Contacts of the helix formed by residues 904 - 920 (chain F) in PDB entry 1ZXE
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 GLU 904 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827F HIS* 3.4 57.5 - - + +
830F GLY 6.4 0.9 - - - -
831F ILE 4.8 0.7 - - - +
832F ILE* 3.6 24.5 - - + +
903F ASN* 1.3 85.2 + - - +
905F LYS* 1.3 90.3 + - + +
906F ILE 3.1 6.9 + - - -
907F ASP* 3.3 10.2 + - - +
908F MSE 3.7 3.3 + - + +
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Residues in contact with LYS 905 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894F GLU* 4.7 0.2 - - - +
903F ASN* 2.8 25.9 + - - +
904F GLU* 1.3 95.2 - - - +
906F ILE* 1.3 64.4 + - - +
907F ASP 3.2 0.2 - - - -
908F MSE 3.3 18.7 + - + +
909F TYR 3.0 15.9 + - - -
966F PRO* 3.6 20.9 + - + +
967F ASN* 4.4 9.9 + - - +
969F ARG* 2.6 64.2 + - + +
971F GLY* 3.9 18.2 - - - +
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Residues in contact with ILE 906 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832F ILE* 3.6 22.4 - - + -
834F ARG* 3.9 24.0 - - + +
890F TYR 4.8 0.2 - - - +
892F ALA* 3.6 32.2 + - + +
894F GLU* 3.8 5.6 - - - +
895F VAL* 3.7 9.0 - - + -
902F TYR* 3.7 37.0 - - + -
903F ASN 3.2 17.0 - - - +
905F LYS* 1.3 79.7 - - - +
907F ASP* 1.3 66.4 + - - +
909F TYR* 3.3 4.0 + - - +
910F SER* 3.0 31.0 + - - -
969F ARG* 3.9 0.2 - - - +
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Residues in contact with ASP 907 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823F LEU* 4.6 10.2 - - + +
827F HIS* 3.1 31.8 + - + +
832F ILE* 3.5 11.5 - - - +
833F HIS* 2.7 36.7 + - - +
834F ARG* 3.0 23.2 + - - -
835F ASN 4.6 0.7 + - - -
836F LEU* 4.0 10.4 + - + +
904F GLU 3.3 2.2 + - - +
906F ILE* 1.3 83.2 - - - +
908F MSE 1.3 61.2 + - - +
910F SER* 3.3 9.4 + - - -
911F LEU* 2.9 29.0 + - - +
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Residues in contact with MSE 908 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820F LEU* 4.0 14.6 - - + -
823F LEU* 4.4 10.1 - - - -
827F HIS* 3.8 18.6 - - + +
904F GLU* 3.9 11.2 - - + +
905F LYS* 3.3 24.0 + - + +
906F ILE 3.2 0.4 - - - -
907F ASP* 1.3 78.2 - - - +
909F TYR* 1.3 61.6 + - - +
911F LEU* 3.1 9.2 + - + +
912F GLY* 2.9 18.4 + - - -
961F LEU* 3.7 31.1 - - + +
969F ARG* 4.8 6.3 - - + -
970F PRO 3.2 29.4 - - - +
971F GLY* 3.4 16.2 - - - +
972F ALA* 3.4 23.8 - - - +
975F LEU* 4.3 0.9 - - + -
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Residues in contact with TYR 909 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890F TYR 4.1 1.3 - - - -
891F VAL 3.4 27.1 - - - -
892F ALA* 3.8 8.7 - - + -
893F THR* 3.2 37.2 - - + +
905F LYS 3.0 13.8 + - - +
906F ILE* 3.3 11.4 - - - +
908F MSE 1.3 76.0 - - - +
910F SER* 1.3 64.2 + - - +
912F GLY* 2.9 11.6 + - - -
913F ILE* 3.1 30.5 + - + -
936F ARG* 3.5 27.7 + - - +
961F LEU 3.6 16.1 + - - -
962F ILE* 3.5 32.5 - - + +
963F ASP 3.9 5.4 - - - -
964F HIS* 4.4 1.0 + + - -
969F ARG* 3.7 23.1 - - - +
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Residues in contact with SER 910 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834F ARG 6.1 0.5 - - - -
836F LEU* 3.8 34.2 + - - +
890F TYR* 2.8 30.6 + - - -
891F VAL* 5.1 0.2 - - - -
892F ALA 5.3 0.2 + - - -
906F ILE* 3.0 15.5 + - - +
907F ASP* 3.5 9.5 + - - -
909F TYR* 1.3 74.9 - - - +
911F LEU* 1.3 53.8 + - - +
913F ILE* 2.9 6.2 + - - +
914F ILE* 2.7 39.3 + - - +
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Residues in contact with LEU 911 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816F PHE* 3.7 29.4 - - + -
819F ILE* 3.9 27.8 - - + -
820F LEU* 3.5 33.4 - - + -
823F LEU* 4.0 14.6 - - + -
836F LEU* 4.2 7.8 - - + +
907F ASP 2.9 14.0 + - - +
908F MSE 3.1 19.0 + - + +
910F SER* 1.3 76.2 - - - +
912F GLY* 1.3 57.3 + - - +
914F ILE* 4.1 15.9 - - + +
915F PHE* 2.8 29.5 + - + +
918F MSE 5.6 0.7 - - - -
961F LEU* 4.5 4.3 - - + -
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Residues in contact with GLY 912 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908F MSE 2.9 10.3 + - - -
909F TYR 2.9 5.5 + - - -
911F LEU* 1.3 77.6 - - - +
913F ILE* 1.3 61.4 + - - +
915F PHE* 3.3 3.5 + - - +
916F PHE* 3.0 22.2 + - - +
958F ILE* 3.8 8.6 - - - +
961F LEU* 3.4 31.4 - - - +
962F ILE* 3.7 8.7 - - - -
