Contacts of the helix formed by residues 834 - 850 (chain B) in PDB entry 4YZC
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955A ARG* 6.2 0.9 - - - -
832B PHE 3.6 3.2 + - - -
833B TRP* 1.3 77.8 - - - +
835B LEU* 1.3 68.4 + - - +
836B GLU* 3.8 10.4 + - - +
837B LYS* 3.3 19.7 + - - +
838B GLN* 3.1 21.1 + - - +
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Residues in contact with LEU 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A ARG* 6.0 0.2 - - - +
800B HIS* 6.1 0.7 - - + -
833B TRP 5.3 0.4 - - - +
834B SER* 1.3 73.3 - - - +
836B GLU* 1.3 65.6 + - - +
838B GLN* 3.8 25.7 - - - +
839B LEU* 3.1 24.3 + - - +
926B PRO* 4.8 1.5 - - - +
927B ASP* 3.6 42.0 - - + +
930B VAL* 3.6 17.6 - - + +
931B CYS* 3.7 29.4 - - - -
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Residues in contact with GLU 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A ARG* 2.5 55.2 + - - +
959A PRO* 6.0 2.4 - - - +
834B SER* 3.3 8.6 + - - +
835B LEU* 1.3 79.0 - - - +
837B LYS* 1.3 51.3 + - - +
839B LEU* 3.3 2.8 + - - +
840B GLN* 2.7 37.5 + - - +
926B PRO* 3.5 23.8 - - + -
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Residues in contact with LYS 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B LYS* 6.4 0.4 - - - +
833B TRP* 3.4 50.7 - - + +
834B SER* 3.3 18.1 + - - +
835B LEU 3.3 0.4 - - - -
836B GLU* 1.3 75.9 - - - +
838B GLN* 1.3 61.0 + - - +
840B GLN* 4.3 5.4 - - + -
841B PHE* 2.8 30.5 + - - +
959B PRO* 3.4 40.0 + - - +
960B TYR* 3.8 12.6 - - + -
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Residues in contact with GLN 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B HIS* 3.5 26.0 - - - -
830B PRO 4.6 5.3 + - - -
833B TRP* 3.5 39.2 + - + +
834B SER 3.1 12.6 + - - +
835B LEU* 3.8 26.0 - - - +
836B GLU 3.3 0.2 - - - -
837B LYS* 1.3 77.2 - - - +
839B LEU* 1.3 57.1 + - - +
841B PHE* 3.2 4.7 + - - +
842B PHE* 2.9 34.7 + - + -
930B VAL* 4.2 8.9 - - + +
934B THR* 4.1 9.2 + - - +
941B LEU* 3.7 27.6 - - + +
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Residues in contact with LEU 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B LEU 3.1 15.1 + - - +
836B GLU* 3.8 4.0 - - - +
838B GLN* 1.3 79.4 - - - +
840B GLN* 1.3 57.3 + - - +
842B PHE* 3.2 6.0 + - + +
843B GLN* 2.8 27.9 + - - +
904B MET* 4.6 13.2 - - + +
908B LYS* 4.0 24.5 - - + +
925B LEU* 3.9 24.2 - - + -
926B PRO* 3.8 28.9 - - + +
929B PHE* 3.5 28.3 - - + -
930B VAL* 3.9 20.1 - - + +
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Residues in contact with GLN 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A GLN* 5.0 14.3 + - - +
836B GLU 2.7 21.8 + - - +
837B LYS* 3.8 7.2 - - - +
839B LEU* 1.3 69.3 - - - +
841B PHE* 1.3 60.9 + - - +
843B GLN* 3.2 30.7 + - - +
844B ASP* 2.9 58.7 + - - +
908B LYS* 3.5 8.1 + - - +
960B TYR* 3.3 14.8 - - - +
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Residues in contact with PHE 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B TRP* 3.5 17.9 - + + -
837B LYS 2.8 18.7 + - - +
838B GLN 3.4 3.4 - - - +
840B GLN* 1.3 76.2 - - - +
842B PHE* 1.3 61.1 + + - +
844B ASP* 3.3 1.0 + - - +
845B VAL* 2.9 59.3 + - + +
941B LEU* 3.7 22.4 - - + -
944B THR* 4.1 11.0 - - + -
945B TYR* 3.8 26.5 - + - -
948B MET* 4.4 0.7 - - + -
957B PHE* 4.0 12.8 - + - -
960B TYR* 3.4 42.7 + + + -
961B TYR* 3.7 24.0 - - - -
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Residues in contact with PHE 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B GLN* 2.9 21.6 + - + -
839B LEU* 3.5 9.2 - - + +
841B PHE* 1.3 80.8 - + - +
843B GLN* 1.3 62.5 + - - +
845B VAL* 3.8 3.5 - - - +
846B SER* 3.0 25.8 + - - -
