Contacts of the helix formed by residues 921 - 932 (chain B) in PDB entry 3BBT
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 921 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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916B GLN* 3.6 1.8 - - - +
920B CYS* 1.3 74.8 - - - +
922B ILE* 1.3 65.3 + - - +
923B ASP* 2.9 24.2 + - - +
924B VAL* 3.1 20.5 - - - +
925B TYR* 3.2 6.9 + - - +
958B ARG 3.9 11.7 - - - +
959B TYR* 2.8 38.7 + - - +
961B VAL* 4.4 18.4 - - + -
971B PRO* 5.7 6.3 - - + -
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Residues in contact with ILE 922 (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 GLN* 3.5 18.7 - - - +
921B THR* 1.3 71.5 - - - +
923B ASP* 1.3 68.3 + - - +
925B TYR* 3.8 25.4 - - + -
926B MET* 2.9 47.9 + - + +
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Residues in contact with ASP 923 (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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921B THR* 2.9 20.0 + - - +
922B ILE* 1.3 87.9 - - - +
924B VAL* 1.3 61.4 + - - +
926B MET* 3.4 10.3 + - - +
927B VAL* 3.5 16.3 + - - +
952B MET* 4.2 7.0 - - + +
958B ARG* 5.4 1.7 - - - +
959B TYR* 3.8 28.2 - - + -
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Residues in contact with VAL 924 (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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796B LEU* 4.3 8.5 - - + -
889B MET* 5.1 3.4 - - + -
920B CYS* 3.7 18.4 - - - -
921B THR* 3.1 22.2 - - - +
923B ASP* 1.3 75.8 - - - +
925B TYR* 1.3 60.8 + - - +
927B VAL* 3.4 8.4 + - - +
928B MET* 3.4 25.4 + - + +
949B PHE* 4.0 17.3 - - + -
952B MET* 3.3 32.8 - - + -
959B TYR* 3.5 31.2 - - + +
960B LEU* 4.0 7.2 - - + -
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Residues in contact with TYR 925 (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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913B ARG* 4.8 3.6 + - - +
914B LEU 2.6 26.5 + - - -
915B PRO* 3.6 5.4 - - - +
916B GLN* 3.5 52.8 + - + -
917B PRO* 3.8 8.7 - - + -
920B CYS* 4.5 4.3 - - + -
921B THR 3.2 15.5 + - - +
922B ILE* 3.8 24.9 - - + +
924B VAL* 1.3 77.7 - - - +
926B MET* 1.3 58.5 + - - +
928B MET* 3.2 14.4 + - - -
929B VAL* 2.9 47.0 + - + +
932B TRP* 4.3 11.1 - + - -
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Residues in contact with MET 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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922B ILE* 2.9 40.3 + - + +
923B ASP* 3.9 5.2 - - - +
924B VAL 3.4 0.2 - - - -
925B TYR* 1.3 74.2 - - - +
927B VAL* 1.3 65.2 + - + +
929B VAL* 3.5 21.7 + - + +
930B LYS* 3.1 46.8 + - + +
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Residues in contact with VAL 927 (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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885B ILE* 5.2 0.9 - - + -
923B ASP 3.6 13.7 - - - +
924B VAL* 3.4 9.1 + - - +
926B MET* 1.3 77.5 - - + +
928B MET* 1.3 61.9 + - - +
930B LYS* 3.5 19.8 + - + +
931B CYS* 3.3 21.5 + - - -
940B PRO* 4.5 2.1 - - + +
945B LEU* 3.8 22.7 - - + -
948B GLU* 4.0 26.7 - - + -
949B PHE* 3.7 28.0 - - + -
952B MET* 4.5 7.6 - - + -
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Residues in contact with MET 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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882B GLY* 4.3 3.4 - - - +
885B ILE* 3.8 25.6 - - + +
886B TRP* 3.7 38.4 - - - +
889B MET* 3.4 37.5 - - + -
917B PRO* 4.3 3.4 - - + -
920B CYS* 4.2 7.9 - - - -
924B VAL 3.4 11.8 + - - +
925B TYR* 3.2 27.7 + - + +
927B VAL* 1.3 75.5 - - - +
929B VAL* 1.3 60.7 + - - +
931B CYS* 2.8 31.1 + - - +
932B TRP* 3.4 26.6 + - + -
949B PHE* 6.1 0.2 - - + -
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Residues in contact with VAL 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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913B ARG* 5.2 9.6 + - + -
925B TYR* 2.9 52.7 + - + +
926B MET* 3.8 22.9 - - + +
927B VAL 3.5 0.2 - - - -
928B MET* 1.3 74.7 - - - +
930B LYS* 1.3 61.2 + - + +
932B TRP* 3.3 23.7 + - + +
933B MET* 3.7 26.2 + - + +
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Residues in contact with LYS 930 (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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926B MET* 3.1 38.8 + - + +
927B VAL* 3.5 19.3 - - + +
928B MET 3.1 0.8 - - - -
929B VAL* 1.3 78.2 - - + +
931B CYS* 1.3 59.6 + - - +
933B MET* 3.2 28.4 - - + +
938B SER 5.6 2.5 - - - +
939B ARG* 3.4 16.0 - - - +
940B PRO* 3.6 20.9 - - + -
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Residues in contact with CYS 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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878B VAL* 3.5 31.6 - - + +
879B TRP* 3.3 20.4 + - - +
881B TYR* 4.6 2.7 - - - -
882B GLY* 4.0 20.2 - - - -
885B ILE* 5.4 0.9 - - - -
927B VAL* 3.3 17.9 - - - -
928B MET* 2.8 11.4 + - - +
930B LYS* 1.3 76.9 - - - +
932B TRP* 1.3 58.3 + - + +
933B MET 3.4 1.3 - - - -
939B ARG* 3.6 15.3 - - - -
940B PRO* 4.0 7.4 - - - -
945B LEU* 3.8 26.7 - - - -
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Residues in contact with TRP 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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879B TRP* 3.3 56.4 + + + -
882B GLY* 3.3 26.5 - - - -
883B VAL* 3.5 11.4 - - + +
886B TRP* 4.2 11.4 - + + -
896B TYR* 5.6 2.7 - - - -
913B ARG* 2.8 68.1 + - + +
914B LEU* 3.9 48.0 - - + -
925B TYR* 4.3 7.2 - + - -
928B MET* 3.5 37.5 - - + -
929B VAL* 3.3 15.7 + - + +
930B LYS 3.2 0.8 - - - -
931B CYS* 1.3 84.6 - - - +
933B MET* 1.3 56.9 + - - +
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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