Contacts of the helix formed by residues 910 - 922 (chain B) in PDB entry 4Q0R
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 PHE 910 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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876B SER* 5.1 0.7 - - - -
879B GLU* 3.5 59.9 - - + -
880B VAL* 4.1 4.5 - - + -
883B GLU* 4.0 17.3 - - + -
884B PHE* 5.5 5.4 - + - -
909B LYS* 1.3 77.4 - - - +
911B GLU* 1.3 70.2 + - + +
913B ASP* 3.5 9.2 + - + +
914B LEU* 3.2 51.7 + - + +
917B LYS* 6.2 2.2 - - - -
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Residues in contact with GLU 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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884B PHE* 5.4 4.3 - - + -
893B TRP* 3.3 44.2 - - + +
909B LYS 3.2 4.7 - - - +
910B PHE* 1.3 86.7 - - + +
912B LYS* 1.3 63.8 + - - +
914B LEU* 3.3 1.6 + - - -
915B ARG* 3.0 24.8 + - - +
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Residues in contact with LYS 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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909B LYS* 3.0 29.3 - - - +
911B GLU* 1.3 82.2 - - - +
913B ASP* 1.3 67.7 + - - +
915B ARG* 3.3 6.3 + - - +
916B LYS* 3.3 19.4 + - - +
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Residues in contact with ASP 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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909B LYS 2.6 19.8 + - - +
910B PHE* 3.5 7.1 + - + +
912B LYS* 1.3 78.0 - - - +
914B LEU* 1.3 58.4 + - - +
916B LYS* 3.5 8.2 + - - +
917B LYS* 3.0 32.9 + - - +
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Residues in contact with LEU 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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872B MSE 4.8 12.1 - - - -
876B SER* 6.3 0.2 - - - -
880B VAL* 3.9 17.0 - - + -
884B PHE* 5.1 3.8 - - + -
890B PHE* 4.2 12.3 - - + -
893B TRP* 4.1 16.2 - - + -
910B PHE* 3.2 49.1 + - + +
911B GLU* 3.6 4.5 - - - +
912B LYS 3.1 0.8 - - - -
913B ASP* 1.3 76.2 - - - +
915B ARG* 1.3 65.3 + - - +
917B LYS* 3.1 21.6 + - + +
918B LEU* 3.0 43.5 + - + +
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Residues in contact with ARG 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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893B TRP* 2.7 68.7 + - + +
894B TYR* 4.1 24.3 - - + -
897B GLY* 4.0 30.9 - - - -
898B GLN* 4.3 5.9 - - - +
911B GLU* 3.0 16.3 + - - +
912B LYS* 3.3 6.0 + - - +
914B LEU* 1.3 75.2 - - - +
916B LYS* 1.3 57.0 + - - +
918B LEU* 4.0 0.9 - - - +
919B VAL* 2.9 35.0 + - + +
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Residues in contact with LYS 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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912B LYS 3.3 10.7 + - - +
913B ASP* 3.5 12.3 - - - +
915B ARG* 1.3 79.0 - - - +
917B LYS* 1.3 56.8 + - - +
919B VAL* 3.7 5.8 - - - +
920B ASN* 2.9 30.4 + - - +
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Residues in contact with LYS 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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871B GLY* 4.1 23.1 - - - +
872B MSE 5.6 3.5 - - - -
876B SER* 3.3 24.0 + - - +
910B PHE* 6.2 2.0 - - - -
913B ASP* 3.0 21.4 + - - +
914B LEU* 3.1 22.3 + - + +
916B LYS* 1.3 74.6 - - - +
918B LEU* 1.3 56.5 + - + +
920B ASN* 3.2 6.7 + - - +
921B ASN* 2.6 36.6 + - + +
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Residues in contact with LEU 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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869B LEU* 4.8 3.4 - - + -
870B LYS 5.4 0.7 - - - +
871B GLY 6.6 0.2 - - - -
872B MSE 4.5 21.3 - - + -
890B PHE* 3.6 31.0 - - + -
893B TRP* 4.6 1.8 - - + -
894B TYR* 3.7 42.8 - - + +
914B LEU* 3.0 31.7 + - + +
915B ARG 4.0 0.2 - - - +
917B LYS* 1.3 75.3 - - + +
919B VAL* 1.3 66.5 + - - +
921B ASN* 3.1 5.5 + - + +
922B GLU 2.9 18.5 + - - -
923B ILE* 3.3 39.2 + - + +
925B LEU* 5.3 0.4 - - + -
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Residues in contact with VAL 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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894B TYR* 3.8 10.3 + - + +
915B ARG* 2.9 23.6 + - + +
916B LYS* 3.7 6.7 - - - +
918B LEU* 1.3 73.2 - - - +
920B ASN* 1.3 56.0 + - - +
922B GLU* 2.8 26.8 + - - +
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Residues in contact with ASN 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 LYS 2.9 20.1 + - - +
917B LYS* 3.6 6.3 - - - +
919B VAL* 1.3 75.8 - - - +
921B ASN* 1.3 59.1 + - - +
922B GLU* 3.2 3.2 + - - +
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Residues in contact with ASN 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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870B LYS* 3.4 33.2 - - + +
871B GLY* 5.2 3.1 - - - -
917B LYS* 2.6 21.3 + - + +
918B LEU* 3.1 9.4 + - + +
920B ASN* 1.3 72.4 - - - +
922B GLU* 1.3 71.0 + - - +
923B ILE* 3.6 13.0 - - + +
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Residues in contact with GLU 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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918B LEU 2.9 2.2 + - - -
919B VAL* 2.8 17.4 + - - +
920B ASN 3.2 3.3 - - - +
921B ASN* 1.3 81.6 - - - +
923B ILE* 1.3 57.8 + - - +
924B ILE* 4.2 6.8 + - - +
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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