Contacts of the helix formed by residues 830 - 844 (chain A) in PDB entry 1Q1O
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 830 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A PHE* 3.8 13.7 - - - -
829A GLY* 1.3 82.4 + - - +
831A ASP* 1.3 70.4 + - - +
832A GLU* 4.3 4.5 - - - -
833A ASP* 2.9 39.9 + - - +
834A TRP 3.6 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 831 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A PHE* 3.7 30.7 - - + +
792A ASP* 5.5 1.9 - - - +
830A SER* 1.3 70.7 - - - +
832A GLU* 1.3 73.0 + - - +
834A TRP* 3.0 16.8 + - - +
835A ASN* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 832 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A SER* 3.4 5.3 - - - -
831A ASP* 1.3 84.4 - - - +
833A ASP* 1.3 63.3 + - - +
835A ASN* 3.2 12.6 + - + +
836A VAL* 3.1 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A TYR* 4.1 16.2 + - - -
827A VAL 3.2 22.4 - - - +
828A LEU* 3.6 18.5 - - + +
829A GLY 4.7 0.2 - - - -
830A SER* 2.9 37.7 + - - +
831A ASP 3.1 0.8 - - - -
832A GLU* 1.3 82.1 - - - +
834A TRP* 1.3 58.9 + - - +
836A VAL* 3.7 7.2 + - - +
837A ALA* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 834 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ILE* 4.3 11.4 - - + -
764A PHE* 4.1 18.4 - + - -
785A VAL* 4.0 21.5 - - + -
786A GLU 4.3 9.4 - - - -
789A TRP* 3.7 13.8 + - + -
790A ASN* 3.9 22.5 - - - +
791A PHE* 3.9 15.0 - - + -
794A LEU* 3.5 32.5 - - + -
828A LEU* 3.9 12.7 - - + +
830A SER 3.6 6.1 + - - +
831A ASP 3.0 11.9 + - - +
833A ASP* 1.3 78.3 - - - +
835A ASN* 1.3 69.4 + - - +
837A ALA* 3.2 24.5 + - + +
838A LYS* 3.3 52.9 + - + +
841A LEU* 6.1 2.9 - - + -
849A LEU* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 835 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A ASP* 3.3 18.2 + - - +
832A GLU* 3.2 16.0 + - + +
834A TRP* 1.3 84.2 - - - +
836A VAL* 1.3 62.9 + - + +
838A LYS* 3.3 33.7 + - - +
839A GLU* 3.3 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A TYR* 5.4 6.5 - - - +
832A GLU* 3.1 21.7 + - + +
833A ASP* 4.1 6.1 - - - +
835A ASN* 1.3 75.9 - - + +
837A ALA* 1.3 59.8 + - - +
839A GLU* 3.1 11.3 + - + -
840A MET* 2.8 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A TYR* 4.5 25.1 + - + -
828A LEU* 4.7 3.8 - - + -
833A ASP 3.2 12.5 + - - +
834A TRP* 3.2 30.4 + - + +
836A VAL* 1.3 79.3 - - - +
838A LYS* 1.3 60.4 + - - +
840A MET* 3.2 21.7 - - - +
841A LEU* 3.4 18.1 + - + +
849A LEU* 5.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ILE* 5.0 7.2 - - + -
787A LYS* 3.7 40.3 + - + +
789A TRP 4.1 5.9 + - - -
834A TRP* 3.3 59.3 + - + +
835A ASN* 3.6 26.7 - - - +
836A VAL 3.2 0.6 - - - -
837A ALA* 1.3 73.2 - - - +
839A GLU* 1.3 57.4 + - + +
840A MET 3.1 5.1 + - - -
841A LEU* 3.4 9.9 + - + +
842A ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A ASN* 3.3 14.8 + - + +
836A VAL* 3.1 14.9 + - + +
838A LYS* 1.3 77.8 - - + +
840A MET* 1.3 61.2 + - - +
842A ALA* 3.6 9.7 - - - +
843A GLU* 3.3 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A TYR* 3.6 28.0 - - + -
819A GLN 3.1 27.6 - - - +
820A ASP* 3.8 17.7 - - + -
821A GLU* 4.3 10.3 - - + +
836A VAL* 2.8 13.5 + - + +
837A ALA* 3.2 15.7 - - - +
838A LYS 3.1 0.2 - - - -
839A GLU* 1.3 78.5 - - - +
841A LEU* 1.3 63.2 + - + +
843A GLU* 4.2 0.4 - - - -
844A ASN* 3.0 43.4 + - - +
846A GLU* 3.7 23.3 - - - +
849A LEU* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ILE* 3.9 34.3 - - + -
764A PHE* 5.7 0.7 - - + -
834A TRP* 6.1 2.5 - - + -
837A ALA* 3.4 19.4 + - + +
838A LYS* 4.2 7.4 - - + +
840A MET* 1.3 76.8 - - - +
842A ALA* 1.3 60.0 + - - +
844A ASN 3.9 0.2 - - - -
845A ASN* 2.9 7.6 + - - -
846A GLU* 2.8 71.3 + - + +
847A LYS* 5.4 0.9 - - - -
848A PHE 3.6 10.8 - - - +
849A LEU* 3.5 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A LYS 3.0 18.8 + - - +
839A GLU* 3.6 13.5 - - - +
840A MET 3.1 0.4 - - - -
841A LEU* 1.3 77.7 - - - +
843A GLU* 1.3 63.1 + - + +
845A ASN* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A GLU* 3.3 16.7 + - - +
840A MET* 4.3 1.6 - - - +
842A ALA* 1.3 78.0 - - + +
844A ASN* 1.3 66.2 + - - +
845A ASN* 3.1 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A GLU* 4.3 20.0 - - - +
840A MET* 3.0 34.4 + - - +
843A GLU* 1.3 80.4 - - - +
845A ASN* 1.3 68.4 + - - +
846A GLU* 2.9 36.6 + - - +
----------------------------------------------------------
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