Contacts of the strand formed by residues 605 - 610 (chain T) in PDB entry 1BGX
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 LEU 605 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600T ALA* 4.3 3.4 - - - -
603T GLY 5.1 4.3 - - - +
604T TRP* 1.3 80.6 - - - +
606T LEU* 1.3 63.2 + - - +
607T VAL* 3.7 2.8 + - - +
790T GLU* 3.6 1.6 - - - -
791T ALA 3.0 37.5 + - - +
796T ALA* 4.0 21.8 - - + -
823T ILE* 4.4 14.1 - - + -
824T GLY* 3.5 15.9 - - - +
825T GLU* 3.9 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 606 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449T VAL* 5.2 1.6 - - + -
598T PHE* 3.5 26.5 - - + +
599T ILE 3.9 12.3 - - - +
600T ALA* 3.9 18.3 - - + +
605T LEU* 1.3 70.3 - - - +
607T VAL* 1.3 61.1 + - - +
608T ALA* 3.8 2.0 + - + +
780T LEU* 3.8 23.8 - - + -
788T VAL* 4.6 12.8 - - + -
789T LEU 3.6 14.4 - - - +
790T GLU* 4.0 4.0 - - + -
822T GLY 3.7 3.3 - - - +
823T ILE* 3.7 0.9 - - - +
824T GLY 2.8 36.6 + - - +
825T GLU 3.9 7.4 + - - +
826T ASP* 3.8 8.5 - - - +
827T TRP* 3.7 21.5 - - + +
830T ALA* 4.3 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 607 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605T LEU 4.1 9.4 - - - +
606T LEU* 1.3 74.6 - - - +
608T ALA* 1.3 57.1 + - - +
609T LEU* 3.4 26.6 + - + +
788T VAL* 5.1 0.2 - - - -
789T LEU* 3.0 41.6 + - + +
791T ALA* 4.7 10.1 - - + +
796T ALA* 3.9 30.1 - - + +
799T VAL* 5.2 2.9 - - + -
800T ALA* 3.9 29.2 - - + +
821T VAL* 5.7 0.7 - - + -
822T GLY 3.5 10.8 - - - +
823T ILE* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 608 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606T LEU* 3.8 2.7 - - + -
607T VAL* 1.3 72.2 - - - +
609T LEU* 1.3 60.6 + - - +
786T GLU* 4.9 3.1 - - - -
787T LEU 3.9 4.3 - - - -
788T VAL* 4.3 13.0 - - + +
822T GLY 3.0 29.7 + - - +
827T TRP* 4.2 24.7 - - + +
830T ALA* 3.9 19.1 - - + -
831T LYS 4.9 1.3 - - - +
832T GLU 3.4 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607T VAL* 3.4 33.7 - - + +
608T ALA* 1.3 74.1 - - - +
610T ASP* 1.3 60.8 + - - +
786T GLU* 3.3 4.3 - - - +
787T LEU* 2.9 39.4 + - + +
789T LEU* 4.0 18.8 - - + -
800T ALA* 4.5 2.0 - - - +
803T ALA* 3.8 24.0 - - + -
804T LYS* 4.1 1.8 - - - +
807T MET* 3.8 28.4 - - - +
819T VAL* 4.0 13.2 - - + -
820T GLU 3.5 4.7 - - - -
821T VAL* 3.8 29.4 - - + -
832T GLU 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 610 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609T LEU* 1.3 76.0 - - - +
611T TYR* 1.3 75.7 + - - +
612T SER* 3.3 6.1 + - - -
785T ASP* 3.1 22.2 + - - +
786T GLU* 3.4 23.9 - - - +
807T MET* 5.5 0.9 - - - -
819T VAL* 3.4 5.6 - - - +
820T GLU* 3.0 34.3 + - + +
832T GLU* 3.5 36.1 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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