Contacts of the helix formed by residues 814 - 824 (chain B) in PDB entry 5PWM
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 TRP 814 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B PHE 3.5 9.2 - - - +
796B ALA 3.2 19.3 - - - -
797B SER* 3.3 26.5 - - - +
798B GLU* 3.6 41.4 - - + +
799B PRO* 3.7 14.6 - - + -
812B PRO* 4.0 26.5 - - + -
813B MET* 1.3 86.6 - - - +
815B LEU* 1.3 65.3 + - - +
816B ASN* 3.8 6.0 - - + +
817B LYS* 3.1 60.7 + - + +
818B VAL* 3.1 13.9 + - - +
840B ILE* 3.6 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B LEU* 3.9 10.5 - - + +
786B VAL* 4.1 13.9 - - + -
787B TYR* 3.1 31.1 + - + +
792B SER* 3.7 38.8 - - - +
795B PHE* 2.8 31.4 + - + +
796B ALA* 4.0 4.9 - - - -
814B TRP* 1.3 71.5 - - - +
816B ASN* 1.3 57.4 + - - +
818B VAL* 3.1 5.5 + - - +
819B LYS* 2.9 24.8 + - - +
837B MET* 3.8 25.6 - - + -
840B ILE* 3.7 18.6 - - + +
841B PHE* 5.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 816 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B TYR* 2.6 34.8 + - - -
796B ALA* 2.9 34.2 + - - +
797B SER* 3.8 13.1 + - - +
814B TRP* 3.9 7.6 - - + +
815B LEU* 1.3 76.7 - - - +
817B LYS* 1.3 57.2 + - - +
819B LYS* 3.4 9.5 + - + +
820B THR* 3.0 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 817 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B LYS* 4.8 7.7 - - - +
812B PRO* 3.7 10.5 + - - +
813B MET* 3.5 34.4 - - + +
814B TRP* 3.1 55.4 + - + +
816B ASN* 1.3 76.4 - - - +
818B VAL* 1.3 60.0 + - - +
820B THR* 3.3 6.8 + - + -
821B SER* 2.9 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 818 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B LEU* 4.2 7.0 - - + -
813B MET* 3.7 22.0 - - + -
814B TRP 3.1 13.4 + - - +
815B LEU* 3.6 6.3 - - - +
817B LYS* 1.3 75.9 - - - +
819B LYS* 1.3 62.3 + - - +
821B SER* 3.2 1.8 + - - -
822B LEU* 2.9 22.9 + - - +
827B TYR* 3.8 13.2 - - - +
833B PHE* 3.5 37.9 - - + +
836B ASP* 4.0 13.9 - - + -
837B MET* 3.9 21.3 - - + -
840B ILE* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 819 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B HIS* 2.8 29.5 + - - +
728B CYS* 4.6 3.0 + - - +
729B HIS 4.7 0.6 + - - -
730B ILE* 3.6 39.6 - - + +
783B LEU* 3.7 15.4 - - + +
787B TYR* 3.9 24.3 - - - +
815B LEU 2.9 12.7 + - - +
816B ASN* 3.5 14.5 + - + +
817B LYS 3.3 0.2 - - - -
818B VAL* 1.3 78.0 - - - +
820B THR* 1.3 64.4 + - - +
822B LEU* 3.4 3.9 + - - +
823B ASN* 3.0 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 820 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B ASN 3.0 17.5 + - - -
817B LYS* 3.6 8.1 - - + -
818B VAL 3.3 0.2 - - - -
819B LYS* 1.3 76.7 - - - +
821B SER* 1.3 60.1 + - - +
823B ASN* 3.2 7.5 + - - +
824B GLU* 2.9 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 821 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B MET* 5.9 0.5 - - - +
817B LYS* 2.9 30.7 + - - +
818B VAL 3.2 0.9 + - - -
820B THR* 1.3 76.6 - - - +
822B LEU* 1.3 60.2 + - - +
824B GLU* 3.3 1.3 + - - -
825B GLN 3.1 3.6 + - - -
826B MET* 2.9 48.4 + - - +
827B TYR* 3.5 31.4 + - - -
836B ASP* 4.9 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 822 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A LYS* 5.1 0.5 + - - -
730B ILE* 5.1 2.7 - - + -
771B MET* 3.6 25.8 - - + -
776B GLN* 3.1 40.6 + - - +
779B CYS* 4.1 9.9 - - + -
780B GLU* 4.0 28.5 - - + +
783B LEU* 3.9 26.5 - - + -
818B VAL 2.9 11.5 + - - +
819B LYS* 3.6 7.4 - - - +
821B SER* 1.3 75.4 - - - +
823B ASN* 1.3 62.9 + - - +
825B GLN* 3.1 13.0 + - - +
827B TYR* 3.9 17.2 - - + -
833B PHE* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 823 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A LYS* 5.5 14.6 - - - +
855A ARG* 4.7 1.9 + - - -
731B PRO* 6.0 4.8 - - - +
776B GLN* 5.3 0.2 - - - +
780B GLU* 5.7 1.1 - - - -
819B LYS* 3.0 19.1 + - + +
820B THR* 3.2 8.1 + - - +
822B LEU* 1.3 75.7 - - - +
824B GLU* 1.3 69.4 + - - +
825B GLN* 3.2 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 824 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LYS* 4.9 0.2 + - - -
855A ARG* 3.2 25.1 + - - +
859A GLN* 4.8 2.4 + - - -
820B THR* 2.9 40.5 + - + +
821B SER* 3.3 0.4 + - - -
823B ASN* 1.3 86.5 - - - +
825B GLN* 1.3 70.6 + - - +
826B MET* 3.2 29.4 + - + +
----------------------------------------------------------
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