Contacts of the helix formed by residues 946 - 956 (chain B) in PDB entry 2R4B
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 THR 946 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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941B GLN* 3.8 1.1 - - - +
944B ILE 3.6 0.2 + - - -
945B CYS* 1.3 75.4 - - - +
947B ILE* 1.3 66.3 + - - +
948B ASP* 2.9 30.4 + - - +
949B VAL* 2.9 14.8 + - - +
950B TYR* 2.9 10.4 + - - +
983B ARG 3.7 12.8 - - - +
984B TYR* 2.7 39.2 + - - +
986B VAL* 4.4 17.9 - - + -
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Residues in contact with ILE 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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941B GLN* 3.5 23.3 - - - +
946B THR* 1.3 71.6 - - - +
948B ASP* 1.3 66.2 + - - +
950B TYR* 3.8 4.5 - - + -
951B MET* 2.9 58.5 + - + +
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Residues in contact with ASP 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946B THR* 2.9 20.1 + - - +
947B ILE* 1.3 88.6 - - - +
949B VAL* 1.3 61.0 + - - +
951B MET* 3.7 4.1 + - - +
952B VAL* 3.4 22.7 + - - +
973B GLU* 5.0 0.5 - - - +
976B ARG* 5.6 2.1 + - - -
977B MET* 3.7 9.0 - - + +
983B ARG 5.0 1.4 - - - +
984B TYR* 3.6 31.9 - - + -
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Residues in contact with VAL 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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821B LEU* 4.4 4.3 - - + -
914B MET* 4.0 20.6 - - + -
945B CYS* 3.8 24.0 - - - -
946B THR* 2.9 11.1 + - - +
948B ASP* 1.3 71.7 - - - +
950B TYR* 1.3 65.7 + - - +
952B VAL* 3.2 14.2 + - - +
953B MET* 3.4 18.7 + - + +
974B PHE* 4.2 10.5 - - + -
977B MET* 3.6 26.9 - - - -
984B TYR* 3.4 30.7 - - + +
985B LEU* 4.0 5.6 - - + -
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Residues in contact with TYR 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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938B ARG* 4.8 4.2 - - - +
939B LEU 2.5 29.8 + - - -
940B PRO* 3.7 4.9 - - - +
941B GLN* 3.4 61.4 + - + -
942B PRO* 4.1 7.4 - - + -
945B CYS* 4.5 3.9 - - + +
946B THR 2.9 15.0 + - - +
947B ILE* 4.0 5.2 - - + +
949B VAL* 1.3 77.8 - - - +
951B MET* 1.3 66.3 + - - +
953B MET* 3.1 16.7 + - - +
954B VAL* 2.9 50.2 + - + +
957B TRP* 4.4 7.0 - + - -
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Residues in contact with MET 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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947B ILE* 2.9 45.8 + - + +
948B ASP* 4.1 4.7 - - - +
949B VAL 3.4 0.2 - - - -
950B TYR* 1.3 86.6 - - - +
952B VAL* 1.3 61.5 + - - +
954B VAL* 3.9 23.8 - - + +
955B LYS* 3.0 42.3 + - + +
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Residues in contact with VAL 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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910B ILE* 4.8 1.1 - - + -
948B ASP 3.4 15.7 + - - +
949B VAL* 3.2 8.7 + - - +
950B TYR 3.1 0.6 - - - -
951B MET* 1.3 74.8 - - + +
953B MET* 1.3 66.0 + - - +
955B LYS* 3.2 23.9 + - + +
956B CYS* 3.2 13.6 + - - -
965B PRO* 4.6 1.7 - - + +
970B LEU* 3.5 31.0 - - + -
973B GLU* 4.1 28.3 - - + +
974B PHE* 3.7 24.5 - - + -
977B MET* 4.2 7.2 - - + -
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Residues in contact with MET 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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907B GLY* 4.1 4.7 - - - +
910B ILE* 3.6 37.2 - - + +
911B TRP* 3.8 28.7 - - - +
914B MET* 3.1 37.0 - - + -
942B PRO* 4.3 3.8 - - + -
945B CYS* 3.8 10.8 - - - -
949B VAL* 3.4 14.1 + - + +
950B TYR* 3.1 22.2 + - + +
952B VAL* 1.3 76.5 - - - +
954B VAL* 1.3 62.9 + - - +
956B CYS* 3.1 25.6 + - - +
957B TRP* 3.2 28.9 - - + -
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Residues in contact with VAL 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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938B ARG* 5.4 11.0 - - + -
950B TYR* 2.9 56.3 + - + +
951B MET* 3.9 23.8 - - + +
953B MET* 1.3 75.0 - - - +
955B LYS* 1.3 59.2 + - + +
957B TRP* 2.9 39.8 + - + +
958B MET* 3.6 10.3 + - - +
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Residues in contact with LYS 955 (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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951B MET* 3.0 36.0 + - + +
952B VAL* 3.2 12.0 + - + +
954B VAL* 1.3 76.5 - - + +
956B CYS* 1.3 60.3 + - - +
957B TRP 3.1 1.3 + - - -
958B MET* 3.2 30.2 + - + +
963B SER 5.3 2.2 - - - +
964B ARG* 3.6 5.5 - - - -
965B PRO* 3.4 30.0 - - + +
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Residues in contact with CYS 956 (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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903B VAL* 3.5 39.7 - - - +
904B TRP* 3.1 22.2 - - - +
906B TYR* 4.3 3.4 - - - -
907B GLY* 3.9 18.2 - - - -
910B ILE* 5.6 0.4 - - - -
952B VAL* 3.5 14.4 - - - -
953B MET* 3.1 13.9 + - - +
955B LYS* 1.3 75.7 - - - +
957B TRP* 1.3 58.3 + - + +
958B MET 3.5 0.4 - - - -
964B ARG* 3.4 14.0 - - - -
965B PRO* 4.0 3.1 - - - -
970B LEU* 3.9 24.0 - - - -
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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