Contacts of the helix formed by residues 834 - 850 (chain A) in PDB entry 4YZ9
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 834 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A PHE 3.7 2.4 + - - -
833A TRP* 1.3 75.8 - - - +
835A LEU* 1.3 65.9 + - - +
836A GLU* 3.8 9.4 + - - +
837A LYS* 2.9 31.7 + - - +
838A GLN* 3.0 13.1 + - - +
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Residues in contact with LEU 835 (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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800A HIS* 6.2 0.7 - - + -
801A GLU* 5.8 3.4 - - - +
833A TRP 4.0 0.4 + - - -
834A SER* 1.3 72.9 - - - +
836A GLU* 1.3 62.7 + - - +
838A GLN* 3.2 24.2 + - - +
839A LEU* 3.1 19.1 + - - +
926A PRO* 5.1 0.9 - - - -
927A ASP* 3.8 37.5 - - + +
930A VAL* 3.7 23.0 - - + +
931A CYS* 3.8 31.2 - - - -
934A THR* 5.9 1.1 - - - +
879C THR* 5.7 1.6 - - - +
880C VAL* 5.1 16.6 - - + -
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Residues in contact with GLU 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A SER* 3.2 9.5 + - - +
835A LEU* 1.3 79.2 - - - +
837A LYS* 1.3 57.4 + - - +
839A LEU* 3.4 3.5 + - - +
840A GLN* 3.0 32.8 + - + +
926A PRO* 3.8 31.9 - - + +
927A ASP* 4.6 2.6 + - - +
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Residues in contact with LYS 837 (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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828A LYS* 5.4 2.8 - - - +
833A TRP* 3.7 40.6 - - + +
834A SER* 2.9 23.6 + - - +
836A GLU* 1.3 77.1 - - - +
838A GLN* 1.3 66.3 + - - +
840A GLN* 3.4 5.6 + - + +
841A PHE* 3.0 21.7 + - - +
959A PRO* 3.1 34.2 + - - +
960A TYR* 3.8 21.0 - - + +
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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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800A HIS* 3.3 26.9 - - - -
830A PRO 4.6 5.2 + - - +
833A TRP* 3.3 40.5 + - + +
834A SER 3.0 16.2 + - - +
835A LEU* 3.2 26.4 + - - +
837A LYS* 1.3 77.4 - - - +
839A LEU* 1.3 62.2 + - - +
841A PHE* 3.1 13.4 + - - +
842A PHE* 3.2 21.6 + - + -
930A VAL* 4.3 7.2 - - + +
934A THR* 4.4 6.6 - - - +
941A LEU* 3.9 23.5 - - + +
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Residues in contact with LEU 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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835A LEU 3.1 9.4 + - - +
836A GLU 3.9 4.0 - - - +
838A GLN* 1.3 79.1 - - - +
840A GLN* 1.3 61.9 + - - +
842A PHE* 3.4 5.9 + - + +
843A GLN* 3.2 20.1 + - - +
904A MET* 4.7 13.7 - - + +
908A LYS* 3.6 30.1 - - + -
925A LEU* 3.7 18.6 - - + -
926A PRO* 3.4 30.7 - - + +
929A PHE* 3.7 28.0 - - + -
930A VAL* 3.8 24.3 - - + +
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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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836A GLU* 3.0 22.1 + - + +
837A LYS* 3.8 6.7 - - + +
838A GLN 3.2 0.2 - - - -
839A LEU* 1.3 73.6 - - - +
841A PHE* 1.3 59.5 + - - +
843A GLN* 3.4 24.3 + - - +
844A ASP* 2.9 40.1 + - - +
908A LYS* 3.4 24.0 + - - +
960A TYR* 3.5 15.3 - - - +
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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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833A TRP* 3.6 9.9 - + + -
837A LYS 3.0 9.4 + - - +
838A GLN 3.1 8.5 + - - +
840A GLN* 1.3 74.9 - - - +
842A PHE* 1.3 64.5 + + - +
844A ASP* 3.3 1.0 + - - -
845A VAL* 2.8 53.0 + - + +
941A LEU* 3.6 28.5 - - + -
944A THR* 3.8 23.6 - - + -
945A TYR* 4.0 16.4 - + - -
948A MET* 4.4 1.3 - - + -
957A PHE* 4.1 10.3 - + - -
960A TYR* 3.4 54.9 + + + -
961A TYR* 3.8 22.2 - + - -
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Residues in contact with PHE 842 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A GLN* 3.2 19.3 + - + -
839A LEU* 3.7 15.5 - - + +
840A GLN 3.4 0.2 - - - -
841A PHE* 1.3 82.3 - + - +
843A GLN* 1.3 58.2 + - - +
845A VAL* 3.6 4.4 - - - +
846A SER* 2.9 30.2 + - - -
