Contacts of the helix formed by residues 837 - 858 (chain A) in PDB entry 1ZUC
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 SER 837 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A ASN 4.6 1.9 + - - -
742A LEU* 3.8 14.8 - - - +
743A HIS* 2.8 34.2 + - - +
746A ASP* 2.7 18.3 + - - +
835A LEU* 4.3 1.1 - - - -
836A ARG* 1.3 69.4 - - - +
838A GLN* 1.3 57.4 + - - +
839A THR 3.4 2.5 - - - -
840A GLN* 3.5 11.8 + - - -
841A PHE* 2.9 28.4 + - - +
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Residues in contact with GLN 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830A ILE* 3.6 23.5 - - - +
834A GLY* 3.6 7.0 - - - -
835A LEU* 2.8 45.7 + - - +
836A ARG 3.3 5.0 + - - +
837A SER* 1.3 75.0 - - - +
839A THR* 1.3 58.6 + - - +
841A PHE* 3.3 13.7 + - - +
842A GLU* 2.7 65.3 + - - +
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Residues in contact with THR 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A SER 3.4 0.4 - - - -
838A GLN* 1.3 77.9 - - - +
840A GLN* 1.3 62.9 + - - +
842A GLU* 3.3 9.1 + - - +
843A GLU* 3.1 41.6 + - + +
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Residues in contact with GLN 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738A GLY* 4.9 6.9 + - - +
741A ASN* 4.3 27.7 - - + +
742A LEU* 3.7 18.2 - - + -
837A SER* 3.5 16.4 + - - +
838A GLN 3.4 0.2 - - - -
839A THR* 1.3 78.4 - - - +
841A PHE* 1.3 58.8 + - - +
843A GLU* 3.3 25.8 + - - +
844A MET* 2.9 30.2 + - + +
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Residues in contact with PHE 841 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742A LEU* 3.6 13.4 - - + +
750A LEU* 4.1 8.7 - - + -
827A LEU* 3.2 56.3 - - + -
830A ILE* 3.4 24.7 - - + -
835A LEU* 3.3 28.0 - - + -
837A SER 2.9 18.7 + - - +
838A GLN* 3.3 24.4 + - - +
840A GLN* 1.3 75.1 - - - +
842A GLU* 1.3 66.8 + - + +
844A MET* 3.3 4.3 + - + +
845A ARG* 2.8 41.0 + - - +
928A LEU* 3.7 14.4 - - + -
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Residues in contact with GLU 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838A GLN* 2.7 54.5 + - - +
839A THR* 3.8 6.8 - - - +
841A PHE* 1.3 85.9 - - + +
843A GLU* 1.3 57.2 + - + +
845A ARG* 3.4 6.4 + - - +
846A SER* 3.0 33.3 + - - +
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Residues in contact with GLU 843 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A THR* 3.1 36.5 + - + +
840A GLN* 3.6 25.0 + - - +
842A GLU* 1.3 72.9 - - - +
844A MET* 1.3 61.1 + - - +
846A SER* 3.4 6.9 + - - -
847A SER* 2.9 34.0 + - - -
850A ARG* 4.6 2.2 + - - +
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Residues in contact with MET 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A LEU* 3.9 21.8 - - + -
737A PRO 3.5 22.0 - - - +
738A GLY* 3.8 21.3 - - - +
739A PHE* 3.7 18.2 - - + +
742A LEU* 4.4 11.7 - - + -
823A VAL* 4.4 0.2 - - + -
827A LEU* 4.0 25.6 - - + -
840A GLN* 2.9 26.2 + - - +
841A PHE* 3.5 5.4 - - - +
843A GLU* 1.3 76.0 - - - +
845A ARG* 1.3 64.0 + - - +
847A SER* 3.2 7.9 + - - -
848A TYR* 3.1 47.4 + - + -
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Residues in contact with ARG 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A LEU* 3.4 25.3 + - + +
827A LEU* 3.0 43.2 + - + +
828A ASN* 3.1 25.9 + - - -
841A PHE* 2.8 28.6 + - + +
842A GLU* 3.7 7.2 - - - +
844A MET* 1.3 74.2 - - - +
846A SER* 1.3 57.3 + - - +
848A TYR* 3.2 2.8 + - - -
849A ILE* 2.9 41.6 + - + +
928A LEU* 3.7 28.4 - - - +
929A LEU 5.1 2.2 + - - +
930A PHE* 3.2 34.7 - - - -
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Residues in contact with SER 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A GLU* 3.0 21.0 + - - +
843A GLU* 3.8 6.2 - - - -
845A ARG* 1.3 72.2 - - - +
847A SER* 1.3 57.4 + - - +
849A ILE* 3.4 13.8 + - - +
850A ARG* 2.9 51.7 + - - +
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Residues in contact with SER 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A LEU* 5.1 7.4 - - - +
843A GLU* 2.9 19.1 + - - +
844A MET* 3.2 13.6 + - - -
846A SER* 1.3 76.3 - - - +
848A TYR* 1.3 64.2 + - - +
850A ARG* 3.2 26.2 + - - +
851A GLU* 3.0 27.0 + - - +
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Residues in contact with TYR 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A LEU* 3.8 26.0 - - + +
691A LEU* 4.0 16.6 - - + -
736A LEU* 3.5 3.8 - - + +
737A PRO* 2.8 53.3 + - + +
820A CYS* 4.4 6.4 - - - +
823A VAL* 3.6 39.9 - - + -
824A LEU* 3.9 20.4 - - + +
