Contacts of the helix formed by residues 919 - 931 (chain A) in PDB entry 4EI4
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 919 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A LEU* 3.6 21.6 - - + +
918A HIS* 1.3 77.0 - - - +
920A ALA* 1.3 64.4 + - - +
921A ASP 3.3 0.3 + - - -
922A LEU* 3.3 4.7 + - - +
923A LYS* 3.1 51.5 + - + +
951A GLY* 3.8 31.6 - - - +
952A ILE* 4.3 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 920 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A HIS* 3.3 1.2 - - - +
919A ILE* 1.3 82.7 - - - +
921A ASP* 1.3 59.3 + - - +
923A LYS* 3.5 10.9 + - + +
924A LYS* 3.0 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 921 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A HIS* 3.4 32.5 + - + +
919A ILE 3.2 0.8 - - - -
920A ALA* 1.3 75.8 - - - +
922A LEU* 1.3 60.4 + - - +
924A LYS* 3.2 19.4 + - - +
925A GLU* 2.9 27.6 + - - +
1023A GLY 5.6 7.2 - - - +
1026A LYS* 4.5 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 922 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A LYS* 4.1 32.5 - - + +
909A SER 4.6 0.4 - - - -
910A LEU* 3.9 31.4 - - + +
918A HIS 3.4 7.9 + - - +
919A ILE 3.3 8.4 + - - +
921A ASP* 1.3 76.4 - - - +
923A LYS* 1.3 58.6 + - - +
925A GLU* 3.2 22.9 + - - +
926A ILE* 2.8 47.1 + - + +
952A ILE* 3.3 35.4 - - + +
953A LYS* 4.8 0.2 - - - -
954A LEU* 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 923 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A ILE* 3.1 45.0 + - + +
920A ALA* 3.6 13.0 - - - +
922A LEU* 1.3 75.7 - - - +
924A LYS* 1.3 62.5 + - + +
926A ILE* 3.5 9.2 + - - +
927A GLU* 3.1 22.7 + - - +
951A GLY 4.9 6.9 + - - +
952A ILE* 4.1 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 924 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920A ALA* 3.0 29.0 + - - +
921A ASP* 3.2 21.5 + - - +
923A LYS* 1.3 75.0 - - + +
925A GLU* 1.3 65.1 + - - +
927A GLU* 3.2 8.3 + - - +
928A ILE* 3.0 33.8 + - + +
1026A LYS* 4.8 8.5 - - - +
1035A PTR 4.4 16.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A LYS* 2.6 45.7 + - - +
921A ASP 2.9 13.1 + - - +
922A LEU* 3.2 18.2 + - + +
924A LYS* 1.3 76.1 - - - +
926A ILE* 1.3 55.1 + - - +
928A ILE* 3.2 13.0 + - - +
929A LEU* 3.0 29.7 + - + +
954A LEU* 4.4 13.0 - - + +
956A MET* 6.1 0.2 - - - +
1021A ASP* 3.6 1.0 - - - +
1022A PHE* 3.2 25.1 + - + +
1023A GLY* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A LEU* 2.8 39.6 + - + +
923A LYS* 3.6 8.3 - - - +
925A GLU* 1.3 74.4 - - - +
927A GLU* 1.3 61.3 + - - +
929A LEU* 3.6 2.2 + - - +
930A ARG* 3.0 33.8 + - + +
940A TYR* 4.0 13.7 - - + +
943A ILE* 3.8 22.2 - - + -
952A ILE* 3.9 30.7 - - + -
954A LEU* 3.7 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A LYS 3.1 16.7 + - - +
924A LYS* 3.6 7.6 - - - +
926A ILE* 1.3 79.4 - - - +
928A ILE* 1.3 62.9 + - - +
930A ARG* 2.9 38.0 + - - -
931A ASN* 3.0 32.7 + - - +
999A TYR* 5.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A LYS* 3.0 27.7 + - + +
925A GLU* 3.5 10.5 - - - +
927A GLU* 1.3 77.7 - - + +
929A LEU* 1.3 62.9 + - - +
931A ASN* 3.3 12.4 + - - +
932A LEU* 3.3 33.3 + - + +
994A LEU* 5.1 0.2 - - + -
999A TYR* 3.8 42.5 + - + +
1022A PHE* 5.1 7.4 - - + +
1025A THR* 3.7 45.8 - - + +
1026A LYS* 5.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A GLU* 3.0 16.4 + - + +
926A ILE* 4.2 4.0 - - - +
928A ILE* 1.3 77.0 - - - +
930A ARG* 1.3 62.7 + - - +
932A LEU* 3.1 25.1 + - + +
937A ILE* 4.0 9.0 - - + -
938A VAL* 3.4 28.0 - - + +
940A TYR* 4.0 17.9 + - + +
954A LEU* 4.2 16.4 - - + -
956A MET* 3.8 36.1 - - + -
1022A PHE* 3.7 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 930 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A ILE* 3.0 22.7 + - - +
927A GLU* 2.9 37.4 + - - +
928A ILE 3.3 0.2 - - - -
929A LEU* 1.3 75.9 - - - +
931A ASN* 1.3 76.3 + - - +
932A LEU 3.5 1.4 + - - +
933A TYR* 3.8 19.1 + - - -
940A TYR* 3.6 54.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 931 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927A GLU* 3.0 38.8 - - - +
928A ILE 3.3 6.5 + - - +
929A LEU 3.1 0.4 - - - -
930A ARG* 1.3 96.8 + - - +
932A LEU* 1.3 63.9 + - - +
933A TYR* 3.7 29.9 + - + -
993A TYR* 4.0 4.3 + - - -
997A ARG* 5.1 4.3 + - - -
999A TYR* 6.1 0.9 - - - +
----------------------------------------------------------
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