Contacts of the helix formed by residues 925 - 940 (chain B) in PDB entry 5B2R
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 ARG 925 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763B MET* 2.7 38.6 + - - +
764B ALA 3.1 22.0 + - - -
765B ARG* 4.0 11.8 - - - +
923B GLU* 2.9 34.1 + - - +
924B THR* 1.3 79.8 + - - +
926B GLN* 1.3 65.1 + - - +
927B ILE* 4.2 13.9 - - + +
928B THR* 3.3 21.1 + - - +
929B LYS* 3.1 21.4 + - - +
959B LYS* 6.0 0.4 - - - +
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Residues in contact with GLN 926 (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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2A G 3.8 22.4 + - - -
924B THR 3.4 4.8 + - - -
925B ARG* 1.3 70.0 - - - +
927B ILE* 1.3 61.5 + - - +
929B LYS* 3.2 19.3 + - - +
930B HIS* 2.9 52.1 + - + +
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Residues in contact with ILE 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B LEU* 3.8 20.6 - - + -
728B ALA 3.5 24.9 - - - +
729B GLY* 5.3 3.1 - - - -
733B ILE* 4.5 13.0 - - + -
734B LYS* 5.0 4.9 - - + -
737B ILE* 3.7 29.2 - - + -
763B MET* 3.8 21.3 - - - -
925B ARG* 4.2 17.0 - - + +
926B GLN* 1.3 77.8 - - - +
928B THR* 1.3 67.6 + - - +
930B HIS* 3.1 9.6 + - + +
931B VAL* 3.1 21.2 + - - +
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Residues in contact with THR 928 (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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761B ILE* 4.0 11.2 - - + +
763B MET* 3.4 41.2 - - + +
923B GLU* 3.6 17.0 - - + +
925B ARG* 3.3 24.7 + - - +
926B GLN 3.2 0.6 - - - -
927B ILE* 1.3 74.2 - - - +
929B LYS* 1.3 65.7 + - - +
931B VAL* 3.2 3.2 + - - +
932B ALA* 3.0 22.2 + - - +
957B THR* 3.7 29.2 - - + -
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Residues in contact with LYS 929 (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 G 2.5 36.6 + - - +
2A G 4.6 16.8 + - - +
923B GLU* 4.1 9.4 - - + +
924B THR* 3.6 34.1 + - - +
925B ARG 3.1 10.8 + - - +
926B GLN* 3.5 25.9 - - - +
928B THR* 1.3 77.5 - - - +
930B HIS* 1.3 56.2 + - + +
932B ALA* 3.3 7.9 + - - +
933B GLN* 2.9 30.0 + - - +
957B THR* 5.9 0.2 - - - -
1010B TYR* 4.0 11.2 - - + -
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Residues in contact with HIS 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B HIS* 4.7 10.9 + + - -
727B LEU* 3.8 42.2 - - + +
728B ALA 5.9 2.0 - - - -
926B GLN* 2.9 47.2 + - + +
927B ILE* 3.1 14.3 + - + +
929B LYS* 1.3 77.4 - - - +
931B VAL* 1.3 58.0 + - - +
933B GLN* 3.3 10.7 + - - +
934B ILE* 2.9 36.8 + - + +
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Residues in contact with VAL 931 (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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11B ILE* 3.8 23.3 - - + -
737B ILE* 3.5 48.0 - - + +
740B THR* 5.1 3.6 - - + -
741B VAL* 6.2 2.0 - - + -
761B ILE* 4.0 12.6 - - + -
763B MET* 3.7 11.7 - - + -
927B ILE 3.1 10.7 + - - +
928B THR* 3.2 7.6 + - - +
930B HIS* 1.3 74.8 - - - +
932B ALA* 1.3 64.7 + - - +
934B ILE* 3.2 9.6 + - + +
935B LEU* 3.0 36.1 + - + +
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Residues in contact with ALA 932 (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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761B ILE* 3.9 3.3 - - + +
928B THR 3.0 13.8 + - - +
929B LYS* 3.5 10.5 - - - +
931B VAL* 1.3 77.7 - - - +
933B GLN* 1.3 57.5 + - - +
935B LEU* 3.3 1.7 + - - +
936B ASP* 2.8 30.8 + - - +
955B VAL* 3.8 21.8 - - + +
957B THR* 3.9 18.2 - - - +
1010B TYR* 3.8 21.3 - - + -
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Residues in contact with GLN 933 (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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723B HIS* 4.3 11.2 + - - -
