Contacts of the helix formed by residues 928 - 943 (chain C) in PDB entry 5ZX2
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 928 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599C HIS* 3.3 33.5 + - + +
922C VAL* 4.4 7.6 - - + -
923C PRO* 5.6 2.9 - - + -
926C MET 3.8 1.0 - - - -
927C ASN* 1.3 71.6 - - - +
929C GLY* 1.3 66.7 + - - +
930C GLN 3.2 2.7 - - - -
931C ILE* 2.9 36.8 + - + -
932C LEU* 3.0 21.1 + - + +
731D VAL* 4.2 14.8 - - + -
732D SER 6.2 0.2 - - - -
733D MET* 6.2 2.0 - - - -
736D VAL* 4.7 9.6 - - + -
817D LEU* 3.9 38.8 - - + -
840D PHE 3.7 10.8 - - - +
841D ARG* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 929 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C PHE* 3.8 21.6 - - - -
599C HIS* 4.0 2.1 + - - -
600C ASP* 3.0 15.0 + - - -
889C HIS* 3.5 16.2 - - - -
928C ILE* 1.3 81.0 - - - +
930C GLN* 1.3 53.7 + - - +
932C LEU* 2.9 5.0 + - - -
933C GLU* 2.6 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 930 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C ILE* 5.9 0.5 - - - +
889C HIS* 3.3 27.0 - - + -
891C ASN* 4.0 20.5 + - - +
917C LEU* 4.6 9.9 - - - +
921C GLY 4.9 2.0 + - - -
922C VAL* 3.8 29.8 - - - +
925C ARG* 5.6 0.2 - - - +
927C ASN* 3.1 46.4 + - - +
929C GLY* 1.3 75.5 - - - +
931C ILE* 1.3 64.9 + - + +
933C GLU* 4.1 1.5 - - - +
934C THR* 2.7 33.4 + - - -
1028C MET* 3.5 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 931 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C ILE* 3.5 28.5 - - + -
922C VAL* 3.7 28.5 - - + -
928C ILE* 2.9 33.3 + - + +
930C GLN* 1.3 83.3 - - + +
932C LEU* 1.3 67.1 + - + +
934C THR* 3.0 7.6 + - - -
935C HIS* 2.9 43.2 + - + +
1024C THR* 5.1 0.4 - - + -
731D VAL* 3.9 23.6 - - + +
732D SER* 4.1 8.5 - - - -
733D MET* 4.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 932 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C PHE* 3.6 24.2 - - + -
599C HIS* 3.5 49.1 - - + +
928C ILE* 3.0 21.8 + - + +
929C GLY* 2.9 6.0 + - - +
931C ILE* 1.3 77.4 - - + +
933C GLU* 1.3 62.6 + - - +
935C HIS* 3.0 7.9 + - + +
936C LEU* 2.9 20.1 + - - +
980C ALA 5.7 0.7 - - - +
982C GLU* 6.1 3.6 - - + -
985C LEU* 3.6 15.0 - - + +
733D MET* 4.0 40.4 - - + -
841D ARG* 5.0 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 933 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595C PRO* 4.4 2.2 - - + -
596C PHE* 3.4 17.1 - - + -
626C VAL* 4.1 23.0 - - + +
888C ARG* 3.2 23.8 + - - +
889C HIS* 3.0 29.2 + - + +
929C GLY 2.6 19.2 + - - +
930C GLN 4.1 1.1 - - - +
932C LEU* 1.3 71.5 - - - +
934C THR* 1.3 51.7 + - - +
936C LEU* 2.9 3.4 + - - +
937C GLY* 2.5 35.5 + - - -
1027C TYR 4.5 1.7 - - - +
1028C MET* 3.5 24.1 - - - +
1029C TYR* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 934 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721C VAL* 3.6 17.2 - - + +
723C ILE* 5.0 8.1 - - + +
930C GLN 2.7 19.0 + - - -
931C ILE* 3.0 12.3 + - - -
933C GLU* 1.3 77.1 - - - +
935C HIS* 1.3 64.3 + - - +
937C GLY 3.4 0.2 + - - -
938C TRP* 3.3 16.8 + - - +
1024C THR* 4.7 12.8 - - + -
1025C VAL* 4.1 5.5 - - - +
1026C GLY* 3.5 32.6 - - - +
1027C TYR 3.6 9.2 + - - -
1028C MET* 3.9 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 935 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931C ILE* 2.9 23.9 + - + +
932C LEU* 3.0 10.3 + - + +
934C THR* 1.3 79.4 - - - +
936C LEU* 1.3 62.9 + - - +
938C TRP* 3.3 13.1 + - - +
939C CYS* 3.3 18.0 + - - -
985C LEU* 3.9 17.0 - - + -
989C LEU* 4.2 16.0 - - + +
1005C ASP 4.0 9.1 + - - -