827A LEU* 4.5 1.1 - - + -
844A MET* 3.1 42.2 + - + +
845A ARG* 3.9 4.9 - - - +
847A SER* 1.3 81.8 - - - +
849A ILE* 1.3 61.9 + - - +
851A GLU* 3.6 6.6 - - + +
852A LEU* 2.9 28.4 + - - +
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Residues in contact with ILE 849 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A LEU* 3.7 19.7 - - + -
845A ARG* 2.9 40.4 + - + +
846A SER* 3.7 10.5 - - - +
848A TYR* 1.3 75.9 - - - +
850A ARG* 1.3 63.0 + - + +
852A LEU* 3.2 5.0 + - - +
853A ILE* 3.1 31.2 + - + +
870A PHE* 3.7 29.4 - - + -
930A PHE* 3.7 24.9 - - + -
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Residues in contact with ARG 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A GLU* 4.6 1.4 + - - +
846A SER* 2.9 40.8 + - - +
847A SER* 3.5 33.6 + - - +
848A TYR 3.2 0.2 - - - -
849A ILE* 1.3 73.2 - - + +
851A GLU* 1.3 59.6 + - - +
853A ILE* 3.3 16.7 + - + +
854A LYS* 3.1 38.4 + - - +
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Residues in contact with GLU 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A PRO* 3.1 30.7 - - - +
687A LEU* 3.6 36.6 - - + +
688A ILE* 3.4 22.8 - - + +
691A LEU* 5.3 0.4 - - + -
820A CYS* 3.7 10.3 - - - -
847A SER 3.0 16.1 + - - +
848A TYR* 3.6 12.1 - - + +
849A ILE 3.2 0.4 - - - -
850A ARG* 1.3 73.3 - - - +
852A LEU* 1.3 61.1 + - - +
854A LYS* 2.8 35.1 + - - +
855A ALA* 2.8 27.7 + - - +
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Residues in contact with LEU 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A GLU* 3.9 20.2 - - - +
820A CYS* 3.8 14.9 - - + -
821A MET* 3.9 28.3 - - + -
824A LEU* 3.9 21.8 - - + -
848A TYR 2.9 13.1 + - - +
849A ILE* 3.5 9.0 - - - +
851A GLU* 1.3 73.8 - - - +
853A ILE* 1.3 59.3 + - - +
855A ALA* 3.2 2.7 + - - +
856A ILE* 2.9 40.9 + - + +
870A PHE* 4.1 19.7 - - + -
873A LEU* 4.3 19.5 - - + -
874A THR* 4.3 13.2 - - + -
877A LEU* 5.1 1.6 - - + -
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Residues in contact with ILE 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849A ILE* 3.1 21.2 + - + +
850A ARG* 3.4 17.3 - - + +
852A LEU* 1.3 74.4 - - - +
854A LYS* 1.3 64.9 + - + +
856A ILE* 3.1 12.2 + - + +
857A GLY* 3.0 19.6 + - - -
866A SER* 6.6 0.4 - - - -
870A PHE* 3.8 28.9 - - + -
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Residues in contact with LYS 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A PRO* 4.1 25.3 - - + +
686A PRO* 5.9 1.8 - - - +
687A LEU* 5.8 0.4 - - - +
688A ILE* 4.8 0.4 - - - -
850A ARG* 3.1 26.2 + - - +
851A GLU* 2.8 41.4 + - - +
853A ILE* 1.3 76.4 - - + +
855A ALA* 1.3 60.7 + - - +
857A GLY* 3.1 13.1 + - - -
858A LEU* 3.2 18.3 + - - +
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Residues in contact with ALA 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A ILE* 4.0 12.0 - - + +
814A SER* 4.7 3.6 + - - -
816A GLU* 3.6 36.7 - - + +
817A GLU* 3.7 14.5 - - - +
820A CYS* 4.2 0.4 - - - -
851A GLU 2.8 16.1 + - - +
852A LEU* 3.2 12.8 + - - +
854A LYS* 1.3 71.7 - - - +
856A ILE* 1.3 62.0 + - - +
858A LEU* 3.4 24.0 + - - +
859A ARG* 4.4 3.6 + - - +
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Residues in contact with ILE 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A GLU* 3.8 21.5 - - + +
852A LEU* 2.9 25.4 + - + +
853A ILE* 3.5 9.4 - - - +
855A ALA* 1.3 75.2 - - - +
857A GLY* 1.3 52.5 + - - +
858A LEU 3.2 0.4 - - - -
859A ARG* 3.3 5.2 + - - +
860A GLN* 2.7 46.1 + - + +
866A SER* 3.8 18.4 - - - +
869A ARG* 3.7 18.4 - - + -
870A PHE* 3.6 46.0 - - + +
873A LEU* 3.9 17.3 - - + -
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Residues in contact with GLY 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853A ILE 3.0 12.4 + - - -
854A LYS* 3.1 7.1 + - - -
856A ILE* 1.3 71.7 - - - +
858A LEU* 1.3 64.6 + - - +
859A ARG 3.1 2.7 + - - -
860A GLN 3.8 16.0 - - - +
861A LYS* 3.8 15.6 + - - +
866A SER* 4.7 2.7 - - - -
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Residues in contact with LEU 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A LEU* 3.6 30.5 - - + +
684A ILE* 4.0 16.2 - - + -
685A PRO* 4.0 16.4 - - + -
688A ILE* 4.8 0.7 - - + -
816A GLU* 3.8 33.9 - - + -
854A LYS 3.2 12.9 + - - +
855A ALA* 3.4 16.4 - - - +
856A ILE 3.2 0.6 - - - -
857A GLY* 1.3 78.6 - - - +
859A ARG* 1.3 70.4 + - + +
861A LYS* 3.7 15.8 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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