Contacts of the helix formed by residues 738 - 754 (chain D) in PDB entry 1SO2
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 738 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731D TYR* 3.5 15.2 - - - -
732D ARG 3.7 18.8 - - - +
733D ASP* 5.2 1.3 - - - -
734D ILE 2.9 23.4 + - - +
735D PRO* 3.5 17.8 + - - +
736D TYR 2.8 12.5 + - - +
737D HIS* 1.3 73.4 - - - +
739D ARG* 1.3 69.9 + - + +
740D ILE* 3.2 22.3 + - + +
741D HIS* 3.0 30.1 + - - +
742D ALA 3.1 9.5 + - - -
951D TRP* 4.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 739 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692D SER 4.8 2.9 - - - -
693D GLY* 2.8 40.8 + - - +
695D ILE* 4.2 12.8 - - + -
696D LEU* 4.4 7.2 - - + +
728D GLU* 2.7 40.7 + - + +
729D ASN* 3.2 31.7 + - - +
731D TYR* 3.2 33.4 + - + +
733D ASP* 6.3 0.2 - - - +
738D ASN* 1.3 75.1 - - + +
740D ILE* 1.3 60.9 + - + +
742D ALA* 3.2 5.6 + - - +
743D THR* 3.0 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 740 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681D ILE* 3.7 21.4 - - + +
682D PHE* 4.2 18.4 - - + -
685D VAL* 3.9 31.9 - - + -
695D ILE* 4.6 9.6 - - + -
738D ASN* 3.2 20.3 + - + +
739D ARG* 1.3 77.7 - - + +
741D HIS* 1.3 60.3 + - - +
743D THR* 3.4 7.7 + - - -
744D ASP* 2.9 27.5 + - - +
951D TRP* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 741 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477D MG 2.6 22.0 - - - -
736D TYR* 3.1 48.9 - + - +
737D HIS* 3.9 14.8 - + - -
738D ASN* 3.0 12.1 + - - +
740D ILE* 1.3 76.8 - - - +
742D ALA* 1.3 63.0 + - - +
744D ASP* 3.2 5.8 + - - +
745D VAL* 3.0 39.1 + - + +
821D HIS* 4.1 3.4 - + - -
822D ASP* 3.4 19.3 - - + -
936D ALA 5.2 0.2 - - - -
937D ASP* 2.8 27.0 + - - -
939D ASN* 6.0 0.2 - - - -
951D TRP* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 742 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696D LEU* 4.1 16.8 - - + -
731D TYR* 3.5 35.6 - - + +
738D ASN 3.1 7.0 + - - +
739D ARG 3.2 9.2 + - - +
741D HIS* 1.3 75.1 - - - +
743D THR* 1.3 65.1 + - - +
745D VAL* 2.8 6.9 + - - +
746D LEU* 2.8 21.2 + - - +
818D ALA 4.1 10.9 - - - +
819D ALA 4.6 0.2 - - - +
821D HIS* 4.1 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 743 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D PHE* 5.4 3.6 - - + -
681D ILE* 4.1 12.6 - - + -
695D ILE* 3.9 12.5 - - + +
696D LEU* 3.3 33.0 + - - +
699D VAL* 3.7 38.6 - - + -
739D ARG 3.0 11.9 + - - -
740D ILE* 3.5 10.8 - - - -
742D ALA* 1.3 76.5 - - - +
744D ASP* 1.3 57.7 + - - +
746D LEU* 3.1 5.5 - - - +
747D HIS* 2.9 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 744 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D PHE* 5.7 1.7 - - - +
681D ILE* 3.9 18.6 - - + +
740D ILE 2.9 16.9 + - - +
741D HIS* 3.5 9.1 + - - +
742D ALA 3.1 0.6 + - - -
743D THR* 1.3 76.6 - - - +
745D VAL* 1.3 62.6 + - - +
747D HIS* 3.5 8.5 + - - +
748D ALA* 3.2 20.3 + - - +
936D ALA 4.6 0.2 - - - +
939D ASN* 2.7 32.0 + - - +
943D LYS* 3.3 20.3 + - - -
951D TRP* 3.7 32.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 745 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741D HIS* 3.0 38.6 - - + +
742D ALA 2.8 6.3 + - - +
744D ASP* 1.3 73.7 - - - +
746D LEU* 1.3 67.2 + - - +
748D ALA* 3.2 3.2 + - - +
749D VAL* 3.1 22.0 + - - +
818D ALA* 4.2 13.7 - - + -
821D HIS* 3.7 25.8 - - + +
933D ILE* 4.4 11.2 - - + -
936D ALA* 3.5 39.5 - - + +
937D ASP* 3.8 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 746 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696D LEU* 4.0 14.8 - - + -
699D VAL* 4.1 18.6 - - + -
700D MET* 2.9 52.0 - - + +
703D LEU* 3.6 18.4 - - + -
742D ALA 2.8 11.5 + - - +
743D THR* 3.1 10.5 - - - +
745D VAL* 1.3 76.0 - - - +
747D HIS* 1.3 63.3 + - - +
749D VAL* 2.8 28.1 - - + +
750D TRP* 3.0 7.4 + - + +
815D TYR* 4.1 23.6 - - + +
818D ALA* 3.8 8.9 - - + +