901A LEU* 3.2 34.8 - - + +
904A MET* 3.5 29.2 - - + -
905A ARG* 5.8 0.7 - - - -
930A VAL* 4.2 14.6 - - + -
934A THR* 4.2 12.3 - - + -
940A LEU* 4.0 15.3 - - + -
941A LEU* 3.7 47.6 - - + -
944A THR* 4.3 9.6 - - + -
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Residues in contact with GLN 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 LEU 3.2 13.6 + - - +
840A GLN* 3.6 29.5 - - - +
841A PHE 3.2 0.2 - - - -
842A PHE* 1.3 73.3 - - - +
844A ASP* 1.3 71.0 + - - +
846A SER* 3.1 6.2 + - - -
847A ASP* 2.9 34.1 + - - +
905A ARG* 3.5 40.4 + - + +
908A LYS* 2.6 42.5 + - + +
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Residues in contact with ASP 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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840A GLN* 2.9 27.9 + - - +
841A PHE 3.8 3.1 - - - +
843A GLN* 1.3 83.7 + - - +
845A VAL* 1.3 61.6 + - - +
847A ASP* 3.7 6.7 + - - +
848A ARG* 3.2 23.0 + - - +
956A LEU* 4.1 34.1 - - + +
957A PHE* 4.0 9.7 - - + -
960A TYR* 2.7 38.1 + - + +
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Residues in contact with VAL 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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841A PHE* 2.8 50.9 + - + +
842A PHE* 3.6 6.1 - - - +
844A ASP* 1.3 75.7 - - - +
846A SER* 1.3 66.8 + - - +
848A ARG* 2.9 16.4 + - - +
849A ILE* 3.0 22.2 + - + +
862A LEU* 4.9 1.1 - - + -
901A LEU* 3.9 24.0 - - + -
944A THR* 4.0 9.9 - - + -
948A MET* 3.9 22.9 - - + -
957A PHE* 3.8 14.8 - - + -
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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 PHE 2.9 17.6 + - - -
843A GLN 3.1 4.2 + - - -
845A VAL* 1.3 78.3 - - - +
847A ASP* 1.3 62.4 + - - +
849A ILE* 3.6 10.4 + - - +
850A GLU* 3.2 31.8 + - - +
901A LEU* 3.4 18.3 + - - +
902A ARG* 3.6 13.0 + - - +
905A ARG* 3.3 32.9 - - - +
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Residues in contact with ASP 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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843A GLN* 2.9 28.4 + - - +
844A ASP* 4.1 8.1 - - - +
846A SER* 1.3 76.2 - - - +
848A ARG* 1.3 61.0 + - - +
850A GLU* 3.8 14.8 - - - +
851A LYS 5.2 0.3 + - - -
905A ARG* 3.2 47.0 + - - +
956A LEU* 5.7 5.4 - - + -
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Residues in contact with ARG 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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844A ASP 3.2 18.0 + - - +
845A VAL* 2.9 6.5 + - - +
847A ASP* 1.3 80.9 - - - +
849A ILE* 1.3 60.6 + - + +
850A GLU 3.3 1.8 + - - -
851A LYS* 4.5 4.5 + - - +
852A GLU* 3.2 29.0 + - - +
858A ILE* 3.5 21.1 - - - +
948A MET* 4.1 10.1 - - + -
951A CYS* 3.9 1.9 - - - -
954A GLU* 2.8 40.7 + - - -
956A LEU* 5.0 8.9 - - + +
957A PHE* 3.7 24.0 - - + -
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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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845A VAL* 3.0 25.5 + - + +
846A SER* 3.8 8.5 - - - +
848A ARG* 1.3 76.4 - - + +
850A GLU* 1.3 65.9 + - - +
851A LYS 3.3 3.1 - - - -
852A GLU* 3.3 19.9 + - + +
858A ILE* 3.5 31.0 - - + -
859A VAL* 4.4 6.3 - - + -
862A LEU* 3.5 26.2 - - + -
898A ARG* 3.2 47.4 + - + +
901A LEU* 4.6 3.4 - - + -
948A MET* 4.2 17.3 - - + -
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Residues in contact with GLU 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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846A SER* 3.2 21.1 + - - +
847A ASP* 3.8 13.2 - - - +
848A ARG 3.3 1.8 - - - -
849A ILE* 1.3 77.8 - - - +
851A LYS* 1.3 59.9 + - + +
852A GLU 4.6 0.7 - - - +
898A ARG* 3.2 22.8 + - - +
902A ARG* 3.3 39.1 + - - +
905A ARG* 6.0 0.7 - - - +
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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
------------------------------------------------------------
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