Contacts of the strand formed by residues 914 - 932 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B ILE* 3.6 25.8 - - + -
907B SER 3.6 10.3 - - - -
908B LYS* 3.5 45.5 - - + -
912B GLY 5.0 0.2 - - - -
913B ARG* 1.3 76.0 + - - +
915B TYR* 1.3 69.7 + - - +
1002B ASP 5.1 0.2 - - - -
1004B TYR* 3.2 40.8 - + - -
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Residues in contact with TYR 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B ILE* 3.5 7.5 - - - -
907B SER 3.1 30.2 + - - +
909B HIS* 3.3 33.7 - + + -
911B ASN* 2.6 38.1 + - - -
913B ARG* 3.4 29.2 - - + +
914B PHE* 1.3 76.0 - - - +
916B GLN* 1.3 72.0 + - - +
917B CYS 3.6 0.3 + - - -
990B PHE* 3.9 12.7 - + + -
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Residues in contact with GLN 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B LYS* 3.2 45.2 - - + +
905B VAL 3.3 10.8 - - - +
906B ILE* 3.6 15.9 - - + +
915B TYR* 1.3 82.4 - - - +
917B CYS* 1.3 62.8 + - - +
990B PHE* 3.9 6.6 - - - -
991B GLU* 4.6 6.8 + - - +
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Residues in contact with CYS 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B LYS* 3.2 12.1 - - - +
905B VAL* 2.8 55.2 + - - +
907B SER* 3.8 22.7 - - - -
916B GLN* 1.3 76.2 - - - +
918B GLU* 1.3 57.4 + - - +
988B VAL* 3.7 18.2 - - - -
989B GLU 3.1 21.3 - - - +
990B PHE* 3.5 22.4 - - + +
991B GLU 5.4 0.2 - - - +
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Residues in contact with GLU 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902B GLY* 3.6 32.0 - - - +
903B GLN 3.5 4.5 - - - +
904B LYS* 2.6 36.6 + - + +
917B CYS* 1.3 73.7 - - - +
919B VAL* 1.3 69.2 + - - +
920B VAL* 3.5 13.8 + - + +
988B VAL* 3.1 5.0 - - - -
989B GLU* 2.6 44.5 + - + +
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Residues in contact with VAL 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899B ILE* 3.7 20.6 - - + -
900B THR 3.8 12.1 - - - +
901B ALA* 3.8 1.5 - - - -
902B GLY* 2.8 32.0 + - - +
903B GLN 2.8 22.1 + - - +
905B VAL* 3.7 23.8 - - + -
918B GLU* 1.3 72.1 - - - +
920B VAL* 1.3 62.5 + - - +
921B ARG 4.2 6.5 - - - +
922B LEU* 3.5 32.1 - - + -
986B TYR* 4.3 10.5 - - + -
987B GLN 3.7 5.6 - - - +
988B VAL* 4.4 6.7 - - + +
1003B VAL* 5.4 1.3 - - + -
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Residues in contact with VAL 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B ALA* 4.6 8.0 - - - +
902B GLY 5.4 0.2 + - - -
918B GLU* 3.9 14.6 - - + +
919B VAL* 1.3 77.6 - - - +
921B ARG* 1.3 65.3 + - + +
987B GLN* 2.8 36.2 + - + +
988B VAL* 5.0 0.7 - - - -
989B GLU* 3.5 37.2 - - + +
995B GLN* 3.5 21.5 - - - +
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Residues in contact with ARG 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B ALA* 5.2 2.0 - - - -
919B VAL* 3.7 0.7 - - - +
920B VAL* 1.3 89.0 + - + +
922B LEU* 1.3 83.7 + - - +
923B THR* 3.8 12.7 + - + +
986B TYR* 3.7 1.9 - - - -
987B GLN* 3.0 47.3 + - + +
947C VAL* 2.9 29.1 + - - -
948C SER* 3.9 28.1 + - - +
949C GLN* 5.6 0.4 - - - +
964C GLN* 4.2 13.3 + - - +
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Residues in contact with LEU 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899B ILE 3.7 20.4 - - - +
900B THR* 4.2 3.8 - - - -
901B ALA* 4.1 20.6 - - + +
919B VAL* 3.5 24.7 - - + -
921B ARG* 1.3 84.4 - - - +
923B THR* 1.3 65.4 + - - +
984B GLN* 3.5 31.9 - - - +
985B MET 3.7 1.1 - - - -
986B TYR* 3.8 16.2 - - + +
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Residues in contact with THR 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B ARG* 3.8 24.6 + - + -
922B LEU* 1.3 79.5 - - - +
924B THR* 1.3 61.3 + - - +
925B GLU* 4.7 4.6 + - - -
984B GLN* 3.3 6.2 - - - +
985B MET* 2.7 57.3 + - - +
987B GLN* 5.8 1.6 + - + -
997B VAL* 5.0 4.0 - - - +
947C VAL* 4.2 18.9 - - + +
949C GLN 6.5 1.1 - - - -
950C ASP* 6.6 0.2 - - + -
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Residues in contact with THR 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A PRO* 4.1 11.5 + - + +
957A PRO* 5.4 0.2 - - - +
958A ALA* 3.7 29.0 + - + +
961A GLU* 5.0 1.0 + - - -
923B THR* 1.3 77.5 - - - +
925B GLU* 1.3 62.0 + - - +
