Contacts of the strand formed by residues 894 - 902 (chain B) in PDB entry 6CNB
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 894 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B VAL* 3.9 3.5 - - - +
795B LEU* 2.8 60.3 + - + +
887B SER 4.0 5.6 - - - +
888B VAL* 4.8 2.7 - - - +
893B GLN* 1.3 74.0 - - - +
895B LEU* 1.3 58.9 + - - +
896B ILE* 6.0 0.4 - - + -
46L VAL* 5.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 895 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU 4.3 12.1 - - - +
121B ARG* 4.3 14.1 - - - +
122B ASP* 3.8 25.8 - - + +
792B THR* 3.7 22.7 - - - +
793B THR 3.7 10.3 - - - +
794B VAL* 3.9 14.4 - - + -
885B MET* 3.8 4.6 - - + +
886B MET* 3.5 0.7 - - - +
887B SER* 2.9 46.4 + - - +
889B SER* 4.5 10.3 - - - +
893B GLN 4.3 4.9 - - - +
894B ALA* 1.3 76.5 - - - +
896B ILE* 1.3 79.9 + - - +
897B LYS* 4.9 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 896 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B THR 4.1 0.2 - - - +
792B THR* 3.8 1.0 - - - -
793B THR* 2.9 42.9 + - - +
795B LEU* 3.9 16.4 - - + -
806B ILE* 3.8 31.2 - - + -
829B LEU* 3.6 24.7 - - + -
843B ILE* 3.5 26.2 - - + -
885B MET 3.3 7.2 - - - +
886B MET* 4.1 23.6 - - + -
894B ALA* 6.0 0.4 - - + -
895B LEU* 1.3 83.4 - - - +
897B LYS* 1.3 66.5 + - - +
898B VAL* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 897 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG 4.5 4.2 + - - -
120B LEU* 3.4 17.2 + - - +
122B ASP* 3.4 26.0 + - - -
721B ILE* 3.7 34.1 + - + +
790B LYS* 4.4 21.7 - - + +
791B THR 3.6 9.6 - - - +
792B THR* 4.3 20.4 - - - -
883B GLN 4.5 0.2 - - - +
884B VAL* 3.4 1.0 - - - -
885B MET* 2.5 69.2 + - + +
895B LEU* 4.9 4.9 - - + -
896B ILE* 1.3 76.6 - - - +
898B VAL* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 898 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B ILE* 5.3 0.7 - - - -
790B LYS* 3.4 4.9 - - - +
791B THR* 2.9 35.4 + - + +
829B LEU* 4.7 9.0 - - + -
830B GLY* 5.8 0.2 - - - -
842B TYR* 3.5 45.1 - - + +
843B ILE* 5.1 4.0 - - + -
881B ILE* 4.8 4.5 - - + -
883B GLN 3.7 4.7 - - - -
884B VAL* 3.5 30.3 - - + -
896B ILE* 4.5 13.2 - - + +
897B LYS* 1.3 78.4 - - - +
899B LEU* 1.3 62.1 + - - +
900B LEU* 3.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 899 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B PHE 5.3 2.0 - - - +
720B ARG 4.4 5.2 - - - +
721B ILE* 3.5 49.1 - - + -
722B ASP 5.2 0.9 - - - +
788B ARG* 3.6 26.5 - - + +
789B ARG 2.9 16.4 - - - +
790B LYS* 4.6 0.2 - - + -
881B ILE* 4.0 2.3 - - - +
882B ASP* 2.7 66.7 + - - +
883B GLN* 3.2 20.7 + - + +
898B VAL* 1.3 76.6 - - - +
900B LEU* 1.3 71.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 900 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B THR 3.5 0.3 - - - +
788B ARG* 3.3 5.9 - - - -
789B ARG* 2.9 42.7 + - + +
791B THR* 4.9 4.5 - - - +
836B VAL* 4.6 4.9 - - + -
842B TYR* 4.2 22.4 - - + -
873B TYR* 3.5 39.3 - - + -
879B SER* 3.8 13.0 - - - +
880B HIS 3.3 10.5 - - - +
881B ILE* 4.3 12.8 - - + -
898B VAL* 3.8 24.5 - - + +
899B LEU* 1.3 82.2 - - - +
901B ARG* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 901 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B GLU* 5.7 1.3 - - + +
787B THR 3.1 11.9 - - - +
788B ARG* 4.2 16.5 - - + +
833B GLY* 4.8 7.1 + - - -
879B SER* 3.5 2.9 - - - -
880B HIS* 2.8 59.6 + - + +
882B ASP* 3.7 32.0 - - + +
900B LEU* 1.3 76.4 - - - +
902B GLN* 1.3 65.5 + - - +
93C GLN* 2.6 49.0 + - - +
94C ASP* 3.4 42.7 + - - +
95C GLU* 3.8 19.1 + - - +
67L PHE* 5.1 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 902 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B GLU* 3.2 3.4 - - - -
787B THR* 2.9 38.3 + - + +
789B ARG* 5.4 3.9 - - - +
873B TYR* 4.3 6.0 + - - -
877B GLU* 2.8 31.7 + - - +
878B PRO 2.9 23.7 - - - +
879B SER* 4.1 6.8 - - - +
880B HIS* 5.6 3.8 - - - -
901B ARG* 1.3 77.6 - - - +
903B ASN* 1.3 60.6 + - - +
904B ARG* 3.0 43.0 + - + +
1032B LEU* 4.3 4.6 - - - +
95C GLU* 4.2 5.2 - - - -
----------------------------------------------------------
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