Contacts of the helix formed by residues 908 - 916 (chain E) in PDB entry 3KKA
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 THR 908 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922C GLU* 5.4 0.9 - - - -
923C HIS* 4.3 14.4 - - + +
906E PHE* 4.0 0.5 - - - +
907E ARG* 1.3 88.4 - - + +
909E VAL* 1.3 66.5 + - - +
910E SER* 3.3 13.1 + - - -
911E GLU* 2.9 34.0 + - - +
912E TRP* 3.1 18.2 + - - +
931E THR 6.1 0.2 - - - -
933E ILE* 3.4 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 909 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908E THR* 1.3 72.5 - - - +
910E SER* 1.3 58.2 + - - +
912E TRP* 3.2 13.4 + - + +
913E LEU* 3.0 32.9 + - + +
922E THR* 5.5 1.8 - - + +
925E PHE* 4.0 30.7 - - + -
926E MET* 4.7 9.2 - - - -
930E TYR 3.5 11.2 - - - +
931E THR 3.4 25.4 + - - +
932E ALA* 3.4 25.5 - - - +
933E ILE* 3.7 9.8 - - - +
936E VAL* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 910 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908E THR* 3.1 10.5 + - - -
909E VAL* 1.3 81.0 - - - +
911E GLU* 1.3 57.5 + - - +
913E LEU* 3.5 2.5 + - - +
914E GLU* 2.9 30.0 + - - +
919E GLN* 4.2 5.7 - - - +
922E THR* 3.8 35.9 + - - +
926E MET* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 911 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905E PRO 4.0 3.5 - - - +
906E PHE* 3.7 20.8 - - + -
907E ARG* 2.9 55.8 + - - +
908E THR* 2.9 25.6 + - - +
910E SER* 1.3 75.6 + - - +
912E TRP* 1.3 62.6 + - - +
914E GLU* 3.4 10.5 - - + +
915E SER* 3.2 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 912 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906E PHE* 3.7 39.4 - + + +
908E THR 3.1 11.6 + - - +
909E VAL* 3.2 24.0 + - + +
911E GLU* 1.3 73.2 - - - +
913E LEU* 1.3 88.0 + - + +
915E SER* 2.8 25.3 + - - -
916E ILE* 3.6 15.2 + - + +
925E PHE* 4.2 11.4 - + - -
933E ILE* 4.6 7.9 - - + -
936E VAL* 3.6 33.2 - - + -
958E ILE* 4.1 16.8 - - + -
961E SER* 3.1 31.9 + - - -
962E LEU* 4.4 15.7 - - + -
965E LEU* 4.1 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 913 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909E VAL* 3.0 25.0 + - + +
910E SER 4.0 1.8 - - - +
912E TRP* 1.3 102.4 - - + +
914E GLU* 1.3 67.4 + - - +
916E ILE* 3.0 18.2 + - + +
918E MET* 2.9 38.7 + - + +
919E GLN* 3.6 17.0 - - - +
921E TYR* 4.0 0.4 - - + -
922E THR* 3.8 29.2 - - - +
925E PHE* 3.6 35.7 - - + -
958E ILE* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 914 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910D SER* 5.9 0.9 - - - -
910E SER* 2.9 20.4 + - - +
911E GLU* 3.4 12.8 - - + +
913E LEU* 1.3 77.1 - - - +
915E SER* 1.3 60.0 + - - +
917E LYS* 3.2 28.2 + - - +
919E GLN* 3.8 29.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 915 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908D THR* 3.5 28.3 - - - -
909D VAL 5.2 0.5 + - - -
910D SER* 5.6 3.9 + - - -
922D THR* 5.8 0.3 - - - +
926D MET* 3.6 18.5 - - - +
931D THR 4.3 2.9 + - - +
906E PHE* 3.4 37.3 - - - -
911E GLU 3.2 5.5 + - - -
912E TRP* 2.8 19.8 + - - -
914E GLU* 1.3 76.3 - - - +
916E ILE* 1.3 65.4 + - - +
917E LYS* 3.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 916 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926D MET* 3.7 11.9 - - - -
931D THR* 3.9 24.5 - - - +
912E TRP* 4.0 17.9 - - + +
913E LEU* 3.0 15.5 + - + +
915E SER* 1.3 88.9 + - - +
917E LYS* 1.3 67.1 + - - +
918E MET* 3.3 19.5 - - + +
957E ARG* 3.0 33.5 + - + +
958E ILE* 4.1 19.3 - - + -
961E SER* 3.6 36.3 - - - +
----------------------------------------------------------
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