Contacts of the helix formed by residues 832 - 849 (chain B) in PDB entry 5V4R
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 832 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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823B GLU* 2.5 54.5 + - - +
824B ARG* 4.2 4.0 - - - -
827B LEU* 4.4 1.1 - - - -
828B GLY 5.0 1.6 - - - -
830B GLY 3.6 2.9 + - - +
831B GLN* 1.3 77.5 - - - +
833B GLN* 1.3 64.4 + - - +
835B MET* 3.0 30.1 + - - +
836B ASN* 3.3 23.3 + - - +
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Residues in contact with GLN 833 (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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905A TYR* 3.5 43.7 + - - +
908A GLY* 5.6 6.7 - - - -
909A GLN 5.7 0.6 + - - -
910A LEU* 3.9 5.8 - - - +
940A LYS* 2.8 41.4 - - + +
823B GLU* 3.8 2.8 + - - +
830B GLY 5.5 4.4 + - - -
831B GLN 4.1 3.6 + - - +
832B SER* 1.3 71.3 - - - +
834B GLU* 1.3 67.9 + - - +
836B ASN* 2.8 28.9 + - - +
837B THR* 3.0 25.8 + - - +
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Residues in contact with GLU 834 (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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797B HIS* 3.0 35.5 + - - -
816B TYR* 4.3 7.3 - - - -
819B ARG* 3.8 28.7 + - + +
820B CYS* 3.3 22.7 - - - +
823B GLU* 3.4 26.5 + - + +
832B SER* 3.2 1.7 + - - +
833B GLN* 1.3 79.2 - - - +
835B MET* 1.3 61.3 + - - +
837B THR* 2.5 29.5 + - - +
838B LEU 3.2 4.0 + - - -
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Residues in contact with MET 835 (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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820B CYS* 4.2 15.8 - - - +
821B LEU* 4.1 19.5 - - - -
824B ARG* 3.8 30.3 - - + +
832B SER* 3.0 28.5 + - - +
833B GLN 3.2 0.2 - - - -
834B GLU* 1.3 75.0 - - - +
836B ASN* 1.3 64.0 + - - +
838B LEU* 3.1 27.2 + - + +
839B PHE* 3.1 44.4 + - + -
842B TRP* 3.9 7.6 - - + -
861B LEU* 3.7 24.0 - - + -
865B ASP* 5.1 1.1 - - - +
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Residues in contact with ASN 836 (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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908A GLY 5.2 6.5 + - - -
910A LEU* 3.6 24.4 - - + +
940A LYS* 4.0 3.1 - - - +
830B GLY* 5.5 7.0 + - - -
832B SER 3.3 9.0 + - - +
833B GLN* 2.8 41.2 + - - +
835B MET* 1.3 79.5 - - - +
837B THR* 1.3 62.4 + - - +
839B PHE* 3.2 14.5 + - - -
840B ARG* 3.0 19.4 + - - +
865B ASP* 4.9 3.3 - - - +
872B TYR* 3.3 35.7 - - + +
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Residues in contact with THR 837 (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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940A LYS* 3.5 19.7 - - + +
944A LEU* 4.2 17.7 - - + -
797B HIS* 3.4 26.9 - - + +
799B SER* 4.5 5.8 - - - -
816B TYR* 2.7 26.3 + - - -
833B GLN 3.0 15.6 + - - +
834B GLU* 2.5 28.2 + - - +
836B ASN* 1.3 75.7 - - - +
838B LEU* 1.3 55.2 + - - +
840B ARG* 3.4 8.9 + - - +
841B PHE* 2.8 24.8 + - - +
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Residues in contact with LEU 838 (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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813B TYR* 4.3 7.9 - - + -
816B TYR* 3.3 26.7 - - + +
817B ARG* 4.5 14.6 - - + +
820B CYS* 3.8 22.2 - - + -
821B LEU* 4.7 3.6 - - + -
834B GLU 3.2 5.4 + - - +
835B MET* 3.1 21.8 + - + +
837B THR* 1.3 78.9 + - - +
839B PHE* 1.3 64.4 + - - +
841B PHE* 3.2 8.6 + - + -
842B TRP* 2.9 74.6 + - + +
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Residues in contact with PHE 839 (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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824B ARG* 4.5 0.7 - - - -
835B MET* 3.1 40.9 + - + -
836B ASN* 3.5 19.3 - - - +
838B LEU* 1.3 76.1 - - - +
840B ARG* 1.3 57.0 + - - +
842B TRP* 3.4 9.1 + + - +
843B SER* 3.0 29.5 + - - -
858B PHE* 3.8 22.4 - + - -
861B LEU* 3.8 19.7 - - + -
862B ALA* 3.6 35.0 - - + -
865B ASP* 3.3 24.2 - - - -
872B TYR* 4.3 1.3 - + + -
873B GLY* 3.5 21.1 - - - -
876B CYS* 3.7 20.3 - - + +
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Residues in contact with ARG 840 (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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914A GLU* 6.1 0.4 - - - -
940A LYS* 5.9 0.7 - - - +
941A PHE* 6.0 2.2 - - - -
944A LEU* 3.7 49.3 + - - +
945A GLU* 4.8 15.6 + - - +
799B SER* 4.4 10.3 + - - -
800B HIS* 5.8 0.6 - - - +
803B LEU* 4.1 21.0 - - - +
836B ASN 3.0 9.9 + - - +
