Contacts of the helix formed by residues 909 - 920 (chain B) in PDB entry 4UN5
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 909 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906B GLY 5.2 2.2 - - - -
907B GLY 3.4 4.7 + - - -
908B LEU* 1.3 78.1 - - - +
910B GLU* 1.3 64.4 + - - +
911B LEU* 3.5 11.7 + - - +
912B ASP* 3.0 42.4 + - - +
913B LYS* 3.2 13.2 + - - +
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Residues in contact with GLU 910 (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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908B LEU 5.2 0.3 - - - +
909B SER* 1.3 71.9 - - - +
911B LEU* 1.3 59.6 + - - +
913B LYS* 3.2 29.8 + - + +
914B ALA* 2.9 30.3 + - - +
1032B ALA* 3.6 12.4 - - + +
1033B THR* 3.6 37.9 - - + +
1036B TYR* 4.9 9.1 - - + -
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Residues in contact with LEU 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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909B SER* 3.6 10.5 - - - +
910B GLU* 1.3 79.7 - - - +
912B ASP* 1.3 62.1 + - - +
914B ALA* 3.5 4.1 + - + +
915B GLY* 2.9 26.5 + - - -
1032B ALA* 3.5 20.8 - - + +
1035B LYS* 6.0 7.0 - - + +
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Residues in contact with ASP 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902B LYS* 4.0 16.7 - - - -
907B GLY 4.0 1.2 - - - +
908B LEU* 3.7 20.0 - - + -
909B SER* 3.0 38.0 + - - +
911B LEU* 1.3 83.3 - - - +
913B LYS* 1.3 56.8 + - - +
915B GLY* 3.4 1.4 + - - -
916B PHE* 2.9 42.3 + - + -
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Residues in contact with LYS 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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846B PHE* 3.5 39.9 - - + -
868B ASP* 4.0 15.0 + - - -
869B ASN* 4.1 9.9 - - - +
908B LEU* 3.1 39.2 + - + +
909B SER 3.6 5.8 + - - +
910B GLU* 3.2 34.0 + - - +
912B ASP* 1.3 75.0 - - - +
914B ALA* 1.3 65.4 + - - +
916B PHE* 3.2 4.2 + - + +
917B ILE* 2.9 27.7 + - - +
1036B TYR* 3.6 22.2 - - + +
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Residues in contact with ALA 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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910B GLU 2.9 12.3 + - - +
911B LEU* 3.8 6.1 - - + +
913B LYS* 1.3 75.1 - - - +
915B GLY* 1.3 57.8 + - - +
917B ILE* 3.3 3.1 + - - +
918B LYS* 2.9 31.8 + - - +
1032B ALA* 3.3 29.4 - - - +
1035B LYS* 3.9 17.0 - - + -
1036B TYR* 3.6 22.9 - - - +
1039B TYR* 4.7 2.8 - - - -
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Residues in contact with GLY 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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911B LEU 2.9 17.8 + - - -
912B ASP* 3.7 2.7 - - - -
914B ALA* 1.3 76.7 - - - +
916B PHE* 1.3 56.2 + - - +
918B LYS* 3.3 4.9 - - - +
919B ARG* 2.7 52.9 + - - +
1035B LYS* 6.2 0.9 - - - -
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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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842B VAL* 4.4 16.8 - - + -
846B PHE* 3.6 40.7 - + + +
847B LEU* 4.2 24.9 - - + -
908B LEU* 4.0 28.5 - - + -
912B ASP* 2.9 30.5 + - + +
913B LYS* 3.6 6.5 - - + +
915B GLY* 1.3 74.2 - - - +
917B ILE* 1.3 62.8 + - - +
919B ARG* 3.0 15.5 + - + +
920B GLN* 3.0 27.8 + - - +
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Residues in contact with ILE 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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845B SER 5.2 4.9 - - - +
846B PHE* 5.1 7.9 - - + -
913B LYS 2.9 18.5 + - - +
914B ALA* 3.7 5.8 - - - +
916B PHE* 1.3 78.1 - - - +
918B LYS* 1.3 62.8 + - - +
920B GLN* 3.1 33.3 + - - +
921B LEU* 3.6 10.7 - - + +
1036B TYR* 3.5 43.5 - - + +
1039B TYR* 3.8 24.9 - - + +
1040B SER* 4.0 25.8 - - - +
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Residues in contact with LYS 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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914B ALA 2.9 12.2 + - - +
915B GLY* 3.3 13.9 - - - +
917B ILE* 1.3 77.1 - - - +
919B ARG* 1.3 79.2 + - + +
921B LEU* 3.2 4.7 + - - +
922B VAL* 2.9 59.6 + - + +
1007B GLU* 4.2 16.2 + - - -
1035B LYS* 3.8 19.9 - - + +
1039B TYR* 3.3 58.6 + - + -
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Residues in contact with ARG 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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1A A 5.5 4.8 + - - -
915B GLY* 2.7 54.2 + - - +
916B PHE* 3.0 18.6 + - + +
918B LYS* 1.3 95.7 - - + +
920B GLN* 1.3 61.9 + - - +
921B LEU 3.1 2.0 + - - -
922B VAL 3.6 9.5 - - - +
924B THR* 4.4 25.7 - - + +
959B LYS* 3.2 26.4 + - - +
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Residues in contact with GLN 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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844B GLN 4.6 0.6 + - - -
845B SER 3.0 24.0 + - - +
846B PHE* 2.9 28.2 + - - +
848B LYS* 4.5 18.7 - - + +
916B PHE 3.0 16.2 + - - +
917B ILE* 3.1 21.6 + - - +
919B ARG* 1.3 78.9 - - - +
921B LEU* 1.3 59.7 + - + +
959B LYS* 3.6 16.1 - - - +
961B LYS* 3.3 51.8 - - + +
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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