Contacts of the strand formed by residues 846 - 852 (chain B) in PDB entry 2B5L
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 GLY 846 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B PHE* 3.8 8.8 - - - -
833B THR* 3.6 11.4 - - - -
834B ALA* 3.9 4.9 - - - -
835B MET* 4.3 1.8 - - - -
845B GLN* 1.3 75.1 - - - +
847B ARG* 1.3 69.4 + - - +
865B GLU* 4.1 2.1 - - - +
866B VAL* 3.0 29.8 + - - +
868B GLY 3.4 14.0 + - - -
870B VAL* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 847 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B SER* 3.4 22.2 + - - -
768B SER* 4.0 13.7 - - - -
770B LEU* 3.8 22.7 - - + -
771B PHE* 3.9 18.4 - - + -
805B HIS* 5.0 0.4 + - - -
807B PHE* 3.8 4.4 - - - -
808B LEU* 3.8 3.4 - - - +
811B GLU* 2.7 37.9 + - - +
833B THR* 2.9 34.3 + - - +
846B GLY* 1.3 81.2 - - - +
848B ILE* 1.3 72.7 + - - +
849B VAL* 3.0 39.3 - - + +
860B THR* 5.8 0.2 - - - +
863B GLU* 3.5 30.7 + - - +
864B LYS 3.7 9.6 - - - +
866B VAL* 4.2 1.1 - - - -
870B VAL* 3.5 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B ILE* 3.8 24.7 - - + -
831B VAL 3.2 5.6 - - - +
832B GLY* 4.6 1.3 - - - -
847B ARG* 1.3 88.2 - - - +
849B VAL* 1.3 59.6 + - - +
850B VAL* 3.8 6.8 + - + +
863B GLU* 2.4 28.5 + - - +
864B LYS* 3.4 8.3 + - + +
866B VAL* 4.0 8.3 - - + -
870B VAL* 3.8 28.7 - - + -
873B MET* 4.1 9.6 - - - -
880B LEU* 4.2 10.8 - - + -
882B ALA* 4.4 7.9 - - + -
884B ILE* 4.5 1.1 - - + -
891B TYR* 4.2 32.5 - - + +
899B VAL* 5.0 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B HIS* 5.5 0.2 - - - +
807B PHE* 4.4 6.3 - - + -
830B ILE* 3.5 4.2 - - - +
831B VAL 3.0 31.3 + - - +
833B THR* 5.4 2.0 - - + -
847B ARG* 3.0 52.3 - - + +
848B ILE* 1.3 74.2 - - - +
850B VAL* 1.3 62.9 + - - +
851B PHE* 3.2 40.6 - - + -
860B THR* 3.6 23.1 - - + -
862B ALA 3.7 6.5 - - - +
863B GLU* 4.2 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 850 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B LEU* 5.7 2.0 - - + -
828B TYR* 3.2 42.4 - - + -
829B PHE 3.9 2.0 - - - -
830B ILE* 4.2 20.0 - - + +
848B ILE* 4.1 9.2 - - + +
849B VAL* 1.3 76.2 - - - +
851B PHE* 1.3 60.5 + - - +
860B THR* 3.7 1.9 - - - -
861B VAL* 2.7 34.1 + - + +
862B ALA* 3.2 28.5 + - + +
893B TRP* 4.2 17.5 - - + -
899B VAL* 5.1 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 851 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B LEU* 4.1 12.3 - - + -
805B HIS* 3.4 39.9 - + + -
807B PHE* 3.7 10.3 - + - -
828B TYR* 3.1 28.1 - - - +
829B PHE* 2.9 34.5 + - + +
831B VAL* 3.9 19.5 - - + -
849B VAL* 3.2 41.7 - - + -
850B VAL* 1.3 75.4 - - - +
852B GLN* 1.3 62.1 + - - +
858B LEU* 3.9 29.8 - - + -
859B GLN 3.6 4.0 - - - +
860B THR* 3.7 19.7 - - - -
861B VAL* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 852 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826B ASN* 4.0 27.6 + - - +
827B THR 3.6 17.0 - - - +
828B TYR* 3.8 23.3 - - + +
829B PHE* 5.8 0.2 - - - -
851B PHE* 1.3 73.7 - - - +
853B TYR* 1.3 83.5 + - - +
854B SER* 3.6 30.5 + - - -
857B LYS 3.3 1.7 - - - +
858B LEU* 3.2 7.7 - - - -
859B GLN* 2.8 55.8 + - + +
861B VAL* 4.2 7.2 - - + -
897B LYS* 6.0 0.4 - - - +
----------------------------------------------------------
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