819D ALA* 4.9 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 747 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674D MET* 3.0 52.8 + - + -
676D ASN 3.4 4.2 + - - -
677D TRP* 3.6 28.1 - + - -
679D PHE* 3.2 33.4 - + + +
699D VAL* 5.6 0.2 - - + -
703D LEU* 4.5 4.3 - - - -
743D THR* 2.9 17.2 + - + +
744D ASP* 3.7 10.7 + - - +
746D LEU* 1.3 77.7 - - - +
748D ALA* 1.3 62.1 + - - +
750D TRP* 3.5 9.6 - + - +
751D TYR* 2.9 43.8 + + + +
943D LYS* 4.9 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 748 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677D TRP* 4.2 21.8 - - + -
744D ASP 3.2 11.8 + - - +
745D VAL 3.5 3.1 - - - +
746D LEU 3.2 0.8 - - - -
747D HIS* 1.3 85.1 + - - +
749D VAL* 1.3 57.8 + - - +
751D TYR* 3.6 1.1 - - - +
752D LEU* 2.9 39.0 + - + +
936D ALA* 3.5 27.6 - - + -
939D ASN* 4.3 8.5 - - - +
943D LYS* 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 749 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745D VAL 3.1 10.3 + - - +
746D LEU* 2.8 31.6 - - + +
748D ALA* 1.3 71.4 - - - +
750D TRP* 1.3 75.2 + - - +
752D LEU* 3.1 0.6 + - - -
753D THR* 2.9 27.2 + - - +
814D LEU* 4.0 27.8 - - + -
815D TYR* 3.9 17.0 - - + -
818D ALA* 4.1 11.0 - - + -
932D CYS* 4.1 13.7 - - - -
933D ILE* 4.0 20.4 - - + -
936D ALA* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 750 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671D ILE* 5.3 3.1 - - + -
674D MET* 3.5 29.6 - - + -
675D SER* 4.5 4.3 - - - -
703D LEU* 3.7 43.1 + - + +
706D ASP* 3.5 21.5 + - - -
707D THR* 3.7 21.3 - - + +
746D LEU* 3.0 17.3 + - + +
747D HIS* 3.5 13.9 - + - +
749D VAL* 1.3 83.5 - - + +
751D TYR* 1.3 76.9 + + + +
753D THR* 2.9 12.0 + - - -
754D THR* 3.1 22.2 + - + +
755D ARG* 2.9 44.6 - - - -
789D SER* 3.5 9.6 + - - -
791D SER* 3.5 9.2 - - - -
815D TYR* 3.8 20.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 751 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674D MET 4.1 5.6 - - - -
675D SER 3.4 24.8 + - - -
676D ASN* 3.7 0.4 - - - -
677D TRP* 3.5 49.1 + + + +
747D HIS* 2.9 29.0 + + + +
748D ALA* 3.6 5.4 - - - +
750D TRP* 1.3 93.6 - + + +
752D LEU* 1.3 65.4 + - + +
753D THR 3.4 0.5 + - - -
754D THR* 3.5 5.0 + - - -
755D ARG* 3.0 64.3 - - + +
1010D PRO* 4.7 11.9 - - + -
1060D GLN* 4.9 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 752 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677D TRP* 4.6 11.4 - - + -
748D ALA* 2.9 38.5 + - + +
749D VAL* 3.1 3.1 + - - +
751D TYR* 1.3 73.9 - - + +
753D THR* 1.3 60.3 + - - +
754D THR 3.4 0.2 - - - -
755D ARG 4.6 1.9 + - - -
757D VAL* 4.9 2.8 - - - +
802D LEU* 3.5 16.4 - - - +
932D CYS* 4.0 33.4 - - - +
935D LEU* 4.6 15.5 - - + -
936D ALA* 4.8 3.1 - - + +
1003D TYR* 4.5 8.3 - - + +
1008D LEU 4.6 0.5 - - - +
1009D LEU* 4.2 14.1 - - + -
1010D PRO* 3.8 39.7 - - + +
1061D LEU* 4.4 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 753 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749D VAL 2.9 15.5 + - - +
750D TRP 2.9 9.2 + - - -
752D LEU* 1.3 79.4 - - - +
754D THR* 1.3 56.8 + - - +
755D ARG 3.8 1.1 - - - -
802D LEU* 3.3 19.1 + - + -
803D SER* 2.7 34.1 + - - -
806D ILE* 5.7 0.7 - - + -
811D LEU* 4.1 18.6 - - + -
814D LEU* 3.8 27.4 - - + -
815D TYR* 2.4 30.3 + - - +
932D CYS* 4.0 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 754 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707D THR* 4.6 6.7 - - + -
750D TRP* 3.1 34.6 + - + +
751D TYR 3.5 0.7 + - - -
752D LEU 3.4 0.2 - - - -
753D THR* 1.3 91.0 - - - +
755D ARG* 1.3 87.9 + - - +
787D ILE* 5.5 2.0 - - + -
789D SER* 4.0 16.4 - - - +
792D CYS* 2.9 13.7 - - - -
801D CYS* 4.1 6.8 - - - -
803D SER* 4.0 18.4 - - - -
811D LEU* 5.4 0.2 - - + -
815D TYR* 3.5 9.9 - - - +
----------------------------------------------------------
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