Contacts of the strand formed by residues 1051 - 1058 (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 VAL1051 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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933C GLY* 4.3 11.7 - - - +
992C GLU* 3.7 25.4 - - + +
993C ILE 3.3 10.3 - - - +
994C PRO* 4.0 18.8 - - + -
995C HIS* 3.5 7.7 + - - -
1046C LEU* 3.1 38.9 + - + +
1047C GLU* 5.2 0.7 - - - -
1049C LYS* 3.8 21.8 - - + +
1050C ARG* 1.3 82.3 - - - +
1052C CYS* 1.3 73.6 + - - +
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Residues in contact with CYS1052 (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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991C VAL 3.7 0.5 - - - +
992C GLU* 3.1 5.2 - - - -
993C ILE* 2.7 38.7 + - + +
995C HIS* 3.7 21.1 - - - -
1006C LEU* 4.2 14.1 - - - -
1008C VAL* 5.2 7.4 - - + -
1046C LEU* 4.7 0.2 - - - -
1051C VAL* 1.3 76.7 - - - +
1053C ARG* 1.3 62.4 + - - +
1054C ILE* 5.1 3.4 - - + -
1065C ILE* 3.9 38.4 - - + -
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Residues in contact with ARG1053 (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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990C ILE* 3.6 27.7 - - + +
991C VAL 3.6 2.2 - - - -
992C GLU* 3.1 18.0 + - + -
1008C VAL* 5.5 3.1 - - - +
1026C GLU* 4.9 4.8 + - - -
1029C LEU* 3.7 40.4 - - - +
1040C LEU* 3.7 10.3 - - - +
1041C GLY 3.0 38.2 + - - +
1042C SER 4.9 0.2 + - - -
1043C LEU* 3.9 25.7 - - + +
1046C LEU* 3.5 29.6 - - + +
1051C VAL 4.2 0.2 + - - -
1052C CYS* 1.3 74.4 - - - +
1054C ILE* 1.3 63.0 + - - +
1055C ILE* 4.0 17.6 + - + +
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Residues in contact with ILE1054 (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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976C ILE* 5.2 0.7 - - + -
989C VAL 3.8 1.2 - - - +
990C ILE* 3.6 3.5 - - - -
991C VAL* 2.8 45.0 + - + +
993C ILE* 3.9 27.6 - - + -
1008C VAL* 4.0 33.4 - - + -
1020C HIS* 3.9 15.3 - - + +
1052C CYS* 5.1 2.0 - - + +
1053C ARG* 1.3 75.0 - - - +
1055C ILE* 1.3 65.5 + - - +
1056C THR* 4.0 5.1 + - + -
1063C PHE* 3.9 45.1 - - + -
1065C ILE* 4.7 8.3 - - + -
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Residues in contact with ILE1055 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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988C PRO* 3.8 14.1 - - + -
989C VAL 3.6 5.4 - - - +
990C ILE* 4.3 16.4 - - + -
1020C HIS* 3.0 19.0 + - - -
1022C SER* 3.4 29.0 - - - +
1025C GLY* 4.1 28.9 - - - +
1026C GLU* 4.8 5.2 - - - +
1029C LEU* 4.3 18.4 - - + -
1032C ILE* 3.7 25.8 - - + -
1053C ARG* 4.0 18.3 + - + +
1054C ILE* 1.3 75.6 - - - +
1056C THR* 1.3 61.3 + - - +
1057C THR* 6.0 0.2 - - + -
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Residues in contact with THR1056 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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988C PRO* 3.4 0.8 - - - +
989C VAL* 2.8 48.4 + - + +
991C VAL* 5.0 6.3 - - + -
1010C ARG* 3.5 14.7 + - - -
1020C HIS* 3.9 12.5 - - - -
1022C SER* 5.5 0.9 - - - -
1054C ILE* 4.3 5.4 - - + -
1055C ILE* 1.3 75.1 - - - +
1057C THR* 1.3 64.4 + - - +
1058C ASP* 2.6 31.6 + - - +
1059C PHE* 4.6 6.5 - - + -
1063C PHE* 4.0 16.3 - - + -
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Residues in contact with THR1057 (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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984C GLN* 3.7 7.1 + - - -
985C PHE* 2.9 43.4 + - - +
986C LEU 5.9 0.2 - - - -
987C SER* 5.0 0.9 - - - -
988C PRO* 3.6 38.4 - - + -
989C VAL 4.8 0.2 - - - +
1022C SER* 6.4 1.6 - - - -
1056C THR* 1.3 77.6 + - - +
1058C ASP* 1.3 62.1 + - - +
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Residues in contact with ASP1058 (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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982C GLY 5.2 1.6 - - - +
983C ALA 3.0 15.7 - - - +
984C GLN* 3.6 26.2 + - - +
985C PHE* 4.6 1.6 - - - -
1010C ARG* 2.9 32.8 + - - -
1012C GLU* 4.5 4.0 - - - +
1056C THR* 2.6 30.0 + - - +
1057C THR* 1.3 82.8 + - - +
1059C PHE* 1.3 68.9 + - - +
1060C PRO* 3.4 5.7 - - - +
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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