Contacts of the helix formed by residues 924 - 937 (chain A) in PDB entry 1ZY5
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 924 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A PHE* 3.3 5.5 - - - +
923A SER* 1.3 96.9 + - - +
925A GLY* 1.3 66.0 + - - +
926A MET* 3.6 7.5 + - - +
927A GLU* 2.8 35.4 + - - +
928A ARG* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A THR* 1.3 74.1 - - - +
926A MET* 1.3 59.8 + - - +
928A ARG* 3.4 11.1 + - - +
929A VAL* 3.3 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A THR* 3.1 7.5 + - - +
925A GLY* 1.3 73.2 - - - +
927A GLU* 1.3 66.1 + - - +
928A ARG 3.1 0.2 - - - -
929A VAL* 3.4 12.1 + - - +
930A ASN* 3.2 47.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
920A TYR* 4.7 4.4 + - - -
921A PRO 4.0 5.0 - - - +
922A PHE* 3.6 10.9 - - + -
923A SER* 2.5 41.8 + - - -
924A THR* 2.8 26.8 + - - +
926A MET* 1.3 78.2 - - - +
928A ARG* 1.3 61.6 + - - +
930A ASN* 3.9 4.5 - - - +
931A ILE* 3.1 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A TYR* 6.1 4.7 - - - -
801A HIS* 5.1 12.5 + - - -
889A MET* 4.4 10.1 - - - +
890A TYR* 2.7 39.6 + - - -
917A GLU* 2.7 19.7 + - - -
922A PHE* 3.5 33.8 - - + -
924A THR 3.0 8.8 + - - +
925A GLY* 3.5 13.4 + - - +
926A MET 3.1 0.2 - - - -
927A GLU* 1.3 75.2 - - - +
929A VAL* 1.3 77.5 + - - +
931A ILE* 3.4 1.0 + - - -
932A LEU* 2.9 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A MET* 4.4 17.3 - - - +
925A GLY 3.3 16.1 + - - +
926A MET* 3.4 13.9 + - - +
928A ARG* 1.3 86.9 - - - +
930A ASN* 1.3 63.4 + - - +
932A LEU* 3.7 1.0 - - - +
933A LYS* 2.8 62.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 930 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A MET* 3.2 37.2 + - - +
927A GLU* 3.9 5.4 - - - +
929A VAL* 1.3 87.9 - - - +
931A ILE* 1.3 63.8 + - + +
933A LYS* 3.3 13.1 + - - +
934A LYS* 3.1 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 931 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A PHE* 3.8 24.2 - - + -
920A TYR* 3.5 33.0 - - + +
922A PHE* 3.6 22.9 - - + -
927A GLU* 3.1 32.0 + - + +
930A ASN* 1.3 76.5 - - + +
932A LEU* 1.3 58.7 + - - +
934A LYS* 3.3 9.9 + - - +
935A LEU* 3.0 25.5 + - + +
941A GLU 4.3 0.7 - - - +
943A PRO* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 932 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A MET* 3.5 31.6 - - + -
913A ILE* 4.2 22.4 - - + -
916A PHE* 3.8 16.2 - - + -
917A GLU* 4.3 7.4 - - + +
922A PHE* 4.0 9.6 - - + -
928A ARG* 2.9 53.0 + - + +
929A VAL 4.0 1.6 - - - +
931A ILE* 1.3 73.6 - - - +
933A LYS* 1.3 60.1 + - - +
935A LEU* 3.3 24.8 + - + +
936A ARG* 2.9 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 933 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A MET* 4.3 16.1 - - + -
929A VAL* 2.8 40.7 + - + +
930A ASN* 3.6 14.4 - - - +
931A ILE 3.3 0.2 - - - -
932A LEU* 1.3 77.7 - - - +
934A LYS* 1.3 57.9 - - + +
936A ARG* 3.3 8.6 + - - +
937A SER* 2.9 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 934 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A ASN* 3.1 19.0 + - - +
931A ILE* 3.4 9.9 - - - +
933A LYS* 1.3 75.8 - - + +
935A LEU* 1.3 63.6 + - - +
937A SER* 2.5 28.6 + - - +
941A GLU* 3.1 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 935 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A TYR* 4.6 1.6 + - - -
913A ILE* 4.9 7.9 - - + -
916A PHE* 3.5 47.8 - - + -
931A ILE* 3.0 13.5 + - + +
932A LEU* 3.3 20.2 + - + +
934A LYS* 1.3 76.4 - - - +
936A ARG* 1.3 59.9 + - - +
937A SER 3.9 0.5 - - - +
940A ILE* 3.4 20.1 - - - +
941A GLU 3.3 25.8 - - - +
942A PHE* 4.1 29.6 - - + -
958A ILE* 5.3 0.4 - - + -
962A ILE* 3.8 35.1 - - + +
964A HIS* 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 936 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A ALA 3.7 13.7 + - - -
889A MET* 3.0 60.8 + - + +
891A VAL* 2.7 32.9 + - - +
893A THR* 3.8 12.6 - - + +
896A LEU* 4.0 23.2 - - - +
909A TYR* 3.5 26.5 - - - +
913A ILE* 4.3 9.2 - - + -
932A LEU* 2.9 22.5 + - - +
933A LYS* 3.8 5.2 - - - +
935A LEU* 1.3 74.1 - - - +
937A SER* 1.3 61.8 + - - +
964A HIS* 3.0 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 937 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933A LYS 2.9 13.1 + - - -
934A LYS* 2.5 26.4 + - - +
936A ARG* 1.3 83.4 - - - +
938A VAL* 1.3 66.5 + - - +
939A SER* 2.9 20.8 + - - -
940A ILE* 2.8 12.6 + - - -
941A GLU* 4.5 0.7 - - - +
964A HIS* 3.1 8.9 + - - -
----------------------------------------------------------
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