837B THR* 3.6 8.5 + - - +
838B LEU 3.2 0.2 - - - -
839B PHE* 1.3 76.5 - - - +
841B PHE* 1.3 62.9 + - - +
843B SER* 3.3 3.2 + - - -
844B PHE* 3.2 57.7 + - + -
872B TYR* 3.5 23.1 - - - +
876B CYS* 3.9 9.4 - - - -
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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
----------------------------------------------------------
799B SER* 4.0 20.0 - - - -
802B LEU* 3.4 35.0 - - + -
803B LEU* 3.6 36.6 - - + -
808B PHE* 4.2 5.2 - + - -
813B TYR* 3.6 26.0 - + - -
816B TYR* 4.2 5.6 - + - +
837B THR 2.8 16.7 + - - +
838B LEU* 3.2 16.5 + - + +
840B ARG* 1.3 77.4 - - - +
842B TRP* 1.3 70.7 + + - +
844B PHE* 3.2 2.3 + - - +
845B PHE* 2.7 69.8 + + + +
854B MET* 4.3 1.1 - - - -
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Residues in contact with TRP 842 (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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813B TYR* 3.0 23.3 + - - -
817B ARG* 5.0 0.9 - - + -
821B LEU* 5.3 0.2 - - + -
835B MET* 3.9 13.5 - - + -
838B LEU* 2.9 55.5 + - + +
839B PHE* 3.8 11.0 - + - +
841B PHE* 1.3 88.8 - + - +
843B SER* 1.3 63.5 + - - +
845B PHE* 4.7 1.3 - - - -
846B LEU* 3.1 34.8 + - + +
854B MET* 3.9 29.7 - - + +
857B GLU* 3.6 38.6 - - + -
858B PHE* 3.5 52.7 - + + -
861B LEU* 4.1 9.0 - - + -
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Residues in contact with SER 843 (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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839B PHE 3.0 18.5 + - - -
840B ARG* 3.6 7.6 - - - -
841B PHE 3.2 0.4 - - - -
842B TRP* 1.3 77.2 - - - +
844B PHE* 1.3 55.7 + - - +
847B ARG* 2.7 52.4 + - - +
858B PHE* 3.9 10.5 - - - -
876B CYS* 2.8 36.3 + - - -
879B ARG* 4.1 3.3 + - - +
880B TYR* 3.7 9.4 + - - +
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Residues in contact with PHE 844 (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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803B LEU* 4.0 22.2 - - + -
840B ARG* 3.2 60.2 + - + +
841B PHE 4.0 1.8 - - - +
843B SER* 1.3 78.9 - - - +
845B PHE* 1.3 65.7 + - - +
846B LEU 3.2 0.2 - - - -
847B ARG* 3.2 52.9 + - - +
848B ASP* 4.2 6.9 + - - +
879B ARG* 6.3 0.9 - - - -
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Residues in contact with PHE 845 (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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802B LEU 4.1 7.9 - - - -
803B LEU* 3.8 9.1 - - + +
808B PHE* 3.6 41.1 - + + -
841B PHE* 2.7 49.0 + + + +
842B TRP* 4.4 1.3 - - - +
844B PHE* 1.3 72.8 - - - +
846B LEU* 1.3 59.1 + - - +
847B ARG 3.2 0.9 + - - -
848B ASP* 3.4 3.4 + - - +
849B HIS* 3.0 74.8 + + + -
851B ASN* 4.5 2.2 - - - -
854B MET* 3.8 36.1 - - + -
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Residues in contact with LEU 846 (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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842B TRP* 3.1 29.9 + - + +
845B PHE* 1.3 75.5 - - + +
847B ARG* 1.3 64.5 + - - +
848B ASP 3.3 0.2 - - - -
849B HIS 3.9 5.2 - - - +
850B PHE* 3.5 22.9 + - + +
851B ASN* 3.7 46.0 - - - +
854B MET* 3.9 13.2 - - + -
855B TYR* 3.8 24.9 - - + +
858B PHE* 3.6 26.9 - - + -
880B TYR* 3.4 25.1 - - + +
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Residues in contact with ARG 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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843B SER* 2.7 42.9 + - - +
844B PHE* 3.5 42.9 - - - +
845B PHE 3.1 1.0 - - - -
846B LEU* 1.3 79.6 - - - +
848B ASP* 1.3 68.7 + - - +
850B PHE* 5.2 0.7 + - - +
879B ARG* 3.9 21.7 + - - +
880B TYR* 4.0 12.5 - - + +
883B TYR* 3.5 38.9 - - - +
884B GLY* 3.9 25.8 - - - +
887B LYS* 5.4 6.5 - - + +
888B LYS* 4.4 19.1 - - - +
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Residues in contact with ASP 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 PHE 4.5 6.6 - - - +
845B PHE* 3.4 2.8 + - - +
847B ARG* 1.3 84.5 - - - +
849B HIS* 1.3 88.2 + - + +
850B PHE 3.8 1.7 + - - -
887B LYS* 5.9 4.3 - - - +
888B LYS* 6.0 4.6 - - - +
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Residues in contact with HIS 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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805B GLU* 6.4 2.2 - - - -
845B PHE* 3.0 63.3 + + + +
846B LEU* 3.9 4.6 - - - +
848B ASP* 1.3 102.0 + - + +
850B PHE* 1.3 66.4 + - - +
851B ASN* 3.4 4.7 + - - +
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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