Contacts of the helix formed by residues 737 - 749 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735D LYS* 2.9 23.9 + - + +
736D ALA* 1.3 74.6 - - - +
738D VAL* 1.3 63.6 + - - +
739D GLU* 3.6 26.7 + - - +
740D PHE* 3.3 12.2 + - - +
741D MET* 3.0 28.7 + - - +
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Residues in contact with VAL 738 (chain D).
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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737D ASN* 1.3 74.9 - - - +
739D GLU* 1.3 61.9 + - - +
741D MET* 3.9 6.3 - - - +
742D ASP* 3.1 38.3 + - - +
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Residues in contact with GLU 739 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737D ASN* 3.3 18.6 + - - +
738D VAL* 1.3 77.9 - - - +
740D PHE* 1.3 61.4 + - - +
742D ASP* 3.5 10.3 + - + +
743D GLU* 3.3 32.7 + - + +
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Residues in contact with PHE 740 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728D LEU* 6.2 0.4 - - + -
734D PRO* 3.8 21.5 - - + -
735D LYS 3.2 28.7 - - - +
736D ALA* 4.8 1.6 - - - -
737D ASN* 3.3 10.4 + - - +
739D GLU* 1.3 78.2 + - - +
741D MET* 1.3 71.7 + - + +
743D GLU* 3.1 11.9 + - + +
744D ALA* 2.9 41.0 + - + +
761D VAL* 4.0 18.2 - - + -
763D LEU* 4.0 10.1 - - + -
767D ILE* 3.4 42.8 - - + -
769D LEU* 4.7 8.7 - - + -
841D ARG 5.7 4.5 - - - -
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Residues in contact with MET 741 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685D LEU* 4.6 11.5 - - + +
687D ILE* 4.4 27.4 - - + -
736D ALA* 5.7 2.0 - - - -
737D ASN 3.0 23.8 + - - +
738D VAL* 3.9 7.2 - - - +
740D PHE* 1.3 89.6 - - + +
742D ASP* 1.3 64.2 + - - +
744D ALA* 3.5 3.1 + - - +
745D LEU* 3.1 43.8 + - + +
761D VAL* 6.5 0.7 - - - -
763D LEU* 5.4 6.7 - - - -
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Residues in contact with ASP 742 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738D VAL* 3.1 28.3 + - - +
739D GLU* 3.5 12.2 - - - +
740D PHE 3.2 0.2 - - - -
741D MET* 1.3 77.6 - - - +
743D GLU* 1.3 65.8 + - - +
745D LEU* 3.5 10.4 + - - +
746D ILE* 3.3 28.6 + - - +
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Residues in contact with GLU 743 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739D GLU* 3.3 22.8 + - + +
740D PHE* 3.1 13.7 + - + +
742D ASP* 1.3 76.6 - - - +
744D ALA* 1.3 65.9 + - - +
746D ILE* 3.2 20.3 - - - +
747D MET* 3.1 31.7 + - + +
841D ARG* 3.2 55.5 + - + +
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Residues in contact with ALA 744 (chain D).
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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685D LEU* 3.6 19.0 - - + +
740D PHE* 2.9 31.6 + - + +
741D MET* 3.9 6.1 - - - +
743D GLU* 1.3 76.9 - - - +
745D LEU* 1.3 57.1 + - - +
747D MET* 3.5 3.2 + - - -
748D ALA* 3.0 27.0 + - - +
758D LEU* 3.6 14.5 - - + +
761D VAL* 4.4 17.0 - - + -
769D LEU* 6.5 0.2 - - + -
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Residues in contact with LEU 745 (chain D).
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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684D GLN* 4.8 6.7 - - + -
685D LEU* 3.9 35.7 - - + +
741D MET* 3.1 36.2 + - + +
742D ASP* 3.8 11.2 - - - +
744D ALA* 1.3 76.4 - - - +
746D ILE* 1.3 61.9 + - + +
748D ALA* 3.1 5.6 + - - +
749D SER* 3.0 26.0 + - - -
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Residues in contact with ILE 746 (chain D).
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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742D ASP 3.3 14.7 + - - +
743D GLU* 3.2 38.1 - - - +
745D LEU* 1.3 77.5 - - + +
747D MET* 1.3 63.4 + - + +
749D SER* 2.9 23.4 + - - +
750D MET* 3.3 24.1 - - + +
812D ARG* 4.9 7.6 - - - +
814D LEU* 6.4 1.8 - - + -
841D ARG* 4.7 15.7 - - - +
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Residues in contact with MET 747 (chain D).
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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91D FMM 3.2 23.3 - - + -
743D GLU* 3.1 22.4 + - + +
744D ALA* 3.7 6.5 - - - +
746D ILE* 1.3 78.9 - - + +
748D ALA* 1.3 63.8 + - - +
749D SER 3.2 1.8 - - - -
750D MET* 3.3 22.4 + - - +
757D ARG* 4.5 0.2 - - - +
758D LEU* 4.2 25.4 + - + +
769D LEU* 5.7 3.6 - - + -
814D LEU* 4.4 12.1 - - - -
837D PHE* 3.2 43.9 - - + +
838D GLY 3.7 15.7 - - - +
839D LEU* 4.7 7.0 - - + -
841D ARG* 5.9 4.9 - - + -
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Residues in contact with ALA 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684D GLN 4.4 6.6 + - - +
685D LEU* 3.7 33.0 - - + +
744D ALA 3.0 17.7 + - - +
745D LEU* 3.1 8.0 + - + +
747D MET* 1.3 75.6 - - - +
749D SER* 1.3 57.9 + - - +
750D MET 3.3 0.7 - - - -
757D ARG* 2.7 32.0 + - - +
758D LEU* 3.8 22.4 - - + +
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Residues in contact with SER 749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684D GLN 6.1 2.0 - - - +
745D LEU 3.0 11.2 + - - -
746D ILE* 2.9 16.0 + - - +
748D ALA* 1.3 76.6 - - - +
750D MET* 1.3 58.2 + - - +
751D ASP* 2.9 15.0 + - - +
808D TYR* 3.5 2.6 + - - -
812D ARG* 2.7 51.6 + - - -
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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