Contacts of the strand formed by residues 914 - 932 (chain A) in PDB entry 5D6Y
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 PHE 914 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A ILE* 3.5 25.6 - - + -
907A SER 3.6 10.5 - - - -
908A LYS* 3.6 44.2 - - + -
912A GLY 5.0 0.2 - - - -
913A ARG* 1.3 75.8 + - - +
915A TYR* 1.3 70.1 - - - +
1004A TYR* 3.2 41.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 915 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A ILE* 3.5 7.0 - - - -
907A SER 3.1 30.7 + - - +
909A HIS* 3.3 32.5 - + + -
911A ASN* 2.6 39.6 + - - -
913A ARG* 3.4 28.6 + - + -
914A PHE* 1.3 77.6 - - - +
916A GLN* 1.3 65.4 + - - +
917A CYS 3.6 0.3 + - - -
990A PHE* 3.8 18.8 - + + -
991A GLU* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 916 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A LYS* 3.3 43.3 - - + +
905A VAL 3.3 11.2 - - - +
906A ILE* 3.6 16.0 - - + +
915A TYR* 1.3 80.7 - - - +
917A CYS* 1.3 63.9 + - - +
990A PHE* 4.0 6.8 - - - -
991A GLU* 4.6 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 917 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A LYS* 3.2 9.8 - - - +
905A VAL* 2.8 54.2 + - - +
907A SER* 3.7 29.6 - - - -
916A GLN* 1.3 75.2 - - - +
918A GLU* 1.3 57.7 + - - +
988A VAL* 3.8 14.1 - - - -
989A GLU 3.1 20.9 - - - +
990A PHE* 3.6 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 918 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A GLY* 3.6 33.5 - - - +
903A GLN 3.5 4.3 - - - +
904A LYS* 2.5 38.1 + - + +
917A CYS* 1.3 74.5 - - - +
919A VAL* 1.3 68.8 + - - +
920A VAL* 3.4 13.8 + - + +
988A VAL* 3.1 5.5 - - - -
989A GLU* 2.6 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 919 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A ILE* 3.7 11.9 - - + -
900A THR 3.9 11.7 - - - +
901A ALA* 4.2 1.1 - - - -
902A GLY* 2.7 33.1 + - - -
903A GLN 2.8 20.0 + - - +
905A VAL* 3.7 32.1 - - + -
918A GLU* 1.3 71.2 - - - +
920A VAL* 1.3 62.5 + - - +
921A ARG 4.2 3.6 - - - +
922A LEU* 3.6 32.1 - - + -
986A TYR* 4.1 12.3 - - + -
987A GLN 3.7 8.5 - - - +
988A VAL* 4.3 7.4 - - + +
1003A VAL* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 920 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A ALA* 4.4 9.6 - - - +
902A GLY 4.9 0.6 + - - +
918A GLU* 3.8 14.4 - - + +
919A VAL* 1.3 77.7 - - - +
921A ARG* 1.3 67.0 + - + +
987A GLN* 2.8 44.1 + - + +
988A VAL* 4.9 0.4 - - - -
989A GLU* 3.6 35.9 - - + +
995A GLN* 3.7 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 921 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A ALA* 5.2 2.0 - - - -
919A VAL* 3.7 1.3 - - - +
920A VAL* 1.3 88.1 + - + +
922A LEU* 1.3 77.8 + - - +
923A THR* 3.9 14.6 + - + +
985A MET 3.9 0.2 - - - +
986A TYR* 3.7 4.2 - - - -
987A GLN* 3.1 46.7 + - + +
947D VAL 3.0 28.6 + - - -
948D SER* 3.9 26.1 + - - +
949D GLN* 5.6 0.2 - - - +
964D GLN* 4.3 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 922 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A ILE 3.7 18.4 - - - +
900A THR* 4.1 4.0 - - - -
901A ALA* 4.1 22.6 - - + +
919A VAL* 3.6 29.4 - - + -
921A ARG* 1.3 77.5 - - - +
923A THR* 1.3 64.8 + - - +
984A GLN* 3.5 31.2 - - - +
985A MET 3.7 1.6 - - - -
986A TYR* 3.6 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 923 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921A ARG* 3.9 25.3 + - + +
922A LEU* 1.3 79.0 - - - +
924A THR* 1.3 61.0 + - - +
925A GLU* 4.8 5.6 + - - -
984A GLN* 3.1 5.7 - - - +
985A MET* 2.7 57.7 + - - +
987A GLN* 5.9 1.9 + - + +
997A VAL* 5.0 3.8 - - - +
947D VAL* 4.3 20.0 - - + +
949D GLN 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 924 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A THR* 1.3 74.5 - - - +
