Contacts of the helix formed by residues 910 - 923 (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 LEU 910 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833A GLN* 4.0 8.5 - - - +
836A ASN* 3.6 30.3 - - + +
872A TYR* 3.5 53.2 - - + +
875A GLU* 5.3 1.0 + - - -
905B TYR* 3.8 34.1 - - + -
908B GLY 5.6 1.1 - - - +
909B GLN* 1.3 75.4 + - - +
911B TYR* 1.3 66.7 + - - +
912B GLY 3.3 3.1 - - - -
913B LEU* 3.3 18.0 + - + +
914B GLU* 3.0 27.2 + - + +
941B PHE* 4.4 15.7 - - + -
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Residues in contact with TYR 911 (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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872A TYR* 5.8 0.4 - - - -
875A GLU* 4.2 25.1 + - - +
879A ARG* 4.9 6.5 - - - -
911A TYR* 3.7 28.7 - + - -
1001A MGT 3.1 17.8 + - - -
871B ARG* 4.2 17.0 - - - +
875B GLU* 3.8 41.3 - - + -
878B PHE* 4.1 9.4 - + + -
879B ARG* 2.7 27.1 + - - +
904B ASP* 3.8 0.8 + - - -
909B GLN* 3.7 2.2 - - + +
910B LEU* 1.3 76.8 - - - +
912B GLY* 1.3 62.7 + - - +
914B GLU* 3.4 6.1 + - + +
915B LYS* 3.1 62.1 + - + +
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Residues in contact with GLY 912 (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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878B PHE* 3.7 33.1 - - - -
901B THR* 3.8 8.9 + - - +
904B ASP* 2.9 18.1 + - - -
911B TYR* 1.3 78.8 - - - +
913B LEU* 1.3 55.6 + - - +
915B LYS* 3.1 4.4 + - - +
916B PHE* 2.9 29.3 + - - +
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Residues in contact with LEU 913 (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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901B THR* 3.6 13.0 + - + +
904B ASP* 4.5 1.6 + - - +
905B TYR* 3.4 39.0 - - + +
909B GLN 5.4 0.2 + - - -
910B LEU* 3.3 23.7 + - + +
912B GLY* 1.3 74.8 - - - +
914B GLU* 1.3 57.7 + - - +
916B PHE* 3.3 2.3 + - - +
917B TRP* 2.9 27.5 + - - +
934B LEU* 3.8 23.6 - - + -
937B TYR* 3.8 21.5 - - + +
938B LEU* 3.6 28.0 - - + +
941B PHE* 3.9 19.7 - - + -
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Residues in contact with GLU 914 (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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840A ARG* 5.0 5.2 + - - -
872A TYR* 2.9 33.7 + - - -
879A ARG* 4.2 17.0 + - - -
1001A MGT 4.2 12.9 + - - +
910B LEU* 3.0 23.7 + - + +
911B TYR* 3.8 6.7 - - + +
913B LEU* 1.3 73.5 - - - +
915B LYS* 1.3 64.0 + - + +
917B TRP* 3.4 3.9 + - - +
918B ALA* 2.8 29.3 + - - +
941B PHE* 3.5 31.9 - - + -
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Residues in contact with LYS 915 (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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1001A MGT 2.5 59.4 + - - +
878B PHE* 4.0 26.2 - - + +
879B ARG* 3.7 15.3 - - + +
882B SER* 3.1 29.2 + - - +
883B TYR* 4.7 3.6 - - + -
897B PHE* 3.8 4.3 - - + -
911B TYR* 3.1 53.7 + - + +
912B GLY 3.1 7.4 + - - +
914B GLU* 1.3 79.3 - - - +
916B PHE* 1.3 57.0 + - - +
918B ALA* 3.3 2.5 + - + -
919B PHE* 3.0 23.0 + - - +
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Residues in contact with PHE 916 (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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894B PHE* 3.6 34.3 - + - -
897B PHE* 3.4 34.3 - + + -
898B GLN* 3.6 24.7 - - + -
901B THR* 3.8 17.0 - - + +
912B GLY 2.9 15.4 + - - +
