Contacts of the helix formed by residues 944 - 954 (chain B) in PDB entry 3O33
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 ASP 944 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924B PHE* 3.6 14.6 - - - +
925B GLN 3.8 0.9 - - - +
926B ASP 3.7 15.7 - - - +
927B PRO* 3.1 37.3 - - + +
928B VAL* 6.6 0.2 - - + -
942B PRO* 5.6 1.0 - - - +
943B MET* 1.3 81.2 + - - +
945B LEU* 1.3 63.5 + - - +
946B SER* 2.8 11.4 + - - -
947B THR* 2.7 47.7 + - - -
948B ILE* 3.3 15.6 + - - +
972B ILE* 3.6 11.4 - - - -
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Residues in contact with LEU 945 (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 LEU* 3.8 11.1 - - + +
915B LEU* 3.9 42.2 - - + -
916B TYR* 3.5 29.8 + - + +
921B SER* 4.2 10.3 - - - -
924B PHE* 2.9 27.6 + - + +
925B GLN* 4.0 20.2 - - + -
944B ASP* 1.3 71.9 - - - +
946B SER* 1.3 58.0 + - - +
948B ILE* 3.2 4.0 + - - +
949B LYS* 2.9 29.1 + - - +
969B PHE* 3.9 12.8 - - + -
972B ILE* 3.7 16.8 - - + +
973B PHE* 6.3 0.2 - - + -
993B LEU* 5.3 2.5 - - + -
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Residues in contact with SER 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916B TYR* 3.2 13.2 + - - -
925B GLN 2.9 18.6 + - - -
926B ASP* 3.8 16.6 + - - -
927B PRO* 3.9 6.2 - - - +
944B ASP* 2.8 19.1 + - - -
945B LEU* 1.3 77.1 - - - +
947B THR* 1.3 56.7 + - - +
949B LYS* 3.5 1.3 + - - -
950B LYS* 2.7 58.2 + - - +
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Residues in contact with THR 947 (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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927B PRO* 4.7 4.0 - - - +
943B MET* 3.8 20.3 - - + -
944B ASP* 2.7 39.8 + - - -
945B LEU 3.2 0.2 - - - -
946B SER* 1.3 71.7 + - - +
948B ILE* 1.3 62.0 + - - +
950B LYS* 3.5 5.0 + - - +
951B ARG* 3.0 61.2 + - + +
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Residues in contact with ILE 948 (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 CYS* 4.2 12.8 - - - -
912B LEU* 3.9 20.9 - - + -
943B MET* 3.9 5.4 - - - -
944B ASP 3.3 8.7 + - - +
945B LEU 3.2 6.1 + - - +
947B THR* 1.3 73.8 - - - +
949B LYS* 1.3 66.3 + - - +
951B ARG* 3.3 1.2 + - - +
952B LEU* 2.9 23.2 + - - +
959B TYR* 3.5 30.5 - - + +
965B PHE* 4.7 2.2 - - + -
968B ASP* 3.8 9.9 - - + -
969B PHE* 3.6 45.1 - - + +
972B ILE* 3.8 23.6 - - + -
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Residues in contact with LYS 949 (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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851B SER 2.7 29.9 + - - -
852B CYS 4.2 2.0 + - - -
853B HIS 3.0 18.0 + - - -
854B VAL* 4.0 26.8 - - + +
855B PRO* 4.7 1.3 - - + -
856B THR* 2.8 28.6 + - - +
912B LEU* 3.6 15.7 - - + +
916B TYR* 4.1 18.2 + - + +
945B LEU 2.9 17.7 + - - +
946B SER* 3.6 6.5 - - - +
948B ILE* 1.3 78.6 - - - +
950B LYS* 1.3 78.2 + - + +
952B LEU* 3.2 3.1 + - - +
953B GLN* 3.2 25.4 + - + +
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Residues in contact with LYS 950 (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 TYR* 4.6 1.0 + - - -
946B SER* 2.7 47.6 + - - +
947B THR* 3.9 5.2 - - + +
949B LYS* 1.3 95.1 - - + +
951B ARG* 1.3 64.4 + - + +
952B LEU 3.2 0.3 + - - -
953B GLN* 3.2 8.1 + - - +
954B GLU* 3.1 36.4 + - + +
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Residues in contact with ARG 951 (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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943B MET* 3.7 20.7 - - - +
947B THR* 3.0 33.2 + - + +
950B LYS* 1.3 76.9 - - + +
952B LEU* 1.3 60.7 + - - +
954B GLU* 3.6 19.4 + - - +
957B SER* 2.8 26.1 + - - -
958B MET* 3.0 47.4 + - + +
959B TYR* 3.6 26.0 - - + -
968B ASP* 2.9 23.0 + - - -
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Residues in contact with LEU 952 (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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854B VAL* 5.2 1.1 - - + -
900B LEU* 3.6 31.2 - - + -
905B LYS* 4.0 27.2 - - + +
908B CYS* 3.7 31.6 - - + -
909B GLU* 3.5 33.4 - - + +
912B LEU* 4.1 9.4 - - + -
948B ILE 2.9 17.5 + - - +
949B LYS 3.5 4.7 - - - +
951B ARG* 1.3 79.3 - - - +
953B GLN* 1.3 60.7 + - - +
954B GLU 3.5 4.2 + - - +
957B SER* 4.3 6.3 - - - +
959B TYR* 3.8 14.3 - - + -
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Residues in contact with GLN 953 (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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855B PRO* 3.8 19.6 - - + +
856B THR* 3.6 33.9 + - - +
882B CYS* 3.8 21.8 - - + +
883B ASP* 5.6 4.0 - - - +
905B LYS* 4.9 9.9 - - - +
949B LYS* 3.2 17.1 + - + +
950B LYS* 3.2 6.4 + - - +
952B LEU* 1.3 78.4 - - - +
954B GLU* 1.3 64.8 + - - +
955B ASP* 3.6 1.4 + - - -
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Residues in contact with GLU 954 (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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899B LYS* 6.0 0.9 - - - -
950B LYS* 3.1 30.7 + - - +
951B ARG* 3.8 18.1 + - - +
952B LEU 3.3 3.1 - - - +
953B GLN* 1.3 79.3 - - - +
955B ASP* 1.3 70.2 + - - +
956B TYR 3.4 2.1 + - - +
957B SER* 3.3 22.6 + - - -
958B MET 5.9 0.3 + - - -
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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