1006C GLY* 4.2 11.1 + - - -
1024C THR* 4.0 25.5 - - + +
1025C VAL 5.1 1.6 + - - -
732D SER* 3.3 14.1 + - - -
733D MET* 3.1 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 936 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.9 35.9 - - + -
596C PHE* 3.8 26.5 - - + -
626C VAL* 3.9 22.4 - - + -
932C LEU 2.9 12.9 + - - +
933C GLU 3.7 4.7 - - - +
935C HIS* 1.3 74.9 - - - +
937C GLY* 1.3 58.4 + - - +
939C CYS* 4.4 11.7 - - + -
940C ALA* 2.9 29.8 + - - +
944C TRP* 5.0 4.0 - - + -
972C VAL* 4.3 11.7 - - + -
974C THR* 4.3 4.5 - - + -
980C ALA* 4.3 7.2 - - + -
985C LEU* 3.7 17.0 - - + +
988C LEU* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 937 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C LEU* 3.8 5.4 - - - +
626C VAL* 3.7 13.8 - - - +
933C GLU 2.5 16.1 + - - -
934C THR 3.9 0.2 - - - -
935C HIS 3.2 0.4 - - - -
936C LEU* 1.3 73.2 - - - +
938C TRP* 1.3 56.3 + - - +
940C ALA* 3.5 3.5 + - - +
941C HIS* 3.0 28.1 + - - +
1027C TYR* 3.4 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 938 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720C LEU* 4.4 9.4 - - + -
907C LEU* 4.7 9.6 - - + -
934C THR 3.3 11.8 + - - +
935C HIS* 3.8 7.9 - - - +
936C LEU 3.2 0.4 - - - -
937C GLY* 1.3 74.2 - - - +
939C CYS* 1.3 71.5 + - - +
941C HIS* 3.0 30.4 + + - +
942C SER* 2.9 41.8 + - - -
989C LEU* 4.8 2.9 - - + -
992C THR* 3.5 27.7 - - + +
993C LEU 5.7 0.4 - - - -
1001C LEU* 4.1 35.0 - - + -
1002C VAL* 3.4 50.3 - - + +
1025C VAL* 4.5 3.8 - - + +
1026C GLY* 4.0 15.9 - - - -
1027C TYR* 3.9 18.0 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 939 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935C HIS 3.3 16.5 + - - -
936C LEU* 3.4 11.2 + - + +
938C TRP* 1.3 79.9 - - - +
940C ALA* 1.3 57.4 + - - +
942C SER* 4.1 4.9 - - - -
943C GLY* 2.8 32.0 + - - -
944C TRP* 3.4 24.3 - - + -
985C LEU* 4.6 5.6 - - - -
988C LEU* 4.1 17.9 - - + +
989C LEU* 3.6 30.5 - - - -
992C THR* 4.1 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 940 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C LEU* 3.8 21.5 - - + +
626C VAL* 5.0 0.2 - - + -
936C LEU 2.9 18.9 + - - +
937C GLY* 3.7 4.9 - - - +
939C CYS* 1.3 75.7 - - - +
941C HIS* 1.3 59.7 + - - +
943C GLY 3.7 2.8 + - - -
944C TRP* 4.3 10.9 - - + -
967C GLN 4.1 0.9 - - - +
969C ASN* 2.9 21.5 + - - -
970C ALA* 3.1 32.5 + - - +
972C VAL* 4.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 941 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C LEU* 4.2 11.2 - - + +
937C GLY 3.0 19.2 + - - +
938C TRP* 3.0 24.5 + + - +
940C ALA* 1.3 77.1 - - - +
942C SER* 1.3 64.7 + - - +
968C PRO* 3.5 6.6 - - - +
969C ASN* 3.0 38.1 + - - +
1027C TYR* 3.3 47.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 942 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938C TRP* 2.9 29.4 + - - -
939C CYS 3.9 0.7 + - - -
941C HIS* 1.3 88.4 - - - +
943C GLY* 1.3 64.8 + - - +
968C PRO* 3.7 15.7 - - - +
992C THR* 3.3 22.9 + - - +
993C LEU* 3.2 29.7 - - - +
994C PRO 4.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 943 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939C CYS 2.8 17.8 + - - +
940C ALA 3.7 2.0 + - - -
941C HIS 3.4 2.6 - - - -
942C SER* 1.3 82.6 + - - +
944C TRP* 1.3 66.2 + - - +
966C ALA* 3.2 14.8 - - - -
967C GLN 3.7 13.9 - - - -
968C PRO* 3.8 0.6 - - - +
992C THR* 3.7 1.9 + - - -
993C LEU* 2.9 24.1 + - - -
----------------------------------------------------------
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