929B LYS 2.9 20.5 + - - +
930B HIS* 3.7 12.1 + - - +
932B ALA* 1.3 72.4 - - - +
934B ILE* 1.3 78.0 + - - +
936B ASP* 3.8 0.5 - - - +
937B SER* 2.9 45.8 + - - -
1010B TYR* 3.0 38.5 - - + +
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Residues in contact with ILE 934 (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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720B LEU* 4.0 16.2 - - + -
723B HIS* 3.7 32.3 - - + +
724B ILE* 4.0 17.5 - - + -
727B LEU* 4.5 9.6 - - + -
737B ILE* 4.5 6.3 - - + -
741B VAL* 4.0 25.4 - - + -
930B HIS 2.9 25.9 + - - +
931B VAL* 3.2 8.7 + - + +
933B GLN* 1.3 86.2 - - - +
935B LEU* 1.3 65.1 + - + +
937B SER* 3.2 7.1 + - - -
938B ARG* 3.0 31.1 + - + +
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Residues in contact with LEU 935 (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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9B LEU* 4.1 8.5 - - + -
740B THR* 4.6 3.4 - - + -
741B VAL* 4.3 27.6 - - + +
744B VAL* 4.2 27.4 - - + -
759B ILE* 4.1 20.4 - - + -
761B ILE* 3.9 28.7 - - + -
931B VAL* 3.0 25.6 + - + +
932B ALA 3.9 2.7 - - - +
934B ILE* 1.3 77.0 - - + +
936B ASP* 1.3 57.4 + - - +
938B ARG* 3.2 6.8 + - + +
939B MET* 2.9 37.2 + - + +
955B VAL* 4.2 13.2 - - + -
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Residues in contact with ASP 936 (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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932B ALA 2.8 18.7 + - - +
933B GLN 3.8 2.6 - - - +
935B LEU* 1.3 76.9 - - - +
937B SER* 1.3 60.4 + - - +
939B MET* 4.8 0.4 - - - -
940B ASN* 2.7 57.9 + - - +
949B LEU* 4.2 6.1 - - - +
951B ARG* 2.8 36.7 + - - -
953B VAL 4.0 2.8 - - - +
955B VAL* 3.7 17.1 + - + +
1010B TYR* 3.7 26.2 - - + +
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Residues in contact with SER 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933B GLN* 2.9 39.1 + - - -
934B ILE* 3.2 9.4 + - - -
936B ASP* 1.3 80.9 + - - +
938B ARG* 1.3 63.4 + - - +
940B ASN 3.7 14.3 - - - +
941B THR* 3.8 8.8 - - - +
949B LEU* 6.3 0.4 - - - -
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Residues in contact with ARG 938 (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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720B LEU* 3.6 26.4 - - - +
741B VAL* 3.3 28.9 - - - +
745B ASP* 2.8 34.8 + - - -
755B LYS* 4.8 4.2 - - - -
934B ILE* 3.0 31.2 + - + +
935B LEU* 3.8 8.0 - - + +
937B SER* 1.3 81.3 - - - +
939B MET* 1.3 72.0 + - + +
941B THR* 3.7 12.1 - - - +
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Residues in contact with MET 939 (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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744B VAL* 3.9 23.3 - - + -
745B ASP* 4.7 11.0 - - - +
748B VAL* 4.4 10.3 - - + -
755B LYS* 3.4 45.7 + - + +
756B PRO* 4.3 13.9 - - - -
759B ILE* 3.9 20.9 - - + -
935B LEU* 2.9 21.8 + - + +
936B ASP* 4.1 2.0 - - - +
938B ARG* 1.3 91.0 - - + +
940B ASN* 1.3 63.6 + - - +
941B THR* 3.7 3.5 + - - +
952B GLU* 4.3 4.3 - - - +
953B VAL* 3.7 29.6 - - + -
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Residues in contact with ASN 940 (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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936B ASP* 2.7 48.0 + - - +
937B SER* 3.7 10.7 - - - +
939B MET* 1.3 80.2 - - - +
941B THR* 1.3 63.0 - - - +
942B LYS 3.9 0.7 - - - -
949B LEU* 3.5 25.0 - - + +
950B ILE 3.4 15.5 - - - +
951B ARG* 3.8 6.1 - - - +
952B GLU* 2.9 15.2 + - - +
953B VAL* 2.8 42.8 + - - +
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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
------------------------------------------------------------
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