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Residues in contact with ILE 913 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889F MSE 3.8 16.4 - - - +
890F TYR* 3.4 30.5 - - + -
909F TYR* 3.1 30.7 + - + +
910F SER 2.9 6.6 + - - +
912F GLY* 1.3 73.5 - - - +
914F ILE* 1.3 61.7 + - - +
916F PHE* 3.3 8.9 + - - +
917F GLU* 3.2 21.4 + - - +
932F LEU* 4.4 22.0 - - + +
935F LEU* 5.0 13.0 - - + -
936F ARG* 4.1 18.4 - - + -
962F ILE* 3.4 25.0 - - + +
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Residues in contact with ILE 914 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796F LEU* 4.1 26.0 - - + -
800F ILE* 5.4 0.4 - - + -
819F ILE* 5.7 2.0 - - + -
836F LEU* 3.9 22.7 - - + +
837F LYS* 3.9 29.4 - - - +
838F PRO* 4.1 10.8 - - + -
841F ILE* 5.3 5.6 - - + -
890F TYR* 3.9 20.6 - - + -
910F SER 2.7 30.7 + - - +
911F LEU* 3.7 11.0 - - + +
913F ILE* 1.3 70.6 - - - +
915F PHE* 1.3 65.8 + - - +
917F GLU* 3.0 9.2 + - - +
918F MSE 2.9 27.8 + - + +
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Residues in contact with PHE 915 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812F TYR* 3.7 37.9 - + - -
813F TRP* 4.1 19.3 - + - -
816F PHE* 3.7 42.2 - + + -
911F LEU* 2.8 22.5 + - + +
912F GLY* 3.3 4.7 + - - +
914F ILE* 1.3 73.7 - - - +
916F PHE* 1.3 62.8 + - - +
918F MSE 3.1 25.6 + - + +
919F ILE* 3.3 18.9 + - + +
954F GLU* 4.1 37.2 - - + -
957F ILE* 4.5 5.4 - - + -
958F ILE* 3.6 23.1 - - + -
961F LEU* 5.2 0.4 - - + -
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Residues in contact with PHE 916 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912F GLY 3.0 12.7 + - - +
913F ILE* 3.3 12.6 - - - +
915F PHE* 1.3 78.0 - - - +
917F GLU* 1.3 58.4 + - - +
919F ILE* 3.1 6.5 + - + +
920F TYR* 3.0 42.8 + + + +
922F PHE* 3.7 18.2 - + - -
931F ILE* 3.6 21.5 - - + -
932F LEU* 3.5 17.7 - - + -
935F LEU* 3.7 21.3 - - + -
942F PHE* 4.1 11.7 - + - -
943F PRO* 3.6 32.1 - - + -
946F PHE* 4.0 17.9 - + - -
958F ILE* 3.7 25.1 - - + +
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Residues in contact with GLU 917 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800F ILE* 3.5 32.3 - - + +
801F HIS* 4.6 12.1 - - - -
806F ASN* 5.3 1.4 - - - +
838F PRO* 4.0 5.7 - - + +
890F TYR* 2.4 45.5 + - - -
913F ILE* 3.2 10.5 + - - +
914F ILE* 3.0 8.3 + - - +
916F PHE* 1.3 76.9 - - - +
918F MSE 1.3 61.5 - - - +
919F ILE 3.2 1.0 + - - -
920F TYR 3.9 18.1 + - - +
921F PRO* 5.6 0.2 - - - +
922F PHE* 4.2 15.4 - - + -
928F ARG* 3.4 32.0 + - - +
932F LEU* 4.4 10.3 - - + -
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Residues in contact with MSE 918 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796F LEU* 4.3 13.0 - - + -
800F ILE* 4.0 14.6 - - + -
805F LEU* 3.5 32.6 - - + +
806F ASN* 3.3 24.3 + - - -
812F TYR* 3.7 31.1 - - + +
815F LEU* 3.8 20.6 - - + -
816F PHE* 4.3 6.3 - - - +
819F ILE* 4.5 11.0 - - + -
911F LEU* 5.6 0.7 - - - -
914F ILE* 2.9 27.5 + - + +
915F PHE* 3.3 34.1 - - + +
916F PHE 3.1 0.6 - - - -
917F GLU* 1.3 79.5 - - - +
919F ILE* 1.3 61.7 + - + +
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Residues in contact with ILE 919 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806F ASN* 3.4 19.6 - - - +
812F TYR* 3.3 40.2 - - + -
915F PHE* 3.5 20.4 - - + +
916F PHE* 3.5 8.7 - - + +
918F MSE 1.3 84.2 - - - +
920F TYR* 1.3 62.4 + - + +
921F PRO* 4.0 1.9 - - - +
946F PHE* 5.0 4.9 - - + -
951F MSE 3.8 34.9 - - + +
954F GLU* 3.7 28.3 - - + -
958F ILE* 3.7 19.3 - - + -
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Residues in contact with TYR 920 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800F ILE* 5.9 0.2 - - - +
806F ASN* 3.9 1.3 - - - +
916F PHE* 3.0 43.6 + + + +
917F GLU 3.9 10.4 + - - +
918F MSE 3.8 1.0 - - - -
919F ILE* 1.3 84.8 - - + +
921F PRO* 1.3 83.3 - - + +
922F PHE* 3.7 19.6 - + - -
931F ILE* 3.6 22.2 - - + +
943F PRO* 3.4 28.7 - - + +
945F ASP* 3.2 43.4 - - + +
946F PHE* 4.6 10.3 - + + -
947F ASP 5.5 0.7 - - - -
951F MSE 5.4 4.5 - - + -
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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) + - + + + + + -
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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