913B LEU 3.7 4.7 - - - +
915B LYS* 1.3 74.6 - - - +
917B TRP* 1.3 64.7 + - - +
919B PHE* 3.1 5.4 + + - +
920B LEU* 3.1 41.8 + - + +
930B ILE* 3.9 9.2 - - + -
934B LEU* 3.7 23.6 - - + -
938B LEU* 3.9 23.1 - - + -
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Residues in contact with TRP 917 (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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913B LEU 2.9 16.8 + - - +
914B GLU* 3.7 4.9 - - - +
915B LYS 3.4 0.2 - - - -
916B PHE* 1.3 76.6 - - - +
918B ALA* 1.3 63.5 + - - +
920B LEU* 3.3 26.0 + - + +
921B LYS* 3.1 33.5 + - + +
938B LEU* 3.8 32.9 - - + +
941B PHE* 3.8 37.3 + + + +
942B ARG* 4.6 27.6 - - + -
945B GLU* 5.0 12.7 - - + +
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Residues in contact with ALA 918 (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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1001A MGT 3.4 46.2 - - + +
882B SER* 4.0 3.4 - - - +
914B GLU 2.8 18.3 + - - +
915B LYS* 3.5 7.0 - - - +
917B TRP* 1.3 79.6 - - - +
919B PHE* 1.3 62.1 + - - +
921B LYS* 3.0 15.8 + - - -
922B TYR* 3.1 23.7 + - + -
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Residues in contact with PHE 919 (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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1001A MGT 4.2 4.9 - - - -
881B TYR 4.5 0.9 - - - -
882B SER* 3.6 24.8 + - - +
885B LEU* 3.5 26.5 - - + -
886B GLU* 3.5 13.0 - - + -
889B PHE* 4.0 23.1 - + - -
894B PHE* 3.5 28.7 - + - -
897B PHE* 3.9 15.7 - + + -
915B LYS 3.0 13.5 + - - +
916B PHE* 3.1 9.4 + + - +
918B ALA* 1.3 75.7 - - - +
920B LEU* 1.3 64.0 + - + +
923B SER* 2.7 61.8 + - - -
928B LEU* 3.8 17.3 - - + -
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Residues in contact with LEU 920 (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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916B PHE* 3.1 41.4 + - + +
917B TRP* 3.3 26.4 + - + +
919B PHE* 1.3 83.7 - - + +
921B LYS* 1.3 61.7 + - - +
923B SER* 4.0 11.9 + - - +
928B LEU* 4.0 25.8 - - + -
930B ILE* 4.2 15.7 - - + -
938B LEU* 3.8 18.2 - - + -
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Residues in contact with LYS 921 (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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917B TRP* 3.1 23.5 + - + +
918B ALA* 3.0 13.4 + - - +
920B LEU* 1.3 79.8 - - - +
922B TYR* 1.3 96.5 + - + +
923B SER 3.9 2.3 + - - +
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Residues in contact with TYR 922 (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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1001A MGT 3.5 75.3 + + + +
886B GLU* 3.8 31.4 - - - +
918B ALA* 3.1 26.1 + - + +
919B PHE 4.5 0.7 - - - +
921B LYS* 1.3 111.6 + - + +
923B SER* 1.3 66.5 + - - +
924B LYS* 3.5 8.3 + - - +
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Residues in contact with SER 923 (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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885B LEU 5.4 0.3 + - - -
886B GLU* 4.3 11.8 + - - +
919B PHE* 2.7 53.1 + - - -
920B LEU* 4.0 10.6 + - - +
921B LYS 3.5 2.9 - - - +
922B TYR* 1.3 73.7 - - - +
924B LYS* 1.3 60.2 + - - +
925B ALA* 3.2 30.8 + - - +
928B LEU* 4.8 3.8 - - - -
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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