926B THR* 4.2 2.3 + - - +
982B PRO* 3.9 27.8 - - + -
983B ILE 3.6 7.0 - - - +
984B GLN* 4.3 5.7 + - - -
950C ASP* 5.8 0.5 - - - +
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Residues in contact with GLU 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923B THR* 3.8 6.2 + - - +
924B THR* 1.3 76.7 - - - +
926B THR* 1.3 66.3 + - - +
927B PHE* 3.4 29.2 - - + -
942B TYR* 4.5 2.6 - - - -
981B HIS 3.3 2.1 - - - +
982B PRO* 4.5 0.4 - - - -
983B ILE 2.9 29.2 + - - +
985B MET* 3.5 26.1 - - + +
997B VAL* 4.8 1.9 - - - +
944C GLU* 4.1 29.2 - - + +
947C VAL* 5.4 3.1 - - - +
966C ARG* 2.4 43.6 + - - -
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Residues in contact with THR 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A PRO* 5.1 6.6 - - - +
924B THR* 4.2 2.5 + - - +
925B GLU* 1.3 77.8 - - - +
927B PHE* 1.3 65.3 + - - +
928B TYR* 3.6 29.2 - - + -
941B LEU 4.5 0.2 - - - +
942B TYR* 5.2 0.7 - - - -
943B PRO* 3.7 22.6 - - + +
980B SER* 3.9 14.4 - - - -
981B HIS 3.2 6.1 - - - +
982B PRO* 4.2 13.7 - - + +
944C GLU* 4.0 7.5 + - - +
952C LEU* 6.2 4.0 - - - -
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Residues in contact with PHE 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925B GLU* 3.4 52.7 - - + -
926B THR* 1.3 76.2 - - - +
928B TYR* 1.3 63.5 + - - +
939B ASP 3.6 16.6 - - - +
940B ASN* 3.6 32.3 - - + -
941B LEU 3.4 7.4 - - - +
942B TYR* 5.5 9.2 - + - -
980B SER* 3.4 2.1 - - - -
981B HIS* 2.8 33.2 + - + +
983B ILE* 3.5 20.6 - - + -
985B MET* 3.9 16.4 - - + -
999B LYS* 4.0 20.4 - - - -
966C ARG* 4.2 7.0 - - - -
19b GLN 5.5 6.3 - - - -
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Residues in contact with TYR 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926B THR* 3.6 15.0 - - + -
927B PHE* 1.3 78.9 - - - +
929B GLU* 1.3 60.5 + - - +
930B VAL* 4.9 1.3 - - + -
938B SER 3.7 0.7 - - - +
939B ASP* 3.3 8.5 - - - -
941B LEU* 2.7 52.3 + - + +
943B PRO* 3.5 37.6 - - + +
946B ILE* 3.8 13.5 - - + -
951B CYS* 3.7 28.8 + - - +
955B GLY* 3.9 1.7 - - - -
956B PRO* 3.4 29.0 - - + +
957B PRO* 4.1 4.9 - - + -
977B PHE* 3.6 18.2 - + + -
979B ALA 3.5 1.6 - - - -
980B SER* 3.5 28.3 - - - -
981B HIS* 4.9 0.2 - - - -
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Residues in contact with GLU 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B TYR* 1.3 72.7 - - - +
930B VAL* 1.3 70.3 + - - +
931B ASN* 5.0 1.6 - - - +
937B PHE* 3.8 19.9 - - + -
938B SER 3.1 12.8 - - - +
939B ASP* 3.7 17.2 - - + +
977B PHE* 4.0 2.4 - - - -
978B VAL* 2.8 48.6 + - + +
979B ALA 2.7 21.0 + - - +
981B HIS* 2.6 39.7 + - - +
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Residues in contact with VAL 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B TYR* 4.9 0.7 - - + -
929B GLU* 1.3 82.5 - - - +
931B ASN* 1.3 60.6 + - - +
932B PHE* 3.5 32.1 - - + -
937B PHE* 3.3 5.9 - - - +
938B SER 2.9 32.4 + - - +
941B LEU* 3.3 33.0 - - + -
946B ILE* 4.3 19.1 - - + -
963B VAL* 4.6 3.1 - - + -
965B VAL* 4.3 4.3 - - + -
975B ALA* 4.0 8.7 - - + -
976B LYS 3.4 12.3 - - - +
977B PHE* 4.4 9.6 - - + -
978B VAL* 4.0 2.9 - - - -
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Residues in contact with ASN 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B GLU* 5.0 1.6 - - - +
930B VAL* 1.3 69.4 - - - +
932B PHE* 1.3 67.6 + - - +
933B ASP* 4.7 0.5 - - - +
936B SER 3.6 4.5 - - - +
937B PHE* 3.3 21.1 - - - +
975B ALA* 3.2 2.3 - - - +
976B LYS* 3.0 40.3 + - + +
978B VAL* 3.6 23.5 - - + +
26b ARG* 3.6 36.2 - - - +
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Residues in contact with PHE 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930B VAL* 3.5 22.7 - - + -
931B ASN* 1.3 78.7 - - - +
933B ASP* 1.3 62.4 + - - +
934B ASP* 3.1 21.5 - - - +
935B GLY* 3.2 13.0 + - - -
936B SER* 2.9 26.1 + - - +
937B PHE* 4.3 3.8 - - - -
938B SER* 3.9 18.8 - - - -
941B LEU* 4.7 0.2 - - + -
965B VAL* 3.8 31.2 - - + -
967B TRP* 3.8 23.6 - + - -
973B TYR* 3.8 19.3 - + + -
974B GLY 3.6 15.9 - - - +
975B ALA* 3.9 3.4 - - + -
23b M3L 3.9 26.7 - - + -
26b ARG* 4.8 2.6 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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