Contacts of the strand formed by residues 898 - 905 (chain A) in PDB entry 2G30
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 TRP 898 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A ASP* 4.1 3.6 - - - -
830A GLY* 3.4 38.8 - - - -
831A LYS 4.2 2.9 - - - -
832A MET* 3.4 55.3 - - + +
840A THR* 6.0 2.0 - - + -
844A ILE* 5.7 2.0 - - + +
890A SER* 4.0 6.3 - - - -
891A LEU 3.4 18.2 - - - -
892A LYS* 3.3 34.4 - - + +
896A GLY 3.4 13.2 + - - -
897A ILE* 1.3 74.5 - - - +
899A ILE* 1.3 62.6 + - - +
900A LEU* 4.2 2.9 - - + -
917A LYS 4.3 0.7 - - - +
918A CYS* 3.5 24.6 - - - -
919A ARG 4.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A SER* 3.5 4.3 - - - -
891A LEU* 3.0 60.9 + - + +
893A LEU* 3.9 17.0 - - + -
897A ILE* 3.9 15.9 - - + +
898A TRP* 1.3 81.0 - - - +
900A LEU* 1.3 75.7 + - - +
901A ALA* 5.3 1.3 - - + +
916A LEU* 4.0 24.2 - - + -
917A LYS 3.7 6.7 - - - +
918A CYS* 3.9 15.7 - - + -
923A VAL* 4.1 11.7 - - + -
924A SER* 5.4 1.3 - - - +
927A ILE* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A MET* 3.6 29.4 - - + -
837A PHE* 3.6 31.6 - - + +
840A THR* 3.8 34.1 - - + -
841A TRP* 3.8 31.1 - - + +
844A ILE* 4.7 5.2 - - + -
889A GLN 3.5 2.0 - - - -
890A SER* 3.9 8.3 - - - -
898A TRP* 4.9 4.3 - - + -
899A ILE* 1.3 84.7 - - - +
901A ALA* 1.3 60.1 + - - +
916A LEU* 3.4 3.6 - - - -
917A LYS* 2.8 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A PHE* 3.9 5.0 - - - -
841A TRP* 3.9 4.2 - - - -
888A TYR* 3.4 4.7 - - - -
889A GLN* 2.8 40.7 + - + +
891A LEU* 6.4 1.1 - - + -
899A ILE* 5.3 1.3 - - + +
900A LEU* 1.3 75.6 - - - +
902A GLU* 1.3 58.7 + - - +
903A LEU 4.1 0.7 - - - -
914A LEU* 3.9 6.1 - - + -
915A SER 3.2 5.4 - - - +
916A LEU* 3.5 20.2 - - + -
931A TYR* 3.5 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A TRP* 3.9 12.5 - - + -
886A MET* 3.4 20.8 - - + +
887A LEU 3.3 4.9 - - - +
888A TYR* 2.8 40.5 + - + -
901A ALA* 1.3 74.5 - - - +
903A LEU* 1.3 66.0 + - - +
904A ARG* 3.4 19.8 + - - +
913A THR* 3.5 4.2 - - - +
914A LEU* 3.5 3.2 - - - +
915A SER* 2.8 44.3 + - - +
15P ARG* 2.8 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A ILE* 3.8 29.2 - - + -
864A VAL* 3.5 32.1 - - + -
885A ASP 3.5 3.8 - - - +
886A MET* 3.6 0.5 - - - -
887A LEU* 2.8 49.5 + - + +
889A GLN* 4.2 13.9 - - - +
901A ALA 4.1 0.4 - - - -
902A GLU* 1.3 75.5 - - - +
904A ARG* 1.3 59.0 + - - +
905A ILE* 4.0 20.9 + - + +
912A TYR* 4.0 16.4 - - + -
913A THR 3.5 11.9 - - - +
914A LEU* 4.0 11.7 - - + -
931A TYR* 4.6 4.3 - - + -
935A LEU* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A GLN* 5.1 7.9 - - - +
884A GLN* 3.1 29.6 - - + +
885A ASP 3.5 4.0 - - - +
886A MET* 3.4 39.9 - - - +
902A GLU* 3.4 23.2 + - - +
903A LEU* 1.3 72.3 - - - +
905A ILE* 1.3 61.9 + - - +
906A GLN* 4.4 9.0 + - + +
911A ASN 4.7 0.7 - - - +
912A TYR* 3.4 10.0 - - - +
913A THR* 2.8 52.3 + - + +
15P ARG* 3.5 22.8 + - - +
16P THR* 3.7 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A LEU 4.6 2.2 - - - +
860A ASN* 5.5 1.3 - - - -
861A ALA* 4.0 32.5 - - + +
864A VAL* 4.2 5.4 - - + -
884A GLN* 3.5 4.4 - - - -
885A ASP* 2.9 49.0 + - + +
887A LEU* 4.3 7.4 - - + -
903A LEU* 4.1 20.4 - - + +
904A ARG* 1.3 79.1 - - - +
906A GLN* 1.3 68.2 + - - +
907A PRO* 4.4 1.2 - - - +
912A TYR* 3.6 49.6 - - + +
----------------------------------------------------------
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