Contacts of the helix formed by residues 870 - 876 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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861A GLU* 3.5 32.6 + - + +
868A ARG 5.0 4.5 - - - +
869A LEU* 1.3 78.4 - - - +
871A LEU* 1.3 66.7 + - - +
872A ARG* 3.2 25.9 - - + +
873A ASP* 3.4 11.2 + - - +
874A LEU* 3.3 22.4 + - - +
1041B ARG* 5.8 5.8 - - - +
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Residues in contact with LEU 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A LEU* 4.2 11.0 - - + -
760A PHE* 3.7 35.9 - - + -
764A MET* 4.8 6.5 - - + -
778A LEU* 4.8 10.5 - - + -
779A PHE* 4.8 4.3 - - + -
840A LEU* 4.5 10.3 - - + -
843A ILE* 4.4 16.4 - - + -
857A MET* 4.1 20.6 - - + -
861A GLU* 3.5 12.9 + - - +
870A GLN* 1.3 75.1 - - - +
872A ARG* 1.3 64.4 + - - +
874A LEU* 3.1 5.5 + - - +
875A ILE* 3.1 49.3 + - + +
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Residues in contact with ARG 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A LEU* 4.5 33.7 + - + +
841A GLU* 5.1 4.9 + - - -
844A LYS* 4.7 22.2 - - - +
870A GLN* 4.4 22.2 - - + +
871A LEU* 1.3 81.8 - - - +
873A ASP* 1.3 70.5 + - - +
875A ILE* 3.8 8.8 - - - +
876A ILE* 3.5 25.1 + - - +
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Residues in contact with ASP 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A LEU* 4.2 19.9 - - + +
870A GLN* 3.4 15.5 + - - +
871A LEU 3.1 0.4 - - - -
872A ARG* 1.3 89.8 + - - +
874A LEU* 1.3 64.8 + - - +
875A ILE 3.3 0.2 - - - -
876A ILE* 3.7 17.0 - - - +
877A SER* 3.9 6.6 + - - -
880A GLN* 4.5 4.0 + - - -
1041B ARG* 4.7 3.1 - - - -
1063B THR* 3.5 21.4 - - - +
1064B SER* 3.0 41.6 + - - +
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Residues in contact with LEU 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A ARG* 6.1 2.2 - - - +
752A THR* 3.8 24.9 - - + +
755A VAL* 4.4 19.3 - - + -
756A LEU* 3.6 24.1 - - + +
760A PHE* 3.7 30.3 - - + -
866A CYS* 4.4 11.9 - - - +
869A LEU* 4.1 33.4 - - + +
870A GLN 3.3 19.5 - - - +
871A LEU* 3.1 5.6 + - - +
873A ASP* 1.3 77.9 - - - +
875A ILE* 1.3 59.1 + - - +
876A ILE 3.4 0.2 - - - -
877A SER* 3.0 24.3 + - - -
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Residues in contact with ILE 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A LEU* 4.0 10.4 - - + +
778A LEU* 3.4 39.3 - - + +
779A PHE* 3.7 18.6 - - + -
832A PHE* 3.8 22.8 - - + -
836A GLN* 3.2 42.7 + - + +
840A LEU* 4.1 17.0 - - + -
871A LEU* 3.1 30.1 + - + +
872A ARG 3.8 6.7 - - - +
874A LEU* 1.3 76.6 - - - +
876A ILE* 1.3 63.8 + - - +
877A SER* 3.1 5.9 + - - -
878A GLU* 3.8 5.9 + - - +
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Residues in contact with ILE 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836A GLN* 4.1 15.5 - - - +
840A LEU* 6.1 2.7 - - + -
872A ARG 3.5 17.7 - - - +
873A ASP* 3.7 12.3 - - - +
875A ILE* 1.3 79.0 - - + +
877A SER* 1.3 64.4 + - - +
878A GLU 3.2 2.8 + - - -
879A MET* 3.2 31.0 + - + -
880A GLN* 3.2 33.3 + - + +
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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