Contacts of the strand formed by residues 966 - 977 (chain B) in PDB entry 3KZ1
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 MET 966 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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929B ASN* 3.1 66.5 + - + +
932B ARG* 4.1 10.3 - - + +
933B LEU* 4.1 29.5 - - + +
936B TYR* 4.8 1.6 - - - -
965B LYS* 1.3 73.8 - - - +
967B ILE* 1.3 62.2 + - - +
968B HIS* 3.7 11.4 - - - +
969B GLU* 3.9 43.7 - - + +
987B LEU* 4.3 7.4 - - - -
988B LEU 3.6 13.5 - - - +
989B LEU* 3.8 11.2 - - + -
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Residues in contact with ILE 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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925B LYS* 5.2 9.7 + - - -
929B ASN* 4.8 5.5 + - - -
965B LYS* 4.5 1.8 - - + +
966B MET* 1.3 77.8 - - - +
968B HIS* 1.3 61.2 + - + +
988B LEU* 2.9 28.6 + - + +
989B LEU 3.7 20.9 - - - +
990B GLU* 4.3 11.7 - - + +
1073B LEU* 4.3 24.2 - - + +
1077B ALA* 3.6 31.4 - - + +
1080B ASN* 6.1 2.2 - - - +
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Residues in contact with HIS 968 (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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966B MET* 3.7 8.0 - - - +
967B ILE* 1.3 82.1 - - - +
969B GLU* 1.3 82.2 + - - +
970B GLY* 5.2 0.2 - - - -
987B LEU 3.7 0.2 - - - -
988B LEU* 2.8 45.8 + - + +
1066B ASP* 5.1 4.5 - - - -
1069B THR* 4.4 12.0 - - + +
1070B TRP* 3.5 42.7 - + - -
1073B LEU* 3.4 32.9 - - + +
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Residues in contact with GLU 969 (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 ARG* 3.2 30.8 + - - +
936B TYR* 2.7 35.0 + - - -
966B MET* 3.9 16.3 - - + +
968B HIS* 1.3 96.0 + - - +
970B GLY* 1.3 59.1 + - - +
985B HIS* 3.1 15.3 - - - +
986B VAL 3.4 8.3 - - - -
987B LEU* 3.6 15.2 - - + +
1070B TRP* 3.9 5.2 - - - -
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Residues in contact with GLY 970 (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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968B HIS* 5.2 0.4 - - - -
969B GLU* 1.3 78.9 - - - +
971B PRO* 1.3 74.8 - - - +
985B HIS* 3.6 14.9 + - - -
986B VAL* 3.0 34.1 + - - +
1070B TRP* 3.8 10.5 - - - -
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Residues in contact with PRO 971 (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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970B GLY* 1.3 83.1 - - - +
972B LEU* 1.3 72.0 + - - +
984B LEU 3.2 11.7 - - - +
985B HIS* 4.4 8.3 - - + -
1060B VAL 4.8 0.2 - - - +
1062B LEU* 4.5 36.3 + - + +
1066B ASP* 4.9 1.6 - - - +
1070B TRP* 6.1 0.7 - - - +
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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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970B GLY 3.6 1.0 + - - -
971B PRO* 1.3 95.6 - - - +
973B THR* 1.3 61.0 + - - +
983B ASP* 4.0 0.8 - - - -
984B LEU* 2.8 47.1 + - + +
986B VAL* 3.4 29.2 - - + -
1043B PHE* 3.8 26.2 - - + -
1059B LEU* 4.3 17.3 - - + -
1060B VAL 3.6 20.2 - - - +
1061B ALA* 4.2 9.0 - - - +
1066B ASP* 4.4 2.5 - - - +
1070B TRP* 3.5 38.6 - - + +
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Residues in contact with THR 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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972B LEU* 1.3 74.7 - - - +
974B TRP* 1.3 61.2 - - - +
975B ARG* 5.6 3.6 - - - +
981B THR* 4.1 24.5 - - + +
982B LEU 3.7 4.7 - - - +
983B ASP* 3.9 20.3 + - - +
1059B LEU* 3.4 4.2 - - - +
1060B VAL* 2.7 58.0 + - + +
1062B LEU* 6.1 0.9 - - - +
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Residues in contact with TRP 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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972B LEU 3.8 0.4 + - - -
973B THR* 1.3 72.9 - - - +
975B ARG* 1.3 58.6 + - - +
976B ILE* 2.9 41.6 + - + +
981B THR* 3.2 6.8 - - - -
982B LEU* 2.8 50.7 + - + +
984B LEU* 3.7 26.5 - - + -
995B LEU* 4.8 6.7 - - + -
1008B HIS* 3.5 36.3 - + + -
1022B PHE* 3.7 33.8 - + + -
1023B SER 5.2 0.7 - - - -
1024B PRO* 6.4 0.4 - - + -
1056B ILE 5.1 0.8 + - - -
1057B TYR* 3.4 43.0 - + - +
1058B GLU 3.2 18.9 - - - +
1059B LEU* 3.5 19.1 - - + -
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Residues in contact with ARG 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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868A ARG* 5.0 9.9 - - - +
973B THR* 4.0 6.0 + - - +
974B TRP* 1.3 71.3 + - - +
976B ILE* 1.3 63.2 + - - +
977B SER* 3.4 14.3 + - - +
980B LYS 4.0 4.7 - - - -
981B THR* 4.1 18.5 - - + +
1039B ASP* 2.5 33.1 + - - -
1041B ARG* 5.2 4.9 - - - +
1058B GLU* 2.9 57.1 + - + +
1060B VAL* 3.5 32.3 - - + +
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Residues in contact with ILE 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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974B TRP* 2.9 47.1 + - + +
975B ARG* 1.3 72.0 - - - +
977B SER* 1.3 63.6 + - - +
980B LYS* 3.3 25.7 + - + +
981B THR* 4.2 6.7 - - - -
982B LEU* 4.8 6.3 - - + +
1008B HIS* 4.1 26.7 - - + -
1009B SER 5.0 0.2 - - - +
1010B LYS* 4.4 26.2 - - - +
1022B PHE* 4.5 23.2 - - + -
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Residues in contact with SER 977 (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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975B ARG* 4.0 15.8 - - - +
976B ILE* 1.3 79.7 - - - +
978B LYS* 1.3 75.2 + - - +
979B ASP 3.5 1.7 + - - -
980B LYS* 3.1 26.6 + - - +
981B THR* 5.6 0.2 - - - +
1010B LYS* 3.3 23.0 + - - -
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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
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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