Contacts of the helix formed by residues 948 - 965 (chain A) in PDB entry 5KHU
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 PRO 948 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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947A LEU* 3.8 28.7 - - - -
949A PHE* 3.8 29.6 - - - -
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Residues in contact with PHE 949 (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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948A PRO* 3.8 29.2 - - - -
950A GLY* 3.7 29.8 - - - +
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Residues in contact with GLY 950 (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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949A PHE* 3.7 29.6 - - - +
951A ILE* 3.8 25.4 - - - +
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Residues in contact with ILE 951 (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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950A GLY* 3.8 29.6 - - - +
952A ALA* 3.8 26.5 - - - +
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Residues in contact with ALA 952 (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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951A ILE* 3.8 26.7 - - - +
953A LEU* 3.7 29.4 - - - +
955A ILE* 4.6 15.7 - - - +
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Residues in contact with LEU 953 (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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952A ALA* 3.7 30.1 - - - +
954A PRO* 3.8 27.1 - - - -
956A ARG* 4.5 15.3 - - - +
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Residues in contact with PRO 954 (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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953A LEU* 3.8 23.3 - - - -
955A ILE* 3.7 29.8 - - - -
957A ASP* 4.4 15.3 - - - -
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Residues in contact with ILE 955 (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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952A ALA* 4.6 15.0 - - - +
954A PRO* 3.7 30.3 - - - -
956A ARG* 3.8 26.5 - - - +
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Residues in contact with ARG 956 (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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953A LEU* 4.5 12.6 - - - +
955A ILE* 3.8 30.1 - - - +
957A ASP* 3.8 26.0 - - - +
959A ILE* 4.3 19.5 - - - +
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Residues in contact with ASP 957 (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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954A PRO* 4.4 17.7 - - - -
956A ARG* 3.8 24.0 - - - +
958A ALA* 3.8 30.3 - - - +
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Residues in contact with ALA 958 (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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957A ASP* 3.8 29.6 - - - +
959A ILE* 3.8 25.8 - - - +
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Residues in contact with ILE 959 (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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956A ARG* 4.3 17.5 - - - +
958A ALA* 3.8 26.2 - - - +
960A TYR* 3.8 28.9 - - - +
962A CYS* 4.4 15.7 - - - +
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Residues in contact with TYR 960 (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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959A ILE* 3.8 25.6 - - - +
961A HIS* 3.8 29.8 - - - +
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Residues in contact with HIS 961 (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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960A TYR* 3.8 28.9 - - - +
962A CYS* 3.8 25.8 - - - +
964A GLU* 4.6 16.4 - - - +
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Residues in contact with CYS 962 (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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959A ILE* 4.4 16.2 - - - +
961A HIS* 3.8 29.8 - - - +
963A ARG* 3.8 23.8 - - - +
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Residues in contact with ARG 963 (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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962A CYS* 3.8 23.8 - - - +
964A GLU* 3.8 30.3 - - - +
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Residues in contact with GLU 964 (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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961A HIS* 4.6 15.9 - - - +
963A ARG* 3.8 29.6 - - - +
965A GLN* 3.8 24.7 - - - +
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Residues in contact with GLN 965 (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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964A GLU* 3.8 28.9 - - - +
966A PRO* 3.8 28.9 - - - -
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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