Contacts of the helix formed by residues 829 - 836 (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 THR 829 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 3.6 35.0 - - + -
828D ARG* 1.3 76.8 - - - +
830D ASN* 1.3 65.2 + - - +
831D ALA* 3.7 9.7 + - - +
832D PHE* 3.0 23.0 + - - +
833D LEU* 3.0 26.5 + - - +
850D LEU* 4.3 5.4 - - - -
959D PHE* 4.9 3.8 - - + -
962D GLN* 2.9 19.9 + - - +
977D MET* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 830 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 5.4 2.4 - - - +
829D THR* 1.3 70.7 - - - +
831D ALA* 1.3 67.2 + - - +
833D LEU* 2.9 8.7 + - - +
834D VAL* 2.8 29.4 + - + +
846D ASP 6.0 1.6 - - - +
848D SER* 4.3 1.5 - - - +
849D VAL* 3.3 18.3 - - + +
850D LEU* 3.0 38.2 + - - +
851D GLU* 3.2 26.9 + - - -
894D ASP* 3.5 15.2 + - - -
896D LYS* 5.8 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 831 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829D THR* 3.9 8.9 - - - +
830D ASN* 1.3 78.7 - - - +
832D PHE* 1.3 56.8 - - - +
834D VAL* 3.4 5.9 + - - +
835D ALA* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 832 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828D ARG* 3.5 24.7 - - + -
829D THR* 3.0 25.2 + - - +
831D ALA* 1.3 76.5 - - - +
833D LEU* 1.3 72.6 + - + +
835D ALA* 3.1 7.7 + - - +
836D THR* 3.0 52.5 + - + +
962D GLN* 3.6 22.4 - - + +
965D GLU* 3.2 34.5 - - + -
966D GLU* 3.7 37.0 - - + -
969D LEU* 4.3 7.6 - - + -
971D LEU* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 833 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826D PRO* 4.7 10.8 - - + -
828D ARG* 4.6 9.2 - - + +
829D THR 3.0 15.3 + - - +
830D ASN* 2.9 9.1 + - - +
832D PHE* 1.3 90.8 - - + +
834D VAL* 1.3 60.0 + - + +
836D THR* 3.2 6.0 + - - -
838D ALA* 2.9 48.2 + - + +
840D GLN* 5.3 12.8 - - + +
841D ALA* 3.4 12.8 - - + +
849D VAL* 4.1 19.3 - - + -
850D LEU* 3.6 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 834 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C LYS* 6.1 5.4 - - + -
883C ARG* 5.7 0.4 - - - +
830D ASN* 2.8 25.6 + - + +
831D ALA* 3.7 6.5 - - - +
833D LEU* 1.3 71.0 - - - +
835D ALA* 1.3 60.3 + - - +
837D ASN* 2.7 33.0 + - - +
841D ALA* 3.9 10.8 - - + -
846D ASP* 3.7 51.1 - - + +
849D VAL* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 835 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A PRO* 5.0 11.8 - - - +
876C HIS* 5.1 9.3 + - - -
880C LYS* 6.0 6.1 - - - -
831D ALA 2.9 19.2 + - - +
832D PHE* 3.5 7.2 - - - +
834D VAL* 1.3 78.6 - - - +
836D THR* 1.3 58.2 + - + +
837D ASN* 3.5 7.4 + - - -
971D LEU* 4.8 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 836 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832D PHE* 3.0 39.7 + - + +
833D LEU* 3.2 11.4 + - - -
834D VAL 2.9 0.2 + - - -
835D ALA* 1.3 76.3 - - - +
837D ASN* 1.3 69.9 + - - +
838D ALA* 3.0 10.0 + - - +
969D LEU* 3.7 29.4 - - + -
971D LEU* 4.2 11.0 - - + -
----------------------------------------------------------
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