Contacts of the strand formed by residues 984 - 994 (chain C) in PDB entry 3KBU
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 GLN 984 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943C CYS* 6.0 0.2 - - - -
944C ALA* 5.9 1.9 + - - +
982C GLY 3.8 11.3 - - - +
983C ALA* 1.3 75.5 - - - +
985C PHE* 1.3 69.9 + - - +
986C LEU* 5.8 0.3 - - - +
1057C THR* 3.7 9.7 + - - -
1058C ASP* 3.6 28.6 + - - +
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Residues in contact with PHE 985 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938C ILE* 4.1 20.0 - - + -
942C THR 3.3 16.4 - - - +
943C CYS* 4.3 23.3 - - + +
944C ALA 6.1 0.2 - - - +
947C THR* 5.7 1.1 - - + -
949C ILE* 4.2 9.2 - - + -
983C ALA* 4.3 15.5 - - + -
984C GLN* 1.3 84.3 + - - +
986C LEU* 1.3 64.2 + - - +
987C SER 3.2 19.5 + - - +
989C VAL* 3.6 24.2 - - + -
1057C THR* 2.9 34.2 + - - +
1058C ASP* 4.8 0.7 - - - -
1059C PHE* 3.6 48.5 - + - -
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Residues in contact with LEU 986 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1867B ALA* 4.5 15.0 - - + -
1868B GLY* 5.3 4.9 - - - +
941C ARG 4.0 19.3 - - - +
942C THR 2.9 15.1 + - - +
944C ALA* 4.2 28.9 - - + +
984C GLN 5.8 0.2 - - - +
985C PHE* 1.3 73.2 - - - +
987C SER* 1.3 60.6 - - - +
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Residues in contact with SER 987 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941C ARG 5.3 1.8 - - - -
942C THR* 3.3 35.0 + - - +
985C PHE* 3.2 14.6 + - - +
986C LEU* 1.3 78.9 - - - +
988C PRO* 1.3 85.0 + - - +
1031C GLN 5.6 0.2 + - - -
1032C ILE* 4.2 10.7 + - - -
1034C ASN* 6.0 0.3 - - - +
1057C THR* 4.6 3.8 - - - -
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Residues in contact with PRO 988 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939C PRO* 3.9 10.0 - - - +
987C SER* 1.3 95.8 + - - +
989C VAL* 1.3 57.8 + - - +
1032C ILE* 3.6 51.4 - - + +
1055C ILE* 3.8 15.0 - - + -
1056C THR 3.4 9.0 - - - +
1057C THR* 3.6 23.5 - - + -
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Residues in contact with VAL 989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936C VAL* 5.9 1.6 - - + -
937C VAL 3.8 8.3 - - - +
938C ILE* 4.2 17.7 - - + -
939C PRO* 4.2 9.6 - - + -
942C THR* 4.4 0.7 - - - +
985C PHE* 3.6 51.4 - - + -
987C SER 4.1 1.6 - - - +
988C PRO* 1.3 78.1 - - - +
990C ILE* 1.3 63.4 + - - +
991C VAL* 4.9 5.6 - - + -
1054C ILE 3.8 0.9 - - - +
1055C ILE* 3.6 4.2 - - - -
1056C THR* 2.8 51.8 + - + +
1059C PHE* 4.4 7.9 - - + -
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Residues in contact with ILE 990 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935C ARG 4.1 0.2 - - - +
936C VAL* 3.6 2.9 - - - +
937C VAL* 2.8 52.6 + - + +
939C PRO* 5.3 1.1 - - + -
989C VAL* 1.3 78.2 - - - +
991C VAL* 1.3 68.2 + - - +
992C GLU* 4.4 9.2 - - + +
1029C LEU* 4.1 14.8 - - + -
1032C ILE* 4.0 26.9 - - + -
1033C LEU* 4.0 21.3 - - + -
1040C LEU* 4.2 10.1 - - + -
1053C ARG* 3.6 28.7 - - + +
1054C ILE 3.6 4.0 - - - -
1055C ILE* 4.3 13.7 - - + -
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Residues in contact with VAL 991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934C LEU* 5.6 1.6 - - + -
935C ARG 3.1 9.6 - - - +
936C VAL* 4.3 19.5 - - + -
978C LEU* 3.8 33.7 - - + -
989C VAL* 4.9 12.1 - - + -
990C ILE* 1.3 78.1 - - - +
992C GLU* 1.3 65.0 + - - +
993C ILE* 3.6 26.4 + - + -
1052C CYS 3.7 0.5 - - - +
1053C ARG* 3.6 0.7 - - - -
1054C ILE* 2.8 47.1 + - + +
1056C THR* 5.0 5.4 - - + -
1059C PHE* 4.9 3.1 - - + -
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Residues in contact with GLU 992 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927C ARG* 5.4 2.1 + - - -
933C GLY 4.0 4.0 - - - +
934C LEU* 3.3 6.4 - - - +
935C ARG* 2.6 76.8 + - + +
937C VAL* 6.0 0.2 - - - -
990C ILE* 4.4 5.2 - - + +
991C VAL* 1.3 75.1 - - - +
993C ILE* 1.3 67.8 + - - +
1040C LEU* 4.2 8.0 - - - +
1041C GLY 4.9 0.7 + - - -
1046C LEU* 4.4 12.5 - - - +
1051C VAL* 3.7 14.9 - - + +
1052C CYS 3.1 9.6 - - - +
1053C ARG* 3.1 41.9 + - + -
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Residues in contact with ILE 993 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934C LEU* 4.1 15.9 - - + -
953C LEU* 5.8 1.3 - - + -
973C SER* 4.3 4.3 - - - -
976C ILE* 3.2 48.2 - - + -
978C LEU* 6.0 0.2 - - + -
991C VAL* 3.6 24.7 - - + -
992C GLU* 1.3 77.6 - - - +
994C PRO* 1.4 78.2 - - + +
995C HIS* 3.9 0.9 + - - -
1051C VAL* 4.0 2.0 - - - -
1052C CYS* 2.7 42.0 + - + +
1054C ILE* 3.9 21.5 - - + -
1065C ILE* 4.2 17.5 - - + -
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Residues in contact with PRO 994 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931C HIS* 5.6 5.2 - - + -
933C GLY* 3.4 38.8 - - - +
934C LEU* 3.7 15.3 - - + +
973C SER* 3.9 7.4 - - - -
993C ILE* 1.4 99.2 - - + +
995C HIS* 1.3 60.5 + - - +
1049C LYS 5.4 0.9 - - - +
1050C ARG 3.3 12.3 - - - +
1051C VAL* 4.0 7.2 - - + -
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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