Contacts of the helix formed by residues 737 - 749 (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 ASN 737 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735B LYS* 2.3 48.1 + - - +
736B ALA* 1.3 89.6 - - - +
738B VAL* 1.3 61.0 + - - +
739B GLU* 3.2 12.0 + - + +
740B PHE* 3.7 15.5 - - + +
741B MET* 2.9 32.8 + - - +
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Residues in contact with VAL 738 (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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737B ASN* 1.3 73.7 - - - +
739B GLU* 1.3 58.6 + - + +
741B MET* 4.0 5.9 - - - +
742B ASP* 3.0 40.0 + - - +
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Residues in contact with GLU 739 (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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737B ASN* 3.2 11.9 + - + +
738B VAL* 1.3 80.0 - - + +
740B PHE* 1.3 60.9 + - - +
742B ASP* 3.5 6.5 + - - +
743B GLU* 3.3 26.4 + - - +
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Residues in contact with PHE 740 (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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734B PRO* 4.2 20.2 - - + -
735B LYS 3.3 26.5 - - - +
736B ALA* 4.7 0.4 - - - -
737B ASN* 3.3 10.0 + - + +
739B GLU* 1.3 75.8 - - - +
741B MET* 1.3 86.0 + - + +
743B GLU* 2.8 11.5 + - + +
744B ALA* 2.8 38.1 + - + +
761B VAL* 4.0 14.4 - - + -
763B LEU* 4.1 3.4 - - + -
767B ILE* 3.3 45.8 - - + -
769B LEU* 4.6 6.3 - - + -
842B LEU* 3.8 29.2 - - + -
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Residues in contact with MET 741 (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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685B LEU* 3.8 28.9 - - + -
687B ILE* 4.1 15.0 - - + -
736B ALA* 5.9 1.1 - - - -
737B ASN 2.9 23.6 + - - +
738B VAL* 4.0 5.6 - - - +
740B PHE* 1.3 107.3 - - + +
742B ASP* 1.3 56.7 + - - +
744B ALA* 3.3 2.3 + - + +
745B LEU* 2.9 44.2 + - + +
761B VAL* 4.7 2.0 - - + -
763B LEU* 3.9 19.7 - - + -
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Residues in contact with ASP 742 (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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738B VAL* 3.0 28.2 + - - +
739B GLU* 3.5 8.5 - - - +
740B PHE 3.1 0.2 - - - -
741B MET* 1.3 76.4 - - - +
743B GLU* 1.3 64.1 + - + +
745B LEU* 3.7 12.0 + - - +
746B ILE* 3.5 29.3 + - - +
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Residues in contact with GLU 743 (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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739B GLU 3.3 13.4 + - - +
740B PHE* 2.8 11.2 + - + +
742B ASP* 1.3 78.4 - - - +
744B ALA* 1.3 64.9 + - - +
745B LEU 3.2 0.4 - - - -
746B ILE* 3.2 24.6 + - - +
747B MET* 3.2 18.9 + - - +
841B ARG* 3.2 55.0 + - - +
842B LEU* 4.6 16.2 - - + -
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Residues in contact with ALA 744 (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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685B LEU* 3.7 28.7 - - + +
740B PHE* 2.8 32.7 + - + +
741B MET* 3.7 7.6 - - - +
743B GLU* 1.3 75.6 - - - +
745B LEU* 1.3 55.7 + - - +
747B MET* 3.2 11.5 + - + +
748B ALA* 2.8 30.1 + - - +
758B LEU* 3.9 4.7 - - + +
761B VAL* 4.5 7.2 - - + -
769B LEU* 5.9 0.7 - - + -
842B LEU* 5.6 1.9 - - + +
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Residues in contact with LEU 745 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683B ALA* 4.2 19.4 - - + +
684B GLN* 4.6 1.1 - - - -
685B LEU* 3.7 37.9 - - + +
741B MET* 2.9 28.3 + - + +
742B ASP* 3.9 11.9 - - - +
744B ALA* 1.3 74.6 - - - +
746B ILE* 1.3 62.5 + - - +
748B ALA* 3.9 3.9 - - + +
749B SER* 3.2 22.5 + - - -
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Residues in contact with ILE 746 (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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742B ASP* 3.5 16.7 + - - +
743B GLU* 3.2 22.0 + - - +
745B LEU* 1.3 77.1 - - - +
747B MET* 1.3 63.4 + - + +
749B SER* 2.6 24.1 + - - +
750B MET* 3.3 14.0 - - - +
812B ARG* 5.8 3.6 - - - +
814B LEU* 4.1 15.0 - - + -
841B ARG* 3.9 28.9 - - - +
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Residues in contact with MET 747 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B FMM 3.6 36.8 - - + -
743B GLU* 3.2 13.5 + - - +
744B ALA* 3.2 9.8 + - - +
746B ILE* 1.3 74.8 - - + +
748B ALA* 1.3 63.6 + - - +
749B SER 3.1 2.0 - - - -
750B MET* 3.3 23.7 + - - +
758B LEU* 4.0 30.0 + - + +
769B LEU* 4.6 7.2 - - + -
814B LEU* 4.9 6.5 - - + -
837B PHE* 3.8 33.0 - - + +
838B GLY* 3.9 4.9 - - - +
839B LEU* 4.9 0.9 - - + -
841B ARG* 6.0 0.9 - - - -
842B LEU* 3.7 38.4 - - + -
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Residues in contact with ALA 748 (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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683B ALA* 5.2 2.8 - - + +
684B GLN 4.3 15.0 + - - +
685B LEU* 3.7 27.6 - - + -
744B ALA 2.8 20.3 + - - +
745B LEU* 4.0 8.7 - - + +
746B ILE 3.4 0.2 - - - -
747B MET* 1.3 73.2 - - - +
749B SER* 1.3 58.3 + - - +
750B MET 3.6 0.7 + - - +
757B ARG* 3.3 31.7 + - - +
758B LEU* 4.2 17.6 - - - +
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Residues in contact with SER 749 (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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683B ALA* 3.8 22.7 - - - -
745B LEU 3.2 14.1 + - - -
746B ILE* 2.6 24.9 + - - -
747B MET 3.1 0.2 - - - -
748B ALA* 1.3 77.0 - - - +
750B MET* 1.3 59.0 - - - +
751B ASP* 3.2 9.7 + - - +
757B ARG* 5.1 2.4 + - - +
808B TYR* 3.7 2.1 + - - -
812B ARG* 2.8 41.1 + - - -
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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