925A GLU* 1.3 62.7 + - - +
926A THR* 4.2 2.8 + - - +
982A PRO* 4.0 27.8 - - + -
983A ILE 3.6 6.5 - - - +
984A GLN* 4.4 5.0 + - - -
956B PRO* 4.0 15.3 + - + +
958B ALA* 3.8 25.5 + - - +
961B GLU* 5.1 1.0 + - - -
950D ASP* 6.2 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A THR* 3.8 6.1 + - - +
924A THR* 1.3 75.0 - - - +
926A THR* 1.3 67.5 + - - +
927A PHE* 3.4 27.7 - - + -
942A TYR* 4.5 3.1 - - - -
981A HIS 3.3 2.4 - - - +
982A PRO* 4.6 0.4 - - - -
983A ILE 2.9 29.1 + - - +
985A MET* 3.6 25.2 - - + +
997A VAL* 4.8 1.9 - - - +
944D GLU* 3.9 30.6 - - + +
947D VAL* 5.4 3.3 - - - +
966D ARG* 2.5 44.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A THR* 4.2 3.4 + - - +
925A GLU* 1.3 76.9 - - - +
927A PHE* 1.3 64.7 + - - +
928A TYR* 3.7 28.7 - - + -
941A LEU 4.4 0.2 - - - +
942A TYR* 5.1 0.3 - - - -
943A PRO* 3.7 23.4 - - + +
980A SER* 4.0 14.8 - - - -
981A HIS 3.2 8.1 + - - +
982A PRO* 4.2 12.0 - - - +
956B PRO* 5.1 6.9 - - - +
944D GLU* 4.0 8.0 + - - +
952D LEU* 6.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A GLU* 3.4 49.8 - - + -
926A THR* 1.3 75.0 - - - +
928A TYR* 1.3 63.7 + - - +
939A ASP 3.6 16.2 - - - +
940A ASN* 3.6 35.2 - - + -
941A LEU 3.4 7.9 - - - +
942A TYR* 5.7 9.4 - + - -
980A SER* 3.5 2.1 - - - -
981A HIS* 2.8 32.7 + - + +
983A ILE* 3.5 24.9 - - + -
985A MET* 3.8 23.3 - - + -
999A LYS* 5.9 2.5 - - + -
966D ARG* 4.1 7.6 - - - -
19a GLN 5.5 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A THR* 3.7 15.0 - - + -
927A PHE* 1.3 76.0 - - - +
929A GLU* 1.3 60.5 + - - +
930A VAL* 4.9 0.9 - - + -
938A SER 3.7 0.7 - - - +
939A ASP* 3.3 9.3 - - - -
941A LEU* 2.7 52.7 + - + +
943A PRO* 3.6 37.7 - - + +
946A ILE* 3.8 13.2 - - + -
951A CYS* 3.5 31.4 + - - +
955A GLY* 3.8 1.6 - - - -
956A PRO* 3.3 28.9 - - + +
957A PRO* 4.0 5.4 - - + -
977A PHE* 3.6 19.1 - + + -
979A ALA 3.5 1.3 - - - -
980A SER* 3.5 29.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A TYR* 1.3 72.8 - - - +
930A VAL* 1.3 70.3 + - - +
931A ASN* 5.0 1.7 - - - +
937A PHE* 3.8 18.2 - - + -
938A SER 3.1 12.6 - - - +
939A ASP* 3.7 17.6 - - + +
977A PHE* 4.0 2.4 - - - -
978A VAL* 2.9 49.4 + - + +
979A ALA 2.7 22.4 + - - +
981A HIS* 2.6 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 930 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A TYR* 4.9 1.1 - - + -
929A GLU* 1.3 83.5 - - - +
931A ASN* 1.3 62.5 + - - +
932A PHE* 3.6 32.8 - - + -
937A PHE* 3.2 6.6 - - - +
938A SER 2.8 28.6 + - - +
941A LEU* 3.4 30.3 - - + -
946A ILE* 4.4 18.4 - - + -
963A VAL* 4.6 2.2 - - + -
965A VAL* 4.3 4.9 - - + -
975A ALA* 4.0 8.7 - - + -
976A LYS 3.4 12.6 - - - +
977A PHE* 4.4 10.8 - - + -
978A VAL* 4.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 931 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929A GLU* 5.0 1.9 - - - +
930A VAL* 1.3 69.8 - - - +
932A PHE* 1.3 67.8 + - - +
933A ASP* 4.7 0.7 - - - +
936A SER 3.6 5.2 - - - +
937A PHE* 3.4 20.4 - - - +
975A ALA* 3.2 1.9 - - - -
976A LYS* 3.0 40.8 + - + +
978A VAL* 3.6 21.8 - - + +
26a ARG* 3.6 35.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 932 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A VAL* 3.6 22.7 - - + -
931A ASN* 1.3 80.0 - - - +
933A ASP* 1.3 62.4 + - - +
934A ASP* 3.1 21.3 - - - +
935A GLY* 3.1 13.2 + - - -
936A SER* 2.9 24.9 + - - +
937A PHE* 4.2 3.8 - - - -
938A SER* 3.8 18.8 - - - -
941A LEU* 4.7 0.2 - - + -
965A VAL* 3.8 30.3 - - + -
967A TRP* 3.7 24.9 - + - -
973A TYR* 3.7 19.5 - + + -
974A GLY 3.6 16.4 - - - +
975A ALA* 3.9 3.8 - - + -
23a M3L 3.9 26.0 - - + -
26a ARG* 4.7 2.9 + - - -
----------------------------------------------------------
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