Contacts of the strand formed by residues 801 - 810 (chain B) in PDB entry 5M64
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 801 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B MET* 5.4 0.9 - - - -
743B ARG 3.2 13.5 - - - -
744B LEU* 4.2 10.3 - - - -
745B GLN* 5.5 0.2 - - - -
799B GLY 3.4 5.2 + - - -
800B TYR* 1.3 80.3 - - - +
802B THR* 1.3 67.9 + - - +
909B ARG* 3.0 37.9 + - - +
1035B ARG* 5.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 802 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B MET* 5.8 0.4 - - - -
742B TYR* 3.7 1.3 - - - -
743B ARG* 2.9 58.0 + - - +
800B TYR* 3.8 17.0 - - + +
801B GLY* 1.3 79.5 - - - +
803B MET* 1.3 62.0 + - - +
804B TYR* 4.6 2.8 - - - -
906B ARG* 3.7 19.0 + - - -
907B ILE 3.4 10.5 - - - +
908B ARG* 3.4 28.7 - - - +
909B ARG* 4.1 4.0 - - - -
93C GLN* 5.2 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 803 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B LEU 3.2 13.2 - - - +
742B TYR* 3.5 21.3 - - + +
802B THR* 1.3 73.8 - - - +
804B TYR* 1.3 73.8 + - - +
805B LYS* 5.0 11.0 - - - -
878B GLU* 5.1 7.9 - - - +
906B ARG* 3.2 0.7 - - - -
907B ILE* 2.9 73.9 + - + +
908B ARG 5.0 5.6 - - - +
909B ARG* 2.7 43.3 - - + +
1041B ASN* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 804 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B LEU* 3.4 28.9 - - + +
740B LYS* 3.2 9.6 - - - +
741B LEU* 2.8 60.1 + - + +
742B TYR 5.2 0.4 - - - -
743B ARG* 3.1 28.4 + - + -
802B THR* 4.6 3.6 - - - -
803B MET* 1.3 83.3 - - - +
805B LYS* 1.3 68.8 + - - +
806B THR* 4.2 2.5 - - - +
883B GLU* 4.5 5.8 - - + -
904B LYS* 4.4 21.8 - - + +
905B TYR 3.1 15.9 - - - +
906B ARG* 2.5 53.4 + - + -
907B ILE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 805 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739B ASN 3.5 4.0 - - - -
740B LYS* 3.5 35.5 - - + +
742B TYR* 5.4 4.4 + - - -
803B MET* 5.0 11.6 - - - -
804B TYR* 1.3 79.4 - - - +
806B THR* 1.3 62.4 + - - +
807B GLU* 3.5 8.2 + - + +
874B TYR* 4.2 10.3 - - - +
878B GLU* 5.0 9.4 - - - -
905B TYR* 3.1 48.1 + - + -
907B ILE* 3.6 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 806 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 6.4 0.4 - - + -
737B SER* 4.7 14.1 - - - +
738B ASP 3.2 20.1 + - - +
739B ASN* 2.8 19.3 + - - +
740B LYS* 5.4 3.9 + - - +
804B TYR* 5.2 1.6 - - - +
805B LYS* 1.3 68.9 + - - +
807B GLU* 1.3 64.6 + - - +
808B LYS* 5.6 3.5 - - - +
902B SER* 4.9 8.3 - - - -
903B ILE 3.3 22.0 - - - +
904B LYS* 2.8 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B LYS* 6.2 2.7 - - - +
805B LYS* 3.5 10.1 + - + +
806B THR* 1.3 78.9 - - - +
808B LYS* 1.3 63.6 + - - +
873B THR 5.5 1.2 - - - +
874B TYR* 3.1 28.4 + - - -
875B HIS 5.5 2.3 + - - +
902B SER* 3.7 1.2 - - - -
903B ILE* 3.0 34.8 + - + +
905B TYR* 3.4 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.4 44.4 - - - +
806B THR* 5.6 3.2 - - - +
807B GLU* 1.3 78.9 - - - +
809B VAL* 1.3 69.5 + - - +
810B ASP* 4.3 4.4 + - + -
872B LYS* 5.4 1.7 + - - -
900B THR* 4.1 22.2 - - + -
901B VAL 3.7 12.6 - - - +
902B SER* 4.6 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B LYS* 1.3 76.3 - - - +
810B ASP* 1.3 64.4 + - - +
811B LEU* 4.3 10.2 - - + +
825B PHE* 5.7 0.7 - - + -
858B ILE* 5.8 4.7 - - + -
859B CYS* 3.6 39.9 - - + -
872B LYS* 3.9 30.3 - - + +
899B GLN 4.4 0.5 - - - +
900B THR* 4.1 0.5 - - - -
901B VAL* 2.9 54.2 + - + +
902B SER* 5.5 0.2 - - - -
903B ILE* 5.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B LYS* 4.3 5.6 + - + -
809B VAL* 1.3 77.9 - - - +
811B LEU* 1.3 105.3 + - - +
812B ALA 4.3 0.3 + - - -
813B LEU* 2.6 44.8 + - - +
861B TYR* 6.0 0.3 - - - -
872B LYS* 5.1 8.0 - - - +
899B GLN* 3.9 8.2 - - - +
900B THR* 3.7 20.5 + - + +
----------------------------------------------------------
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