Contacts of the helix formed by residues 861 - 872 (chain B) in PDB entry 5YWB
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 ASP 861 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B ARG* 5.3 0.2 + - - -
860B LEU* 1.3 76.8 - - - +
862B VAL* 1.3 66.4 + - - +
863B HIS* 3.4 13.7 - - + +
864B LEU* 3.6 18.4 - - - +
865B SER* 2.6 32.3 + - - -
890B LYS* 5.0 1.3 + - - -
1379B GLY 4.5 3.8 - - - +
1380B ARG* 3.6 6.0 - - - -
1381B THR* 3.3 45.9 + - - +
1385B LYS* 4.2 11.6 + - - -
1507B GLU* 5.3 3.0 - - - +
1538B HIS* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 862 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861B ASP* 1.3 75.9 - - - +
863B HIS* 1.3 77.1 + - + +
865B SER* 3.4 3.6 + - - -
866B ASP* 2.8 50.6 + - - +
890B LYS* 5.9 1.6 - - - +
892B GLN* 5.5 4.3 - - - +
1538B HIS* 3.6 27.6 - - + +
1540B VAL* 4.9 14.6 - - + -
1578B VAL* 5.0 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 863 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861B ASP* 3.4 4.9 - - + -
862B VAL* 1.3 87.5 - - + +
864B LEU* 1.3 64.8 + - + +
866B ASP* 3.3 8.6 + - - +
867B HIS* 2.9 29.5 + - - +
1379B GLY 5.5 2.0 + - - -
1380B ARG* 3.5 62.1 + - + +
1578B VAL* 4.3 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 864 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B SER* 4.1 25.2 + - - +
837B ARG* 3.3 33.2 - - - +
860B LEU* 3.9 14.8 - - + +
861B ASP* 3.6 20.8 + - - +
862B VAL 3.5 0.2 - - - -
863B HIS* 1.3 81.6 - - + +
865B SER* 1.3 57.8 + - - +
867B HIS* 3.4 5.1 + - + +
868B LEU* 2.9 31.7 + - - +
1381B THR* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 865 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B PHE* 4.1 13.6 - - - +
860B LEU* 3.3 24.2 + - - +
861B ASP 2.6 24.2 + - - -
862B VAL* 3.7 4.3 - - - -
863B HIS 3.2 0.6 - - - -
864B LEU* 1.3 77.5 - - - +
866B ASP* 1.3 60.4 + - - +
868B LEU* 3.9 1.4 - - - +
869B MET* 2.9 33.3 + - - +
890B LYS* 4.2 10.8 + - - -
892B GLN* 4.6 2.9 - - - -
893B TYR* 3.8 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 866 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B VAL* 2.8 37.0 + - - +
863B HIS* 3.6 7.8 + - - +
865B SER* 1.3 75.3 - - - +
867B HIS* 1.3 58.2 + - - +
869B MET* 3.8 3.5 - - - +
870B GLN* 2.9 32.6 + - - +
892B GLN* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 867 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B GLU 3.8 23.0 + - - -
805B ALA 3.9 9.6 + - - -
807B SER* 3.1 25.2 + - - +
863B HIS 2.9 16.9 + - - +
864B LEU* 3.9 5.8 - - + +
866B ASP* 1.3 75.6 - - - +
868B LEU* 1.3 56.9 + - - +
870B GLN* 3.9 4.5 - - + +
871B ALA* 2.9 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 868 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B ALA 3.6 22.9 - - - +
806B CYS* 3.9 24.7 - - + +
807B SER* 4.6 4.7 - - - +
837B ARG* 5.4 4.0 - - + -
840B VAL* 4.5 24.0 - - + -
844B LEU* 5.0 8.1 - - + -
856B PRO* 4.6 7.9 - - + +
857B PHE* 4.2 18.4 - - + -
860B LEU* 4.0 21.1 - - + -
864B LEU 2.9 18.3 + - - +
865B SER 3.9 2.7 - - - +
867B HIS* 1.3 78.1 + - - +
869B MET* 1.3 58.4 + - - +
872B GLY* 3.0 27.0 + - - +
873B ILE* 3.6 9.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 869 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B LEU* 6.0 0.2 - - - -
710B MET* 5.6 3.8 - - + -
857B PHE* 4.2 5.6 - - + -
865B SER 2.9 17.9 + - - +
866B ASP* 4.0 2.9 - - - +
868B LEU* 1.3 77.2 - - - +
870B GLN* 1.3 65.6 + - + +
873B ILE* 3.4 34.3 - - + +
874B LEU* 3.2 41.6 + - + +
886B LEU* 5.7 0.4 - - + -
892B GLN* 3.6 17.5 - - + +
893B TYR* 3.4 44.6 - - + -
896B HIS* 4.1 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 870 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866B ASP 2.9 19.7 + - - +
867B HIS* 3.9 3.6 - - + +
869B MET* 1.3 82.2 - - + +
871B ALA* 1.3 60.7 + - + +
874B LEU* 3.4 24.6 - - - +
875B GLU* 3.2 53.4 + - - +
896B HIS* 4.6 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 871 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B ALA* 4.1 22.9 - - + +
867B HIS* 2.9 32.7 + - + +
870B GLN* 1.3 79.3 - - - +
872B GLY* 1.3 59.5 + - - +
875B GLU* 3.1 19.3 - - - +
876B LEU* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 872 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B ALA* 4.3 8.1 + - - +
844B LEU* 4.1 18.2 - - - +
868B LEU* 3.0 12.7 + - - -
871B ALA* 1.3 78.5 - - - +
873B ILE* 1.3 59.1 + - - +
876B LEU* 3.3 10.4 - - - +
877B LEU* 2.6 39.8 + - - +
----------------------------------------------------------
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