Contacts of the helix formed by residues 729 - 740 (chain D) in PDB entry 3A8P
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 729 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D GLU* 6.2 0.2 - - - -
711D LEU* 3.8 14.6 - - - +
722D LEU* 4.9 0.2 - - - +
727D VAL* 3.5 15.4 - - - +
728D LEU* 1.3 77.2 - - - +
730D VAL* 1.3 65.7 + - - +
731D SER* 3.4 11.3 + - - -
732D SER* 2.8 23.1 + - - -
733D PHE* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 730 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708C LYS* 6.4 0.2 - - - -
572D ILE* 4.4 12.3 - - + -
574D GLN* 4.1 19.5 - - + +
687D MET* 4.2 1.5 - - - +
690D PHE* 3.8 18.8 - - + -
707D PRO* 3.5 41.1 - - + +
710D LEU* 3.7 29.6 - - + -
711D LEU* 3.8 13.6 - - + +
729D SER* 1.3 74.4 - - - +
731D SER* 1.3 52.7 + - - +
733D PHE* 3.2 4.0 + - - +
734D HIS* 2.8 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 731 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D ILE* 5.5 0.4 + - - -
574D GLN* 4.3 13.0 - - - +
587D CYS* 3.3 42.1 + - - +
589D SER* 3.7 20.2 + - - -
595D VAL* 3.9 10.3 - - - +
729D SER* 3.1 10.5 + - - -
730D VAL* 1.3 78.7 - - - +
732D SER* 1.3 62.0 - - - +
734D HIS* 3.2 4.3 + - - +
735D ALA* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 732 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517D VAL* 5.6 2.2 - - - -
525D LEU* 4.3 0.7 - - - +
595D VAL* 4.7 4.7 - - - -
722D LEU* 3.7 16.1 - - - +
725D LEU* 4.4 8.3 - - - -
727D VAL* 2.9 32.6 + - - -
728D LEU* 3.6 0.9 - - - -
729D SER* 2.8 37.4 + - - -
731D SER* 1.3 78.0 - - - +
733D PHE* 1.3 56.6 + - - +
735D ALA* 3.2 9.0 + - - +
736D LEU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 733 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D GLU* 3.7 40.8 - - + -
687D MET* 3.4 18.6 - - + -
710D LEU* 3.9 32.5 - - + -
711D LEU* 4.1 8.3 - - + -
713D ALA* 4.3 2.0 - - + -
714D THR* 3.2 42.8 - - + -
718D SER* 4.6 3.6 - - - -
722D LEU* 3.7 16.6 - - + -
729D SER 2.9 17.6 + - - +
730D VAL* 3.4 4.7 - - - +
732D SER* 1.3 77.0 + - - +
734D HIS* 1.3 61.9 + - - +
736D LEU* 3.2 7.3 + - + +
737D VAL* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 734 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D ASP 3.8 19.2 + - - -
572D ILE* 3.7 22.0 - - + +
589D SER* 2.7 42.2 + - - +
590D ASN 3.5 11.6 + - - -
591D SER* 4.8 1.2 - - - -
687D MET* 3.3 32.9 - - + +
691D ARG* 4.7 6.1 + - - -
730D VAL* 2.8 14.3 + - + +
731D SER* 3.4 9.4 - - - +
733D PHE* 1.3 77.1 - - - +
735D ALA* 1.3 58.3 + - - +
737D VAL* 3.1 3.6 + - + +
738D CYS* 2.9 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 735 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517D VAL* 5.0 2.0 - - + -
525D LEU* 3.8 15.3 - - + +
589D SER* 4.9 0.6 - - - -
590D ASN 5.3 1.6 - - - -
593D GLY* 3.5 32.0 - - - +
594D ASP 4.8 0.4 - - - +
595D VAL* 3.8 16.2 - - + -
725D LEU* 6.2 0.2 - - + -
731D SER 3.0 13.4 + - - +
732D SER* 3.5 9.9 - - - +
734D HIS* 1.3 76.6 - - - +
736D LEU* 1.3 61.8 + - - +
738D CYS* 3.4 4.0 + - - +
739D SER* 3.1 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 736 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D LEU* 3.6 14.1 - - + +
718D SER* 3.6 40.4 - - - +
721D ALA* 4.7 12.3 - - + -
722D LEU* 3.9 25.4 - - + -
732D SER 2.9 13.8 + - - +
733D PHE* 3.5 13.2 - - + +
735D ALA* 1.3 74.3 - - - +
737D VAL* 1.3 64.7 + - - +
739D SER* 2.7 27.0 + - - +
740D ARG* 3.5 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 737 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D GLU 4.5 8.5 - - - +
684D LYS* 3.4 41.1 - - + +
687D MET* 4.1 26.7 - - + -
688D ASP* 5.8 0.2 - - - +
733D PHE* 3.0 33.8 + - + +
734D HIS* 3.6 6.7 - - + +
736D LEU* 1.3 75.6 - - + +
738D CYS* 1.3 64.4 + - - +
740D ARG* 3.3 34.2 + - - +
741D ASP* 3.7 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 738 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519D LEU* 5.3 2.1 - - - +
590D ASN 3.5 22.4 - - - -
591D SER* 3.6 27.4 - - - +
592D CYS 5.7 0.4 - - - -
593D GLY* 3.9 11.7 - - - +
734D HIS* 2.9 38.3 + - - +
735D ALA 3.7 5.4 - - - +
736D LEU 3.2 0.2 - - - -
737D VAL* 1.3 74.5 - - - +
739D SER* 1.3 57.9 + - - +
740D ARG 3.0 4.9 - - - -
741D ASP* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 739 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519D LEU* 3.5 41.3 - - - +
523D ARG* 2.9 42.2 + - - +
525D LEU* 4.5 5.1 - - - +
735D ALA 3.1 12.3 + - - -
736D LEU* 2.7 31.7 + - - +
738D CYS* 1.3 75.5 - - - +
740D ARG* 1.3 58.4 + - - +
741D ASP 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 740 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D ARG* 2.8 34.6 + - - +
680D GLN* 3.2 40.1 + - - +
683D GLU* 2.6 30.9 + - - +
684D LYS 5.6 0.2 - - - +
715D SER* 5.1 0.2 + - - -
717D PRO* 6.3 0.2 - - - +
718D SER* 2.7 28.7 + - - +
733D PHE* 5.8 0.2 - - - -
736D LEU* 3.5 36.9 + - + +
737D VAL* 3.3 21.2 + - - +
738D CYS 3.0 1.4 - - - -
739D SER* 1.3 75.7 - - - +
741D ASP* 1.3 63.1 + - - +
----------------------------------------------------------
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