Contacts of the helix formed by residues 964 - 986 (chain B) in PDB entry 5XA0
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 ASP 964 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961B GLU 4.2 3.7 + - - +
962B LYS* 3.7 1.2 - - - +
963B GLU* 1.3 74.5 - - - +
965B ILE* 1.3 59.5 + - - +
967B VAL* 2.4 32.8 + - - +
968B MET* 3.0 8.0 + - - +
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Residues in contact with ILE 965 (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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962B LYS 5.5 0.8 - - - +
964B ASP* 1.3 78.5 - - - +
966B MET* 1.3 60.4 + - - +
967B VAL 3.4 0.9 + - - -
968B MET* 4.0 10.0 + - - +
969B ASP* 4.3 5.7 + - - +
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Residues in contact with MET 966 (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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962B LYS 4.5 4.0 + - - +
963B GLU* 3.3 30.2 - - + +
964B ASP 3.2 0.4 - - - -
965B ILE* 1.3 77.0 - - - +
967B VAL* 1.3 56.2 + - - +
968B MET 3.6 0.2 - - - -
969B ASP* 3.3 12.0 - - - +
970B THR* 2.9 22.3 + - - -
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Residues in contact with VAL 967 (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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963B GLU 2.3 27.2 + - - +
964B ASP* 2.4 31.2 + - - +
966B MET* 1.3 66.6 - - - +
968B MET* 1.3 57.7 + - - +
969B ASP 3.2 1.1 - - - -
970B THR* 3.5 11.1 - - - -
971B LYS* 2.9 29.8 + - - +
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Residues in contact with MET 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964B ASP 3.0 7.3 + - - +
965B ILE* 4.0 8.0 + - - +
966B MET 3.6 0.4 - - - -
967B VAL* 1.3 74.8 - - - +
969B ASP* 1.3 59.1 + - - +
971B LYS* 4.0 5.4 - - - +
972B LEU* 3.0 27.0 + - - +
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Residues in contact with ASP 969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965B ILE 4.3 3.4 + - - +
966B MET* 3.3 16.9 + - - +
968B MET* 1.3 76.3 - - - +
970B THR* 1.3 53.2 + - - +
972B LEU* 3.0 7.9 + - - +
973B LYS* 2.7 36.7 + - - +
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Residues in contact with THR 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963B GLU* 6.2 1.1 - - - -
966B MET 2.9 16.3 + - - -
967B VAL* 3.3 14.3 + - - -
969B ASP* 1.3 73.3 - - - +
971B LYS* 1.3 59.3 + - - +
973B LYS* 2.9 10.5 + - - +
974B ILE* 2.9 28.3 + - - +
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Residues in contact with LYS 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B PRO* 5.2 17.7 - - + +
967B VAL 2.9 19.9 + - - +
968B MET* 4.1 5.4 - - - +
970B THR* 1.3 72.8 - - - +
972B LEU* 1.3 57.1 + - - +
974B ILE* 3.4 9.5 + - - +
975B ILE* 3.0 26.7 + - - +
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Residues in contact with LEU 972 (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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864B PHE* 6.0 6.9 - - + +
968B MET 3.0 19.7 + - - +
969B ASP* 3.0 9.5 + - - +
971B LYS* 1.3 75.7 - - - +
973B LYS* 1.3 59.5 + - - +
975B ILE* 3.0 10.6 + - - +
976B GLU* 2.9 26.5 + - - +
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Residues in contact with LYS 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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860B ASN* 5.5 12.3 - - + +
863B THR* 6.4 2.0 - - - -
864B PHE* 6.0 6.0 - - + +
969B ASP 2.7 15.5 + - - +
970B THR* 3.3 12.8 - - - +
972B LEU* 1.3 70.1 - - - +
974B ILE* 1.3 67.0 + - - +
976B GLU* 3.1 17.4 + - - +
977B ILE* 3.1 14.4 + - - +
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Residues in contact with ILE 974 (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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773B LEU* 5.7 12.3 - - + +
970B THR 2.9 12.1 + - - +
971B LYS* 3.6 12.3 - - - +
973B LYS* 1.3 76.3 - - - +
975B ILE* 1.3 57.0 + - - +
977B ILE* 3.6 5.8 + - - +
978B LEU* 3.0 30.5 + - - +
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Residues in contact with ILE 975 (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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971B LYS 3.0 14.9 + - - +
972B LEU* 3.0 14.3 + - - +
974B ILE* 1.3 75.0 - - - +
976B GLU* 1.3 58.8 + - - +
978B LEU* 4.1 5.0 - - - +
979B GLN* 2.9 28.9 + - - +
