Contacts of the helix formed by residues 811 - 822 (chain A) in PDB entry 1DQA
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 LEU 811 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A TYR* 3.7 18.4 - - - +
518A ASN 5.7 0.2 - - - +
521A LEU* 3.7 40.4 - - + +
522A VAL* 4.1 9.0 - - + -
526A CYS* 4.1 17.0 - - - -
808A GLY 3.2 9.0 + - - +
809A THR 4.1 0.2 - - - +
810A ASN* 1.3 81.5 - - + +
812A LEU* 1.3 60.0 + - - +
813A PRO* 3.5 3.1 - - + -
814A GLN* 3.3 25.6 + - - +
815A GLN* 3.0 29.2 + - - +
537B PRO* 4.3 10.3 - - + -
558B THR* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 812 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ASN* 5.3 11.9 - - + +
521A LEU* 3.9 23.3 - - + +
810A ASN 3.8 0.4 + - - +
811A LEU* 1.3 69.6 - - - +
813A PRO* 1.3 74.9 - - + +
815A GLN* 3.2 25.4 + - + +
816A ALA* 3.0 21.1 + - - +
511B TYR* 3.7 50.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 813 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A TYR* 4.6 13.2 - - + -
811A LEU* 3.8 3.1 - - + -
812A LEU* 1.3 91.7 - - + +
814A GLN* 1.3 76.6 + - - +
816A ALA* 3.0 19.3 + - + +
817A CYS* 3.3 4.9 + - - -
511B TYR 3.4 23.1 - - - +
512B LEU* 4.6 0.9 - - - +
513B PRO* 4.0 8.5 - - + -
534B MET* 3.6 24.8 - - + +
535B PRO* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 814 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A TYR* 4.7 0.7 + - - -
762A ILE 4.6 2.8 + - - -
763A ALA 3.7 12.8 - - - +
764A CYS 3.7 0.9 - - - -
765A GLY* 3.4 28.9 - - - +
808A GLY 2.9 27.4 - - - +
809A THR* 4.9 1.3 - - - -
811A LEU* 3.3 31.2 - - + +
812A LEU 3.2 0.2 - - - -
813A PRO* 1.3 89.3 - - - +
815A GLN* 1.3 60.3 + - - +
817A CYS* 3.2 4.2 + - - +
818A LEU* 3.1 27.6 + - - +
534B MET* 3.3 21.8 - - - +
535B PRO 3.7 15.1 + - - +
536B ILE* 4.0 9.9 - - - +
558B THR* 4.4 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 815 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A THR 3.0 28.8 + - - +
810A ASN* 3.4 20.7 + - - +
811A LEU 3.0 21.2 + - - +
812A LEU* 3.2 24.5 + - + +
814A GLN* 1.3 73.4 - - - +
816A ALA* 1.3 55.5 + - - +
818A LEU* 3.2 5.1 + - + +
819A GLN* 2.7 48.6 + - - +
824A GLN* 3.6 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 816 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A LEU 3.0 11.5 + - - +
813A PRO 3.0 13.8 + - - +
815A GLN* 1.3 77.6 - - - +
817A CYS* 1.3 55.0 + - - +
819A GLN* 3.3 8.5 + - - +
820A MET* 3.0 31.0 + - - +
508B SER* 3.1 26.5 - - - +
509B LEU* 4.8 0.2 - - - -
511B TYR* 4.1 4.0 - - + -
512B LEU* 3.9 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 817 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL* 4.5 4.0 - - - -
554A PRO* 3.7 23.4 - - + +
763A ALA* 3.3 34.5 - - - +
764A CYS* 4.0 4.7 - - - -
813A PRO 3.3 0.6 + - - -
814A GLN 3.2 2.9 + - - +
816A ALA* 1.3 76.4 - - - +
818A LEU* 1.3 65.1 + - - +
820A MET* 3.3 39.1 + - - +
821A LEU* 3.4 16.3 + - - +
512B LEU* 4.1 10.8 - - - -
534B MET* 3.6 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 818 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A CYS* 3.6 39.5 - - + +
766A GLN* 4.3 1.3 - - - +
804A THR* 4.3 14.8 - - + +
809A THR* 3.7 28.5 - - + +
814A GLN 3.1 17.7 + - - +
815A GLN* 3.2 12.5 + - - +
817A CYS* 1.3 75.5 - - - +
819A GLN* 1.3 61.6 + - - +
821A LEU* 3.2 3.4 + - - -
822A GLY 3.1 4.5 + - - -
823A VAL* 3.1 37.2 + - + +
824A GLN* 3.7 19.7 - - + -
838A LEU* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A GLN* 2.7 33.6 + - - +
816A ALA* 3.6 3.1 - - - +
817A CYS 3.2 0.4 - - - -
818A LEU* 1.3 68.8 - - - +
820A MET* 1.3 64.7 - - - +
821A LEU 3.1 2.2 - - - -
822A GLY* 3.0 14.4 + - - +
824A GLN* 3.4 34.1 + - + +
503B LEU* 6.0 0.2 - - - +
504B SER* 5.0 2.8 + - - -
505B GLU* 4.2 21.9 + - + +
507B SER 4.8 0.5 - - - +
508B SER* 3.4 35.7 + - - +
511B TYR* 6.2 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 820 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A VAL* 5.6 1.8 - - - -
551A PHE* 5.7 0.9 - - - -
552A GLN* 4.3 18.5 + - - +
554A PRO* 3.8 17.9 - - + -
816A ALA 3.0 16.3 + - - +
817A CYS* 3.3 43.9 + - - +
819A GLN* 1.3 76.3 - - - +
821A LEU* 1.3 61.8 + - + +
822A GLY 3.7 0.2 + - - -
499B LEU* 4.6 7.9 - - - -
503B LEU* 4.0 28.3 - - + +
504B SER* 5.3 4.2 + - - -
508B SER* 3.8 16.3 + - - +
509B LEU* 3.6 29.6 - - + -
512B LEU* 3.8 4.5 - - + -
531B ILE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 821 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A PHE* 3.7 34.1 - - + -
552A GLN 3.5 24.0 - - - +
553A VAL* 4.1 9.2 - - + -
554A PRO* 3.9 20.4 - - + -
760A ILE* 5.2 2.0 - - + -
764A CYS* 4.1 14.4 - - - -
817A CYS 3.4 6.3 + - - +
818A LEU 3.2 9.3 + - - +
819A GLN 3.1 0.6 - - - -
820A MET* 1.3 80.0 - - - +
822A GLY* 1.3 59.5 + - - +
823A VAL* 3.6 14.2 + - + +
837A GLN* 5.3 0.2 - - - +
838A LEU* 3.7 28.0 - - + -
841A ILE* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 822 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A LEU 3.1 0.2 + - - -
819A GLN* 3.0 16.7 + - - -
820A MET 3.3 0.8 + - - -
821A LEU* 1.3 77.9 - - - +
823A VAL* 1.3 61.9 + - - +
824A GLN 3.8 1.3 - - - -
834A ASN* 4.1 7.3 + - - +
504B SER* 4.8 11.9 + - - -
----------------------------------------------------------
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