Contacts of the strand formed by residues 972 - 990 (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 VAL 972 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947B VAL* 4.1 8.5 - - + -
964B GLN* 3.6 31.6 - - + +
965B VAL 3.4 9.0 - - - +
966B ARG* 4.4 5.4 - - + -
970B GLY 4.8 0.4 - - - +
971B GLN* 1.3 86.6 + - - +
973B TYR* 1.3 69.1 - - - +
987C GLN* 3.9 22.0 - - + +
995C GLN* 3.0 29.0 + - + +
996C LEU 4.7 0.9 - - - -
997C VAL* 3.8 28.9 - - + -
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Residues in contact with TYR 973 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932B PHE* 3.8 22.0 - + + -
964B GLN* 3.4 3.1 - - - -
965B VAL* 2.8 38.4 + - - +
967B TRP* 3.5 28.9 - - + -
969B ASP* 3.2 23.2 + - - -
971B GLN* 3.4 35.0 + - + -
972B VAL* 1.3 77.7 - - - +
974B GLY* 1.3 64.4 + - - +
23b M3L 3.5 40.0 - - - -
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Residues in contact with GLY 974 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B PHE* 3.6 6.9 - - - +
933B ASP* 3.3 38.0 + - - +
962B VAL* 6.2 1.1 - - - -
963B VAL 3.7 6.3 - - - -
964B GLN* 4.7 5.8 - - - -
973B TYR* 1.3 75.8 - - - +
975B ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 975 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930B VAL* 4.0 11.2 - - + -
931B ASN 3.2 22.7 - - - +
932B PHE* 3.9 12.8 - - + -
933B ASP* 3.9 9.2 + - - +
962B VAL* 3.4 10.2 - - - +
963B VAL* 2.9 42.2 + - + -
965B VAL* 4.1 5.2 - - + -
974B GLY* 1.3 75.1 - - - +
976B LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 976 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930B VAL* 3.4 3.8 - - - -
931B ASN* 3.0 38.9 + - + +
933B ASP* 5.1 7.6 + - - +
960B GLY* 4.0 22.7 - - - +
961B GLU 3.2 6.3 - - - +
962B VAL* 4.1 22.4 - - + +
963B VAL* 4.3 2.9 - - - -
975B ALA* 1.3 79.2 - - - +
977B PHE* 1.3 66.4 + - - +
978B VAL* 3.9 1.8 - - + +
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Residues in contact with PHE 977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A PRO* 3.6 17.5 - - + -
928B TYR* 3.6 28.7 - + + -
929B GLU 4.0 7.4 - - - -
930B VAL* 4.4 10.8 - - + -
946B ILE* 4.9 2.7 - - + -
956B PRO* 3.8 9.4 - - + -
957B PRO* 3.4 60.3 - - + -
958B ALA 3.4 19.5 - - - +
959B GLU* 3.9 3.1 - - - -
960B GLY* 2.8 29.3 + - - -
961B GLU 2.7 15.3 + - - +
963B VAL* 4.1 4.3 - - + +
976B LYS* 1.3 71.9 - - - +
978B VAL* 1.3 61.2 + - - +
979B ALA* 3.4 32.8 - - - -
980B SER* 3.5 3.4 - - - -
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Residues in contact with VAL 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B GLU* 2.8 41.8 + - + +
930B VAL 4.0 2.5 - - - -
931B ASN* 3.6 50.0 - - - +
959B GLU* 2.9 29.8 - - - +
976B LYS* 3.9 2.0 - - + +
977B PHE* 1.3 77.2 - - - +
979B ALA* 1.3 66.1 + - + +
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Residues in contact with ALA 979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980A SER 5.5 2.5 - - - +
981A HIS* 5.9 2.9 - - + +
982A PRO* 5.1 0.9 - - - -
927B PHE 4.1 0.2 - - - +
928B TYR* 3.5 0.2 - - - -
929B GLU* 2.7 28.8 + - - +
959B GLU* 4.7 8.1 - - - +
977B PHE* 3.4 17.0 - - - -
978B VAL* 1.3 89.6 - - + +
980B SER* 1.3 61.8 + - - +
981B HIS* 3.8 27.4 - - + +
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Residues in contact with SER 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959A GLU* 5.0 0.2 - - - +
979A ALA* 5.4 2.3 - - - +
980A SER* 3.7 26.2 + - - +
982A PRO* 4.2 11.9 - - - +
926B THR* 3.9 9.4 - - - -
927B PHE 3.4 4.0 - - - -
928B TYR* 3.5 30.3 - - - -
956B PRO* 4.3 10.2 - - - +
977B PHE* 3.5 7.5 - - - -
979B ALA* 1.3 74.9 - - - +
981B HIS* 1.3 63.7 + - - +
982B PRO* 3.5 10.0 - - - +
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Residues in contact with HIS 981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959A GLU* 3.3 24.3 + - - +
979A ALA* 5.9 1.2 - - - +
925B GLU 3.3 2.3 - - - +
926B THR* 3.2 5.6 - - - -
927B PHE 2.8 38.2 + - - +
929B GLU* 2.6 44.8 + - + +
939B ASP* 4.1 14.9 - - + +
979B ALA* 3.8 15.2 - - + +
980B SER* 1.3 74.9 + - - +
982B PRO* 1.3 65.7 - - - +
983B ILE* 3.4 25.2 + - + +
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Residues in contact with PRO 982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956A PRO* 3.6 25.1 - - + -
