Contacts of the strand formed by residues 880 - 888 (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 ALA 880 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851B TYR* 3.8 1.3 - - - -
852B VAL* 3.0 36.7 + - + +
874B TYR* 5.8 1.6 - - + +
878B GLU* 3.0 11.8 + - + +
879B PRO* 1.3 74.6 - - - +
881B TYR* 1.3 76.1 + - - +
905B TYR* 5.3 3.1 - - + -
906B ARG 3.2 15.9 - - - +
907B ILE* 3.6 26.5 - - + +
908B ARG 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 881 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849B GLY* 5.6 1.3 - - - -
850B THR 3.1 22.2 - - - +
851B TYR* 3.4 33.5 - + + -
852B VAL* 4.5 1.8 - - - +
880B ALA* 1.3 85.1 - - - +
882B ILE* 1.3 75.0 + - - +
883B GLU* 4.9 4.7 - - - +
905B TYR* 3.3 10.9 - - - +
906B ARG* 2.9 33.0 + - + +
908B ARG* 3.2 32.5 + - - -
93C GLN* 4.8 3.8 - - - -
94C ASP* 4.1 20.4 - - - +
95C GLU* 4.9 3.3 + - + +
67L PHE* 3.2 42.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 882 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B LYS* 4.4 13.0 - - - +
846B PRO* 5.5 0.2 - - + -
847B TYR 3.1 27.4 - - - +
848B ILE* 3.7 15.2 - - + +
849B GLY* 4.2 14.3 + - - +
850B THR* 4.0 14.6 + - - +
852B VAL* 4.4 13.2 - - + -
858B ILE* 5.9 0.7 - - + -
881B TYR* 1.3 82.8 - - - +
883B GLU* 1.3 86.5 + - - +
884B GLU* 3.9 10.1 - - - +
885B VAL* 4.8 0.9 - - + -
903B ILE* 4.1 13.7 - - + -
904B LYS 3.3 10.8 - - - +
905B TYR* 3.5 25.4 - - + +
94C ASP* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 883 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B TYR* 4.5 3.1 - - + -
848B ILE* 3.5 17.4 - - - +
881B TYR* 4.9 2.1 - - - +
882B ILE* 1.3 90.6 - - - +
884B GLU* 1.3 80.6 + - + +
904B LYS* 2.7 42.0 + - + +
905B TYR 4.4 0.9 - - - -
906B ARG* 2.6 66.3 + - + +
94C ASP* 5.4 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 884 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B CYS* 5.2 16.6 - - - +
848B ILE* 4.5 11.6 - - - +
882B ILE* 3.9 2.8 - - - +
883B GLU* 1.3 91.9 - - + +
885B VAL* 1.3 67.8 + - - +
886B ASN* 4.0 21.8 - - - +
903B ILE* 3.2 25.5 - - - +
904B LYS* 3.7 12.6 + - + +
57L LEU* 5.1 8.5 - - + +
58L LYS* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 885 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B LEU* 4.0 36.1 - - + -
846B PRO* 3.7 40.2 - - + +
847B TYR 4.6 5.8 - - - +
848B ILE* 4.9 1.8 - - + +
882B ILE* 4.8 0.9 - - + -
884B GLU* 1.3 83.5 + - - +
886B ASN* 1.3 63.9 + - - +
887B LEU* 3.8 7.3 + - + +
901B VAL* 4.1 14.8 - - + -
902B SER 3.9 4.3 - - - +
903B ILE* 4.5 4.0 - - + -
29L TYR* 5.6 0.2 - - - -
56L LEU 4.1 1.2 - - - +
57L LEU 4.3 0.3 - - - -
58L LYS* 3.7 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 886 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN* 4.0 24.1 + - - +
734B CYS 5.6 2.4 + - - -
736B ARG 5.6 0.5 - - - +
737B SER* 4.9 3.9 + - - -
884B GLU* 4.5 17.8 - - - +
885B VAL* 1.3 75.7 + - - +
887B LEU* 1.3 66.3 + - - +
888B ILE* 3.6 9.8 - - + +
901B VAL* 4.0 2.9 - - - +
902B SER* 3.2 47.7 + - - +
903B ILE* 5.4 1.7 + - - -
904B LYS* 5.5 9.0 + - - +
55L ILE* 5.6 3.9 - - + +
56L LEU 3.8 3.3 + - - +
57L LEU* 4.0 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 887 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B LEU* 4.3 17.5 - - + -
885B VAL* 4.5 5.4 - - + +
886B ASN* 1.3 80.8 - - - +
888B ILE* 1.3 62.3 + - - +
898B LEU* 4.2 22.4 - - + -
900B THR 4.8 0.9 - - - +
901B VAL* 4.3 22.4 - - + -
29L TYR* 3.6 39.3 - - + +
46L VAL* 5.5 1.3 - - + -
54L ARG 3.6 2.9 - - - +
55L ILE* 3.3 8.5 - - - +
56L LEU* 3.0 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 888 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN 3.3 19.3 - - - +
129B ARG* 3.3 36.8 - - + +
130B LEU* 3.8 15.0 - - + -
886B ASN* 3.6 17.5 - - + +
887B LEU* 1.3 77.2 - - - +
889B GLY* 1.3 64.7 + - - +
890B ASP* 5.4 2.0 - - - +
898B LEU* 4.0 15.3 - - - +
899B GLN 5.0 0.3 + - - -
900B THR* 3.4 38.3 + - + +
901B VAL 5.1 0.2 - - - -
902B SER* 3.3 31.9 - - - +
54L ARG 5.0 0.4 - - - -
55L ILE* 3.7 11.0 - - + -
----------------------------------------------------------
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