Contacts of the strand formed by residues 843 - 852 (chain B) in PDB entry 3N57
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 ILE 843 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768B GLU* 3.6 34.1 - - + +
794B TYR* 4.6 2.4 + - - -
796B GLN* 3.5 27.4 - - + +
798B ASP 3.8 15.0 - - - +
799B MET* 3.6 27.1 - - + -
800B GLN* 3.3 6.7 - - - +
839B ARG* 3.5 0.2 - - - -
840B ALA 2.8 27.4 + - - +
841B ASN 3.8 7.6 - - - +
842B GLY* 1.3 88.0 - - - +
844B GLN* 1.3 76.6 + - - +
1005B PHE* 3.6 28.0 - - + -
1006B PRO 4.4 4.5 - - - +
1008B VAL 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 844 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B TYR* 3.4 13.1 + - - -
796B GLN* 3.8 0.3 - - - -
797B THR* 3.0 31.1 + - - +
798B ASP 3.2 11.2 + - - +
799B MET 3.6 8.1 + - - -
800B GLN* 4.0 3.7 - - + +
804B GLU* 3.2 37.3 + - - +
805B ASN* 3.0 26.7 + - - +
808B LEU* 3.7 7.7 - - + +
838B ARG 3.0 14.1 - - - +
839B ARG* 2.9 40.2 + - + +
843B ILE* 1.3 81.6 - - - +
845B GLY* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 845 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B TYR* 3.5 9.8 - - - -
795B TYR 3.1 13.9 - - - -
797B THR* 3.9 10.3 - - - -
808B LEU* 3.3 15.6 - - - +
837B PRO* 3.4 0.5 - - - +
838B ARG 2.7 31.1 + - - -
844B GLN* 1.3 79.4 - - - +
846B LEU* 1.3 58.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 846 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B ILE 3.6 0.7 - - - +
794B TYR* 3.5 2.9 - - - -
795B TYR* 2.8 50.0 + - + +
797B THR* 4.9 0.8 - - - +
808B LEU* 4.0 21.9 - - + +
811B PHE* 3.7 28.0 - - + -
812B ALA* 4.5 8.1 - - + -
815B ILE* 4.0 16.6 - - + -
836B GLY 3.7 23.8 - - - +
845B GLY* 1.3 73.7 - - - -
847B ARG* 1.3 60.7 + - - +
848B PHE* 3.9 26.0 - - + -
867B LEU* 4.8 4.7 - - + -
944B LEU* 4.4 13.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
683B MET* 5.0 7.7 - - - +
792B GLU* 3.5 28.3 + - + +
793B ILE 3.0 10.1 - - - +
794B TYR* 4.7 4.3 - - + -
834B PHE* 3.7 33.3 - - + -
835B SER* 3.3 20.3 - - - -
836B GLY 3.0 20.1 + - - +
837B PRO 3.5 17.7 + - - -
838B ARG* 3.7 32.7 - - + +
845B GLY 4.1 0.2 + - - -
846B LEU* 1.3 76.3 - - - +
848B PHE* 1.3 71.2 + - - +
849B ILE* 4.2 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B ILE* 3.7 1.5 - - + +
792B GLU* 3.1 6.8 - - - +
793B ILE* 2.9 40.0 + - + +
795B TYR* 3.9 22.4 - + - -
815B ILE* 4.0 20.9 - - + -
819B ALA* 4.4 4.5 - - + -
823B LEU* 4.4 9.2 - - + -
833B VAL* 6.4 0.4 - - + -
834B PHE 3.3 7.2 - - - +
835B SER* 3.6 22.7 - - - -
846B LEU* 3.9 21.8 - - + -
847B ARG* 1.3 77.2 - - - +
849B ILE* 1.3 63.4 + - - +
850B ILE* 4.3 5.2 - - + -
863B VAL* 3.8 36.8 - - + -
866B PHE* 4.2 21.1 - + - -
867B LEU* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B HIS* 3.8 36.6 - - + +
682B ALA* 5.9 0.2 - - + -
683B MET* 3.7 28.9 - - + -
791B ILE 3.3 7.4 - - - +
792B GLU* 3.9 24.9 - - + +
832B ILE* 3.9 7.7 - - + +
833B VAL* 3.6 2.3 + - - -
834B PHE* 2.8 60.6 + - + +
847B ARG* 4.2 14.1 - - + +
848B PHE* 1.3 78.5 - - - +
850B ILE* 1.3 68.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 850 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B HIS* 4.5 2.3 - - - +
789B SER 4.0 0.2 - - - +
790B GLY* 3.4 3.5 - - - -
791B ILE* 2.9 50.9 + - + +
823B LEU* 4.8 12.8 - - + -
829B LEU* 4.4 18.6 - - + -
830B GLY 4.7 0.2 - - - +
832B ILE 3.5 11.0 - - - +
833B VAL* 4.3 18.2 - - + -
834B PHE 5.4 0.2 - - - +
848B PHE* 5.2 4.9 - - + -
849B ILE* 1.3 87.0 - - - +
851B GLN* 1.3 74.7 + - - +
852B SER* 4.3 10.1 - - - -
859B LEU* 4.4 17.6 - - + +
863B VAL* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 851 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER* 4.9 0.7 + - - -
192B LYS* 3.9 23.8 - - - +
677B GLN* 3.1 24.0 - - - +
678B PRO* 3.4 12.4 - - + +
679B HIS* 2.9 38.2 + - + -
786B HIS* 5.8 1.2 - - - -
788B ASN* 3.9 24.6 + - + +
789B SER 3.2 16.4 - - - +
830B GLY* 3.2 23.4 - - - -
831B TYR 4.1 2.1 + - - -
832B ILE* 3.3 24.3 + - + +
850B ILE* 1.3 75.9 - - - +
852B SER* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 852 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER* 5.3 1.8 - - - -
788B ASN* 3.4 13.5 - - - -
789B SER* 2.7 41.1 + - - -
829B LEU* 2.5 34.5 - - - -
830B GLY* 4.4 1.3 - - - -
850B ILE* 4.3 4.9 - - - -
851B GLN* 1.3 74.4 - - - +
853B GLU* 1.3 56.0 + - - +
854B LYS* 3.1 21.4 + - - +
859B LEU* 3.5 19.9 - - - +
----------------------------------------------------------
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