Contacts of the helix formed by residues 893 - 904 (chain A) in PDB entry 3KSS
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 ARG 893 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A TYR* 4.8 2.1 - - - +
891A PHE 2.9 12.7 + - - +
892A ARG* 1.3 100.8 - - - +
894A VAL* 1.3 85.0 + - - +
895A GLY* 3.2 21.7 - - - +
896A GLU* 3.2 33.3 + - + +
897A ALA* 3.8 8.7 + - - +
949A ARG* 6.0 3.4 - - - -
1035A TYR* 6.1 0.9 - - - -
1038A MET* 4.7 18.2 + - - +
1039A TRP* 6.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 894 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A PHE* 5.2 12.8 - - + -
888A TYR* 5.9 1.8 - - + -
892A ARG 3.7 1.9 + - - -
893A ARG* 1.3 93.8 - - - +
895A GLY* 1.3 63.4 + - - +
896A GLU 3.3 0.7 - - - -
897A ALA* 4.3 5.6 - - + -
898A LEU* 2.7 67.1 + - + +
1038A MET* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 895 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A ARG* 3.2 13.2 - - - +
894A VAL* 1.3 84.4 - - - +
896A GLU* 1.3 55.8 + - - +
898A LEU* 3.9 0.6 - - - -
899A LEU* 2.9 27.2 + - - +
1038A MET* 3.4 46.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU 4.7 6.1 - - - +
888A TYR* 5.8 0.2 - - - -
891A PHE* 2.8 51.1 + - - +
892A ARG 4.2 0.5 + - - -
893A ARG* 3.2 29.4 - - + +
895A GLY* 1.3 73.5 - - - +
897A ALA* 1.3 69.2 + - - +
899A LEU* 3.0 9.6 + - - +
900A ILE* 2.8 32.4 + - - +
945A LEU* 3.1 43.9 - - + +
949A ARG* 4.2 8.0 - - - -
1035A TYR* 5.1 3.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A PHE* 5.2 5.6 - - + +
887A LEU* 3.9 25.0 - - + +
888A TYR* 4.4 12.8 - - + +
893A ARG 3.8 14.1 - - - +
894A VAL* 3.3 8.5 + - + +
896A GLU* 1.3 83.3 - - + +
898A LEU* 1.3 64.7 + - + +
900A ILE* 3.0 24.4 - - - +
901A ILE* 3.3 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A PHE* 5.7 4.7 - - + -
894A VAL* 2.7 52.2 + - + +
895A GLY* 4.0 4.7 - - - +
897A ALA* 1.3 76.9 - - + +
899A LEU* 1.3 60.4 + - - +
901A ILE* 3.8 15.4 - - + +
902A SER* 2.9 32.3 + - - -
1038A MET* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A GLY 2.9 16.7 + - - +
896A GLU* 3.2 13.0 - - - +
898A LEU* 1.3 76.9 - - - +
900A ILE* 1.3 55.9 + - + +
902A SER* 3.1 8.7 + - - -
903A SER* 2.5 43.9 + - - +
906A PHE* 5.8 1.8 - - + -
941A GLY* 6.3 0.2 - - - -
945A LEU* 5.5 9.6 - - + -
1030A ILE* 3.4 42.6 - - + +
1034A ALA* 3.5 31.6 - - + -
1038A MET* 5.1 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ILE* 5.7 0.9 - - + -
883A ILE* 5.3 2.2 - - + -
887A LEU* 3.3 41.5 - - + -
896A GLU 2.8 15.7 + - - +
897A ALA* 3.0 25.8 - - - +
899A LEU* 1.3 77.0 - - + +
901A ILE* 1.3 62.5 + - + +
903A SER* 2.9 27.2 + - - +
904A VAL* 3.0 14.5 + - + +
938A ALA* 4.2 31.9 - - + +
941A GLY* 6.0 5.4 - - - -
942A VAL* 6.0 3.1 - - + +
1030A ILE* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A LEU* 5.2 22.4 - - + +
883A ILE* 4.7 10.5 - - + -
884A PHE* 4.8 13.2 - - + -
887A LEU* 3.7 21.3 - - + -
897A ALA* 3.3 20.0 + - + +
898A LEU* 3.8 16.8 - - + +
899A LEU 3.2 0.4 - - - -
900A ILE* 1.3 79.1 - - + +
902A SER* 1.3 61.9 + - - +
903A SER 2.9 5.5 + - - -
904A VAL* 3.9 8.4 + - - +
905A PRO* 3.8 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A LEU 2.9 20.1 + - - -
899A LEU* 3.3 9.4 - - - +
901A ILE* 1.3 77.3 - - - +
903A SER* 1.3 62.5 + - - +
905A PRO* 3.3 13.4 - - - +
906A PHE* 4.5 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A LEU* 2.5 30.5 + - - -
900A ILE* 2.9 20.3 + - - +
901A ILE 2.9 2.0 - - - -
902A SER* 1.3 71.6 - - - +
904A VAL* 1.3 53.0 + - - -
905A PRO* 2.7 26.7 - - - +
906A PHE* 2.7 46.5 - - - -
937A ALA* 6.2 0.9 - - - +
1026A LEU* 3.8 8.5 - - - +
1030A ILE* 3.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A ILE* 3.0 12.7 + - + +
901A ILE* 3.9 10.8 - - - +
903A SER* 1.3 79.0 + - - +
905A PRO* 1.3 76.9 - - + +
906A PHE* 4.2 2.5 - - - -
907A ALA* 2.8 24.3 + - + +
908A LEU* 3.4 16.3 + - + +
934A ALA* 3.4 42.6 - - + +
937A ALA* 5.1 3.8 - - + -
938A ALA* 6.0 2.9 - - + +
----------------------------------------------------------
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