Contacts of the helix formed by residues 944 - 954 (chain C) in PDB entry 3O37
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924C PHE* 3.3 15.0 - - - +
925C GLN 2.9 9.9 - - - +
926C ASP 3.6 13.7 - - - +
927C PRO* 3.3 25.9 - - + +
928C VAL* 5.4 0.9 - - + +
943C MET* 1.3 79.9 - - - +
945C LEU* 1.3 62.8 + - - +
946C SER* 2.3 32.9 + - - -
947C THR* 2.6 33.2 + - - -
948C ILE* 3.4 14.9 + - - +
972C ILE* 3.5 11.0 - - - -
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Residues in contact with LEU 945 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912C LEU* 3.7 9.5 - - + +
915C LEU* 3.8 44.2 - - + -
916C TYR* 3.4 27.1 + - + +
921C SER* 4.1 21.1 - - - -
924C PHE* 2.8 27.8 + - + +
925C GLN* 3.8 12.3 - - + +
944C ASP* 1.3 71.4 - - - +
946C SER* 1.3 57.7 + - - +
947C THR 3.3 0.3 + - - -
948C ILE* 3.3 4.7 + - - +
949C LYS* 3.0 27.4 + - - +
969C PHE* 4.0 11.9 - - + -
972C ILE* 3.7 19.7 - - + +
973C PHE* 6.3 0.2 - - + -
993C LEU* 4.9 3.1 - - + -
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Residues in contact with SER 946 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916C TYR* 3.1 13.0 + - - -
925C GLN 2.8 18.6 + - - -
926C ASP* 3.8 10.8 + - - -
927C PRO* 3.6 13.5 - - - +
944C ASP* 2.3 24.3 + - - -
945C LEU* 1.3 73.4 - - - +
947C THR* 1.3 58.1 + - - +
949C LYS* 3.5 8.6 - - - +
950C LYS* 3.1 33.4 + - - +
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Residues in contact with THR 947 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927C PRO* 4.5 4.9 - - - +
942C PRO 5.8 0.4 - - - +
943C MET* 3.7 23.5 - - + -
944C ASP* 2.6 30.8 + - - -
946C SER* 1.3 77.2 + - - +
948C ILE* 1.3 68.9 + - - +
950C LYS* 3.2 14.4 + - + +
951C ARG* 2.9 49.4 + - + +
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Residues in contact with ILE 948 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908C CYS* 4.3 4.7 - - - -
912C LEU* 4.1 19.1 - - + -
943C MET* 3.9 5.8 - - - -
944C ASP 3.7 7.4 - - - +
945C LEU* 3.3 6.8 + - + +
947C THR* 1.3 76.0 - - - +
949C LYS* 1.3 63.0 + - - +
951C ARG* 3.2 2.2 + - - +
952C LEU* 2.9 23.2 + - - +
959C TYR* 3.4 25.2 - - + +
965C PHE* 4.7 1.6 - - + -
968C ASP* 3.8 15.5 - - + +
969C PHE* 3.5 57.7 - - + +
972C ILE* 3.6 21.3 - - + -
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Residues in contact with LYS 949 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851C SER 2.8 29.1 + - - -
852C CYS* 4.2 4.6 + - - +
853C HIS 3.1 21.8 + - - -
854C VAL* 4.0 19.6 - - + +
855C PRO* 5.5 1.6 - - + -
856C THR* 3.1 25.2 + - - +
912C LEU* 3.5 14.5 - - + +
916C TYR* 4.0 24.2 + - + +
945C LEU 3.0 17.7 + - - +
946C SER* 3.5 8.3 - - - +
948C ILE* 1.3 78.2 - - - +
950C LYS* 1.3 62.5 + - - +
952C LEU* 3.4 3.9 + - - +
953C GLN* 3.3 21.5 + - - +
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Residues in contact with LYS 950 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946C SER* 3.1 24.6 + - - +
947C THR* 3.2 15.0 + - + +
949C LYS* 1.3 73.2 - - - +
951C ARG* 1.3 65.8 + - + +
953C GLN* 3.2 5.6 + - - +
954C GLU* 2.8 56.5 + - - +
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Residues in contact with ARG 951 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943C MET* 3.4 23.6 - - - +
947C THR* 2.9 33.7 + - + +
948C ILE* 3.6 4.3 - - - +
950C LYS* 1.3 80.4 - - + +
952C LEU* 1.3 62.1 + - - +
954C GLU* 3.7 9.3 + - - +
957C SER* 3.6 22.2 - - - -
958C MET* 3.3 50.4 + - + +
959C TYR* 3.6 24.1 - - + -
968C ASP* 2.9 24.2 + - - -
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Residues in contact with LEU 952 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854C VAL* 5.2 1.1 - - + -
900C LEU* 3.5 31.9 - - + -
905C LYS* 3.2 37.9 + - + +
908C CYS* 3.7 27.1 - - + -
909C GLU* 3.4 35.9 - - + +
912C LEU* 4.2 8.3 - - + -
948C ILE 2.9 17.1 + - - +
949C LYS 3.6 6.3 - - - +
950C LYS 3.2 0.2 - - - -
951C ARG* 1.3 79.7 - - - +
953C GLN* 1.3 58.5 + - - +
957C SER* 3.7 12.3 + - - -
959C TYR* 3.9 14.5 - - + -
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Residues in contact with GLN 953 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855C PRO* 3.4 29.0 - - + +
856C THR 5.9 1.3 - - - +
882C CYS* 3.4 36.9 + - + +
905C LYS* 3.5 23.0 + - - +
909C GLU* 4.4 3.1 - - - +
949C LYS* 3.3 11.8 + - + +
950C LYS* 3.2 5.8 + - - +
952C LEU* 1.3 79.1 - - + +
954C GLU* 1.3 68.8 + - - +
955C ASP* 3.4 3.1 + - - -
957C SER* 4.6 0.6 + - - -
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Residues in contact with GLU 954 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950C LYS* 2.8 45.3 + - - +
951C ARG* 3.9 10.8 - - - +
952C LEU 3.5 0.8 - - - -
953C GLN* 1.3 75.1 - - - +
955C ASP* 1.3 78.0 + - - +
956C TYR* 4.6 6.5 - - + +
957C SER* 2.7 30.4 + - - +
958C MET 5.4 0.4 - - - +
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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