901B LEU* 3.7 22.4 - - + +
904B MET* 3.5 32.1 - - + -
905B ARG* 6.1 0.2 - - - -
930B VAL* 4.2 10.5 - - + -
934B THR* 4.0 23.8 - - + -
940B LEU* 3.8 23.6 - - + -
941B LEU* 3.6 46.0 - - + -
944B THR* 4.1 13.0 - - + -
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Residues in contact with GLN 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A GLN* 5.6 0.4 - - - +
843A GLN* 3.8 20.4 - - - +
839B LEU 2.8 14.4 + - - +
840B GLN* 3.2 28.0 + - - +
842B PHE* 1.3 76.6 - - - +
844B ASP* 1.3 61.5 + - - +
846B SER* 3.2 2.5 + - - -
847B ASP* 2.8 37.0 + - - +
905B ARG* 3.5 48.3 + - - +
908B LYS* 2.5 41.6 + - + +
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Residues in contact with ASP 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B GLN* 2.9 35.9 + - - +
841B PHE 4.0 2.5 - - - +
843B GLN* 1.3 77.0 + - - +
845B VAL* 1.3 61.4 + - - +
847B ASP* 3.7 7.8 - - - +
848B ARG* 2.9 30.8 + - - +
956B LEU* 3.5 38.0 - - + +
957B PHE* 3.6 10.5 - - + -
960B TYR* 2.6 30.2 + - + +
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Residues in contact with VAL 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B PHE* 2.9 48.3 + - + +
842B PHE* 3.8 4.9 - - - +
844B ASP* 1.3 76.6 - - - +
846B SER* 1.3 59.6 + - - +
848B ARG* 2.9 3.7 + - - +
849B ILE* 2.9 36.1 + - + +
862B LEU* 4.8 0.7 - - + -
901B LEU* 3.7 15.5 - - + -
944B THR* 3.7 21.8 - - + -
948B MET* 3.8 22.0 - - + -
957B PHE* 3.5 24.2 - - + -
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Residues in contact with SER 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B PHE 3.0 18.5 + - - -
843B GLN 3.6 3.1 - - - -
845B VAL* 1.3 76.5 - - - +
847B ASP* 1.3 62.9 + - - +
849B ILE* 3.5 11.7 - - - +
850B GLU* 3.1 30.5 + - - +
901B LEU* 3.4 29.5 + - - -
902B ARG* 3.5 16.3 + - - +
905B ARG* 3.4 19.0 - - - +
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Residues in contact with ASP 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909A HIS* 3.6 22.1 + - + -
843B GLN* 2.8 25.3 + - - +
844B ASP* 3.9 9.4 - - - +
846B SER* 1.3 73.5 - - - +
848B ARG* 1.3 58.2 + - - +
850B GLU* 3.0 18.8 - - - +
905B ARG* 2.6 48.9 + - - +
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Residues in contact with ARG 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844B ASP 2.9 19.4 + - - +
845B VAL 2.9 4.4 + - - +
847B ASP* 1.3 78.6 - - - +
849B ILE* 1.3 65.7 + - + +
850B GLU 4.1 2.4 - - - +
852B GLU* 3.6 27.4 + - - +
858B ILE* 3.5 22.1 - - + +
948B MET* 4.3 5.4 - - + -
951B CYS* 3.9 7.4 - - - -
954B GLU* 2.7 42.4 + - - -
956B LEU* 4.6 9.4 - - + +
957B PHE* 3.6 22.9 - - + -
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Residues in contact with ILE 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845B VAL* 2.9 22.0 + - + +
846B SER* 3.5 14.6 - - - +
848B ARG* 1.3 77.7 - - - +
850B GLU* 1.3 60.1 + - + +
852B GLU* 2.8 35.3 + - - +
858B ILE* 3.9 26.0 - - + -
859B VAL* 4.3 12.1 - - + +
862B LEU* 3.6 24.7 - - + -
898B ARG* 3.5 41.0 + - + +
901B LEU* 4.2 7.2 - - + -
902B ARG* 5.8 0.4 - - + -
948B MET* 4.0 19.5 - - + -
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Residues in contact with GLU 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A GLU* 5.4 1.2 - - - +
846B SER* 3.1 17.5 + - - +
847B ASP* 3.0 21.5 - - - +
848B ARG 4.1 2.2 - - - +
849B ILE* 1.3 78.1 - - + +
851B LYS* 1.3 61.5 + - + +
898B ARG* 3.4 22.1 + - - +
902B ARG* 3.3 42.6 + - + +
905B ARG* 6.0 1.7 - - - +
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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
------------------------------------------------------------
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