Contacts of the helix formed by residues 863 - 877 (chain A) in PDB entry 5NK4
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 LYS 863 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A ALA* 5.2 12.7 - - + +
800A VAL* 4.5 2.7 - - + -
858A ARG 5.1 5.7 + - - -
859A ALA* 5.0 12.2 + - - +
861A ARG 3.6 8.9 + - - +
862A PRO* 1.3 79.0 - - - +
864A PHE* 1.3 67.5 + - - +
865A ALA* 3.1 11.9 - - + +
866A ASP* 2.9 28.5 + - - +
867A ILE* 3.0 13.6 + - - +
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Residues in contact with PHE 864 (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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724A ALA* 4.2 11.4 - - + +
727A MET* 3.5 48.9 - - + -
728A LYS* 3.6 23.1 - - + -
731A ALA* 4.3 14.1 - - + -
796A SER* 3.7 14.1 - - - -
799A ASP* 3.7 25.8 - - + -
800A VAL* 3.6 23.7 - - + +
803A PHE* 3.6 27.8 - + + -
863A LYS* 1.3 74.1 - - - +
865A ALA* 1.3 64.2 + - - +
867A ILE* 3.1 14.0 + - + +
868A VAL* 2.8 27.9 + - - +
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Residues in contact with ALA 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A LYS* 3.8 37.2 + - + +
732A ASN* 5.7 0.9 - - - +
863A LYS* 3.1 8.8 - - + +
864A PHE* 1.3 78.3 - - - +
866A ASP* 1.3 64.3 + - - +
868A VAL* 3.6 1.6 + - - +
869A SER* 3.1 24.3 + - - -
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Residues in contact with ASP 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A PRO* 3.8 15.5 - - + +
863A LYS* 2.9 35.7 + - - +
865A ALA* 1.3 77.1 - - - +
867A ILE* 1.3 66.4 + - - +
869A SER* 3.3 6.2 + - - -
870A ILE* 3.0 37.7 + - + +
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Residues in contact with ILE 867 (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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724A ALA* 3.7 14.4 - - + -
800A VAL* 3.9 26.0 - - + -
803A PHE* 3.5 28.9 - - + -
849A LEU* 4.2 20.4 - - + -
853A CYS* 4.0 12.1 - - - -
862A PRO* 4.0 14.8 - - + -
863A LYS 3.0 13.6 + - - +
864A PHE* 3.6 26.5 - - + +
866A ASP* 1.3 76.6 - - - +
868A VAL* 1.3 62.9 + - - +
870A ILE* 3.3 2.8 + - - +
871A LEU* 3.0 32.2 + - + +
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Residues in contact with VAL 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A ARG* 4.1 21.3 - - - +
724A ALA* 3.5 39.0 - - + +
725A ALA* 3.6 9.9 - - + +
728A LYS* 4.2 18.6 - - + +
864A PHE 2.8 23.2 + - - +
865A ALA 4.0 3.4 - - - +
867A ILE* 1.3 70.4 - - - +
869A SER* 1.3 57.7 + - - +
871A LEU* 3.4 3.8 + - - +
872A ASP* 2.9 44.2 + - - +
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Residues in contact with SER 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A ALA 3.1 18.5 + - - -
866A ASP* 3.6 6.3 - - - -
868A VAL* 1.3 80.3 - - - +
870A ILE* 1.3 63.5 + - - +
872A ASP* 3.5 7.1 - - - +
873A LYS* 3.0 49.4 + - - +
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Residues in contact with ILE 870 (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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845A ALA* 5.6 2.2 - - + +
849A LEU* 4.1 35.0 - - + -
862A PRO* 5.8 1.6 - - + -
866A ASP* 3.0 28.4 + - + +
867A ILE 3.9 3.1 - - - +
869A SER* 1.3 76.6 - - - +
871A LEU* 1.3 64.6 + - - +
873A LYS* 3.2 12.8 + - + +
874A LEU* 3.0 42.1 + - + +
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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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717A VAL* 4.0 11.0 - - + -
720A LEU* 3.7 16.8 - - + +
721A ARG* 3.7 38.4 - - + +
724A ALA* 4.1 2.9 - - + -
803A PHE* 4.3 3.8 - - + -
807A MET* 4.9 2.5 - - + -
846A ILE* 3.6 30.7 - - + -
849A LEU* 3.9 15.7 - - + -
867A ILE* 3.0 36.7 + - + +
868A VAL 4.0 2.7 - - - +
870A ILE* 1.3 75.0 - - - +
872A ASP* 1.3 63.0 + - - +
874A LEU* 3.3 6.0 + - + +
875A ILE* 3.0 31.7 + - - +
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Residues in contact with ASP 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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721A ARG* 2.4 53.5 + - - +
868A VAL* 2.9 24.1 + - - +
869A SER* 3.5 7.5 - - - +
871A LEU* 1.3 76.5 - - - +
873A LYS* 1.3 58.5 + - + +
875A ILE* 3.2 6.5 + - - +
876A ARG* 2.9 54.5 + - - +
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Residues in contact with LYS 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 SER* 3.0 40.6 + - - +
870A ILE* 3.2 10.1 + - + +
872A ASP* 1.3 77.8 - - + +
874A LEU* 1.3 63.4 + - + +
876A ARG* 3.4 7.9 + - - +
877A ALA* 3.1 25.6 + - - +
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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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717A VAL* 5.1 2.0 - - + -
845A ALA* 3.7 34.5 - - + +
846A ILE* 3.9 24.2 - - + -
849A LEU* 5.7 0.2 - - + -
870A ILE* 3.0 38.5 + - + +
871A LEU* 3.7 7.2 - - + +
873A LYS* 1.3 77.2 - - + +
875A ILE* 1.3 63.3 + - - +
877A ALA 3.0 21.5 - - - +
878A PRO* 3.4 4.9 - - - +
880A SER* 3.3 29.8 + - - +
881A LEU* 3.9 16.8 - - + +
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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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714A LEU* 4.2 26.0 - - + +
717A VAL* 3.7 20.0 - - + +
718A GLY* 3.8 19.5 - - - +
721A ARG* 3.8 31.6 - - + -
871A LEU 3.0 21.5 + - - +
872A ASP* 3.7 6.5 - - - +
874A LEU* 1.3 75.3 - - - +
876A ARG* 1.3 66.1 + - + +
878A PRO* 3.3 18.2 - - - +
881A LEU* 4.9 0.4 - - + -
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Residues in contact with ARG 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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872A ASP* 2.9 38.0 + - - +
873A LYS* 4.0 6.7 - - - +
874A LEU 3.3 0.2 - - - -
875A ILE* 1.3 81.9 - - + +
877A ALA* 1.3 57.2 + - - +
878A PRO* 3.4 6.8 - - - +
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Residues in contact with ALA 877 (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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873A LYS 3.1 13.2 + - - +
874A LEU 3.1 2.2 - - - -
876A ARG* 1.3 76.9 - - - +
878A PRO* 1.3 57.5 - - - +
879A ASP* 3.2 3.6 - - - -
880A SER* 2.7 40.8 + - - +
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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