Contacts of the helix formed by residues 870 - 876 (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 GLN 870 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041A ARG* 4.0 25.1 - - - +
1062A LEU 5.4 3.2 + - - -
861B GLU* 3.4 26.2 - - + +
869B LEU* 1.3 77.4 - - - +
871B LEU* 1.3 70.2 + - - +
872B ARG* 3.3 27.7 - - + +
873B ASP* 3.1 20.7 + - + +
874B LEU* 3.3 12.4 + - - +
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Residues in contact with LEU 871 (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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756B LEU* 3.9 12.1 - - + -
760B PHE* 3.7 40.4 - - + -
764B MET* 4.0 8.7 - - + -
778B LEU* 4.9 8.3 - - + -
779B PHE* 4.4 7.4 - - + -
840B LEU* 4.6 7.0 - - + -
843B ILE* 5.1 8.1 - - + -
857B MET* 4.0 22.4 - - + -
861B GLU* 3.2 14.0 + - - +
870B GLN* 1.3 72.8 - - - +
872B ARG* 1.3 55.0 + - - +
874B LEU* 2.8 25.2 + - - +
875B ILE* 2.8 45.7 + - + -
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Residues in contact with ARG 872 (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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1063A THR* 6.5 1.6 - - - -
840B LEU* 4.2 40.3 + - + +
841B GLU* 5.6 1.4 - - - +
844B LYS* 4.0 36.8 - - - +
870B GLN* 3.9 26.7 - - + +
871B LEU* 1.3 77.2 - - - +
873B ASP* 1.3 62.4 + - + +
875B ILE* 3.9 10.8 - - - +
876B ILE* 3.3 27.7 + - - +
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Residues in contact with ASP 873 (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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1041A ARG* 4.3 5.5 + - - -
1062A LEU 4.8 0.3 - - - +
1063A THR* 3.5 29.2 - - - +
1064A SER* 3.4 33.5 + - - +
1065A SER* 5.1 0.5 + - - -
869B LEU* 3.9 26.5 - - + +
870B GLN* 3.1 21.3 + - - +
871B LEU 3.1 0.4 - - - -
872B ARG* 1.3 81.2 - - - +
874B LEU* 1.3 64.8 + - - +
876B ILE* 3.8 16.2 - - - +
877B SER* 3.9 5.7 + - - -
880B GLN* 4.4 5.2 + - - -
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Residues in contact with LEU 874 (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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1040A LYS* 5.8 3.1 - - - +
752B THR* 3.8 24.4 - - + +
755B VAL* 4.3 13.2 - - + -
756B LEU* 3.8 21.0 - - + +
760B PHE* 4.2 23.6 - - + -
865B GLN 6.0 0.2 - - - +
866B CYS* 4.3 18.4 - - + +
869B LEU* 3.8 38.8 - - + +
870B GLN 3.3 14.1 + - - +
871B LEU 2.8 6.0 + - - +
873B ASP* 1.3 79.6 - - - +
875B ILE* 1.3 59.3 + - - +
877B SER* 2.5 31.7 + - - +
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Residues in contact with ILE 875 (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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756B LEU* 3.9 9.1 - - + +
778B LEU* 3.6 30.3 - - + +
779B PHE* 3.6 28.7 - - + -
832B PHE* 4.0 19.7 - - + -
836B GLN* 3.1 39.0 + - + +
840B LEU* 3.5 32.5 - - + -
871B LEU* 2.8 25.6 + - + +
872B ARG 3.9 6.5 - - - +
874B LEU* 1.3 74.4 - - - +
876B ILE* 1.3 60.4 + - - +
877B SER* 3.1 9.6 + - - -
878B GLU* 4.2 3.1 + - - +
879B MET 5.3 0.2 + - - -
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Residues in contact with ILE 876 (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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836B GLN* 3.8 17.5 - - - +
840B LEU* 5.8 4.5 - - + -
872B ARG 3.3 21.7 + - - +
873B ASP* 3.8 14.6 - - - +
874B LEU 3.3 1.4 - - - -
875B ILE* 1.3 79.3 - - + +
877B SER* 1.3 56.3 + - - +
878B GLU 3.4 0.9 - - - -
879B MET* 3.3 23.4 + - + -
880B GLN* 3.0 47.0 + - + +
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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