 1.3 65.1 + - - +
601E GLU* 3.5 31.6 - - - +
602E ASN* 3.3 37.0 + - - +
603E LYS* 3.4 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 600 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599E CYS* 1.3 73.3 - - - +
601E GLU* 1.3 66.7 + - - +
603E LYS* 3.0 17.9 + - + +
604E ALA* 2.9 25.7 + - + +
645E LEU* 3.7 29.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 601 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564E ARG* 3.4 36.6 + - - +
599E CYS* 3.5 29.9 - - - +
600E THR* 1.3 81.7 + - - +
602E ASN* 1.3 55.7 + - - +
604E ALA* 3.3 8.9 + - + +
605E ASP* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 602 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560E LYS 5.7 1.0 + - - -
563E LEU* 6.2 0.2 - - - +
564E ARG* 3.4 30.6 + - - +
569E VAL* 3.6 29.6 - - + +
595E LEU* 3.0 33.2 + - - +
596E SER* 4.6 1.1 - - - -
598E HIS* 3.6 21.2 + - - +
599E CYS* 3.3 22.4 + - - +
600E THR 3.2 0.4 - - - -
601E GLU* 1.3 76.4 - - - +
603E LYS* 1.3 63.0 + - - +
605E ASP* 3.4 3.4 + - - -
606E ILE* 3.2 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 603 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596E SER 2.9 28.7 + - - +
597E ALA* 4.2 0.4 - - - +
599E CYS* 3.6 17.5 - - - +
600E THR* 3.0 16.9 + - + +
602E ASN* 1.3 78.0 - - - +
604E ALA* 1.3 61.5 + - - +
606E ILE* 3.3 4.3 + - - +
607E CYS* 3.1 27.4 + - - -
641E ASN 3.1 22.4 + - - +
642E VAL* 3.9 21.3 - - + +
644E SER* 3.6 16.4 - - - +
645E LEU* 3.6 15.5 - - + -
498J ASP* 2.8 39.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 604 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600E THR* 2.9 13.8 + - + +
601E GLU* 3.6 11.7 - - + +
603E LYS* 1.3 76.4 - - - +
605E ASP* 1.3 59.2 + - - +
607E CYS* 3.3 6.2 + - - +
608E ALA* 2.9 31.0 + - - +
645E LEU* 3.3 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 605 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564E ARG* 2.8 31.4 + - - -
569E VAL* 4.0 13.5 - - + +
570E LYS* 3.3 47.6 + - + +
601E GLU* 2.9 17.7 + - - +
602E ASN* 3.7 7.2 - - - +
603E LYS 3.3 0.2 - - - -
604E ALA* 1.3 76.1 - - - +
606E ILE* 1.3 61.4 + - - +
608E ALA* 3.4 1.4 + - - +
609E VAL* 3.4 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 606 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569E VAL* 3.5 20.2 - - + -
573E MET* 4.1 14.1 - - + -
592E LEU* 4.2 18.2 - - + +
595E LEU* 6.0 0.2 - - + -
596E SER* 3.6 33.2 - - - +
602E ASN 3.2 16.8 + - - +
603E LYS 3.6 6.1 - - - +
604E ALA 3.3 0.2 - - - -
605E ASP* 1.3 76.0 - - - +
607E CYS* 1.3 63.1 + - - +
608E ALA 3.2 0.9 + - - -
609E VAL* 3.3 13.6 + - - +
612E ALA* 3.4 17.2 - - + +
613E LEU* 5.0 0.9 - - + -
616E LEU* 4.0 26.7 - - + -
638E ILE* 4.2 7.9 - - + -
642E VAL* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 607 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603E LYS 3.1 22.6 + - - +
604E ALA* 3.3 7.2 + - - +
606E ILE* 1.3 77.1 - - - +
608E ALA* 1.3 58.4 + - - +
609E VAL 3.4 5.6 + - - +
613E LEU* 4.0 32.8 - - + +
642E VAL* 4.0 19.5 - - - -
645E LEU* 4.7 9.2 - - + -
646E ILE* 4.2 14.1 - - - -
652E HIS* 3.6 35.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 608 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570E LYS* 4.1 13.4 + - - +
604E ALA 2.9 16.9 + - - +
605E ASP* 3.9 5.2 - - - +
606E ILE 3.2 0.6 - - - -
607E CYS* 1.3 76.3 - - - +
609E VAL* 1.3 64.1 + - - +
610E ASP* 3.3 4.3 + - - +
652E HIS* 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 609 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570E LYS* 4.2 23.3 - - + +
573E MET* 3.9 23.8 - - + -
574E GLU* 3.4 33.9 - - + +
577E LEU* 3.9 13.5 - - + -
605E ASP 3.4 16.3 + - - +
606E ILE 3.3 8.4 + - - +
607E CYS 4.0 4.7 - - - +
608E ALA* 1.3 76.8 - - - +
610E ASP* 1.3 73.7 + - - +
611E GLY 3.3 0.9 + - - -
612E ALA* 3.1 24.4 + - + +
613E LEU 4.7 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