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Residues in contact with GLU 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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863B THR* 3.8 7.0 - - - +
864B PHE* 4.6 6.3 - - - +
867B VAL* 3.4 30.1 - - + +
868B ASN* 3.8 13.7 - - + +
972B LEU 2.9 11.1 + - - +
973B LYS* 3.1 10.5 + - - +
975B ILE* 1.3 73.7 - - - +
977B ILE* 1.3 70.3 + - - +
979B GLN* 3.1 8.5 + - - +
980B PHE* 2.9 20.4 + - - +
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Residues in contact with ILE 977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B VAL* 4.6 4.3 - - - +
895B LEU* 5.8 8.1 - - + -
973B LYS 3.1 9.4 + - - +
974B ILE* 3.9 8.7 - - - +
976B GLU* 1.3 77.1 - - - +
978B LEU* 1.3 59.8 + - - +
980B PHE* 2.9 10.4 + - - +
981B ILE* 2.8 29.2 + - - +
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Residues in contact with LEU 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B ASP* 4.5 24.0 - - + +
974B ILE 3.0 19.4 + - - +
975B ILE* 4.1 4.9 - - - +
977B ILE* 1.3 76.0 - - - +
979B GLN* 1.3 64.4 + - - +
981B ILE* 4.4 6.7 - - - +
982B LEU* 2.8 29.7 + - + +
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Residues in contact with GLN 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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868B ASN* 5.2 3.8 - - - +
871B ARG* 3.2 27.1 - - + +
975B ILE 2.9 20.6 + - - +
976B GLU* 3.1 8.0 + - - +
978B LEU* 1.3 79.7 - - - +
980B PHE* 1.3 63.7 + - - +
982B LEU* 3.8 2.4 - - - +
983B ASN* 3.1 18.7 + - - +
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Residues in contact with PHE 980 (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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867B VAL* 4.6 3.8 - - + +
870B ALA* 4.6 12.6 - - + -
871B ARG* 3.3 21.3 - - - +
874B ILE* 5.2 1.2 - - - +
976B GLU 2.9 10.0 + - - +
977B ILE* 2.9 11.5 + - - +
979B GLN* 1.3 77.4 - - - +
981B ILE* 1.3 62.9 + - - +
983B ASN* 4.2 0.5 - - - +
984B VAL* 2.9 29.9 + - - +
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Residues in contact with ILE 981 (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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977B ILE 2.8 18.9 + - - +
978B LEU* 4.1 6.1 - - - +
980B PHE* 1.3 73.7 - - - +
982B LEU* 1.3 56.8 + - - +
984B VAL* 4.8 2.9 - - - -
985B ARG* 2.8 39.1 + - + +
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Residues in contact with LEU 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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978B LEU* 2.8 20.0 + - + +
979B GLN* 3.8 2.9 - - - +
981B ILE* 1.3 74.8 - - - +
983B ASN* 1.3 67.6 + - - +
985B ARG 5.1 0.7 - - - -
986B LEU* 2.9 35.8 + - + +
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Residues in contact with ASN 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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871B ARG* 3.4 27.1 - - + +
874B ILE* 5.0 2.1 - - + +
875B TYR* 4.8 15.4 + - + +
979B GLN 3.1 12.8 + - - +
980B PHE 4.2 0.9 - - - +
982B LEU* 1.3 80.0 - - - +
984B VAL* 1.3 63.5 + - - +
986B LEU* 4.1 5.9 + - - +
988B TYR* 4.4 15.9 + - - +
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Residues in contact with VAL 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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874B ILE* 4.1 21.4 - - + +
891B LEU* 5.8 8.7 - - + -
980B PHE 2.9 19.4 + - - +
981B ILE* 4.3 2.7 - - - +
983B ASN* 1.3 80.1 - - - +
985B ARG* 1.3 58.2 + - + +
986B LEU 3.5 0.2 - - - -
988B TYR* 4.4 1.0 - - - +
989B ARG* 2.8 23.0 + - - +
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Residues in contact with ARG 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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981B ILE* 2.8 23.2 + - + +
982B LEU* 3.6 1.6 - - - -
984B VAL* 1.3 77.2 - - + +
986B LEU* 1.3 58.2 + - - +
989B ARG* 3.1 15.4 - - - +
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Residues in contact with LEU 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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982B LEU* 2.9 23.5 + - + +
983B ASN* 4.1 3.7 + - - +
984B VAL 3.5 1.6 - - - -
985B ARG* 1.3 77.0 - - - +
987B ASP* 1.3 69.5 + - + +
988B TYR 3.6 0.4 - - - -
989B ARG* 3.2 12.2 + - - +
990B ILE* 4.2 4.5 + - - +
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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
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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