957A PRO 3.5 22.9 - - - +
959A GLU* 2.6 47.2 + - - +
977A PHE* 3.6 18.8 - - + -
980A SER* 4.2 11.4 - - - +
924B THR* 3.9 14.8 - - + -
925B GLU 3.9 3.6 - - - +
926B THR* 4.2 8.9 - - + +
980B SER* 3.5 11.0 - - - +
981B HIS* 1.3 82.1 - - - +
983B ILE* 1.3 55.0 + - - +
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Residues in contact with ILE 983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958A ALA* 4.1 2.9 - - - -
959A GLU* 4.6 8.7 - - + +
924B THR* 3.6 0.9 - - - +
925B GLU 2.9 35.8 + - - +
927B PHE* 3.5 28.3 - - + -
939B ASP 5.0 4.0 - - - +
981B HIS* 3.7 26.5 - - + +
982B PRO* 1.3 76.2 - - - +
984B GLN* 1.3 76.4 + - - +
985B MET* 3.2 18.8 + - - +
999B LYS* 3.9 24.0 - - + +
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Residues in contact with GLN 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958A ALA* 3.6 29.1 - - + +
959A GLU 4.8 7.8 + - - +
961A GLU* 4.6 13.5 + - - +
922B LEU* 3.5 30.0 - - - +
923B THR 3.3 21.9 - - - +
924B THR* 4.3 5.2 + - - -
983B ILE* 1.3 81.3 - - - +
985B MET* 1.3 68.5 + - - +
986B TYR* 3.4 37.1 - - + +
999B LYS* 4.0 13.5 - - - -
1000B ARG* 4.1 5.4 + - + -
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Residues in contact with MET 985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922B LEU* 3.7 2.6 - - - -
923B THR* 2.7 42.9 + - - +
925B GLU* 3.5 33.7 - - + +
927B PHE* 3.9 17.9 - - + -
983B ILE* 3.7 17.0 - - - +
984B GLN* 1.3 81.6 - - - +
986B TYR* 1.3 64.7 + - - +
987B GLN 4.2 0.2 - - - -
997B VAL* 3.8 26.0 - - + +
998B VAL* 3.5 15.3 - - - -
999B LYS* 3.6 35.7 - - + -
966C ARG* 4.8 2.9 - - - +
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Residues in contact with TYR 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898B SER* 4.9 4.2 - - - -
899B ILE* 3.4 46.2 + - + +
919B VAL* 4.3 5.2 - - + -
921B ARG 3.7 3.1 - - - +
922B LEU* 3.8 36.3 - - + -
984B GLN* 3.4 27.3 - - + +
985B MET* 1.3 74.6 - - - +
987B GLN* 1.3 62.5 + - - +
988B VAL* 3.5 15.3 + - + -
997B VAL* 3.5 3.0 - - - -
998B VAL* 2.7 47.0 + - - +
999B LYS 4.2 2.9 - - - -
1000B ARG* 3.8 43.4 - - + -
1003B VAL* 4.6 11.9 - - + -
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Residues in contact with GLN 987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919B VAL* 3.7 2.9 - - - +
920B VAL* 2.8 41.8 + - + +
921B ARG* 3.0 39.7 + - + +
923B THR* 5.8 1.5 + - + -
985B MET* 4.2 0.6 - - - +
986B TYR* 1.3 71.6 - - - +
988B VAL* 1.3 58.5 + - - +
995B GLN* 2.4 33.1 + - + +
996B LEU 3.2 11.7 - - - +
997B VAL* 4.1 12.1 - - + +
947C VAL* 3.8 14.4 - - + +
964C GLN* 3.1 22.4 + - - +
972C VAL* 4.1 16.7 - - + +
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Residues in contact with VAL 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905B VAL* 4.3 7.0 - - + -
907B SER* 4.6 3.4 - - - -
917B CYS* 3.7 27.6 - - - -
918B GLU 3.1 9.2 - - - +
919B VAL* 4.4 8.1 - - + -
920B VAL* 5.0 0.4 - - - -
986B TYR* 4.1 9.2 - - + +
987B GLN* 1.3 77.1 - - - +
989B GLU* 1.3 60.0 + - - +
990B PHE* 4.2 10.9 - - + -
994B SER 3.9 0.7 - - - +
995B GLN* 3.1 8.7 - - - +
996B LEU* 2.9 53.2 + - + +
998B VAL* 4.3 10.1 - - + -
1003B VAL* 4.2 22.0 - - + -
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Residues in contact with GLU 989 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B LYS* 5.5 0.3 - - - -
917B CYS* 3.1 5.5 - - - +
918B GLU* 2.6 43.1 + - + +
920B VAL* 3.5 25.6 - - + +
987B GLN 4.4 0.2 + - - -
988B VAL* 1.3 73.6 - - - +
990B PHE* 1.3 70.8 + - - +
993B GLY* 4.0 17.9 - - - +
994B SER 3.7 4.0 - - - +
995B GLN* 3.7 28.6 + - + -
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Residues in contact with PHE 990 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907B SER 3.7 19.7 - - - -
908B LYS 3.6 21.3 - - - -
909B HIS* 3.6 31.9 - + + -
915B TYR* 3.9 22.2 - + + -
916B GLN 3.9 0.9 - - - -
917B CYS* 3.5 26.5 - - + +
988B VAL* 4.2 12.8 - - + -
989B GLU* 1.3 80.2 - - - +
991B GLU* 1.3 67.6 + - - +
992B ASP* 3.1 15.5 - - - +
993B GLY* 2.9 16.3 + - - -
994B SER* 3.0 21.4 + - - +
996B LEU* 3.5 27.1 - - + -
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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
------------------------------------------------------------
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