Contacts of the helix formed by residues 897 - 907 (chain A) in PDB entry 4CKR
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 897 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895A ARG 3.6 4.0 - - - +
896A PRO* 1.3 90.4 - - + +
898A PHE* 1.3 60.5 + - - +
899A SER* 3.2 12.1 - - - +
900A GLN* 2.9 29.7 + - + +
901A LEU* 3.0 11.3 + - - +
1002A EDO 3.2 28.0 - - - +
1004A EDO 3.7 11.4 - - - +
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Residues in contact with PHE 898 (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 ALA* 3.9 13.6 - - - +
754A MET* 3.4 48.0 - - + -
755A ARG* 3.6 22.9 - - + +
758A ALA* 4.4 0.4 - - + -
767A LEU* 4.8 0.2 - - + -
822A THR* 3.9 12.3 - - + -
825A ASP* 3.6 39.3 - - + -
826A VAL* 3.7 14.8 - - + -
829A PHE* 3.6 27.4 - + + -
896A PRO 3.9 0.2 + - - -
897A PRO* 1.3 67.9 - - - +
899A SER* 1.3 59.8 + - - +
901A LEU* 3.7 16.8 - - + +
902A HIS* 2.8 32.2 + - - +
1002A EDO 2.9 20.9 + - - +
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Residues in contact with SER 899 (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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755A ARG* 3.8 23.1 - - - +
897A PRO* 3.9 11.6 - - - +
898A PHE* 1.3 76.1 - - - +
900A GLN* 1.3 57.9 + - - +
902A HIS* 3.8 3.5 + - - +
903A ARG* 3.0 30.2 + - - +
1002A EDO 2.9 19.1 + - - -
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Residues in contact with GLN 900 (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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883A LEU* 5.9 3.4 - - + -
896A PRO* 4.4 11.9 - - + -
897A PRO* 2.9 27.8 + - + +
899A SER* 1.3 79.4 + - - +
901A LEU* 1.3 60.2 + - - +
903A ARG* 3.8 10.9 - - - +
904A PHE* 2.9 33.7 + - + +
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Residues in contact with LEU 901 (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 ALA* 4.3 5.8 - - + -
826A VAL* 3.9 13.5 - - + -
829A PHE* 3.8 28.3 - - + -
883A LEU* 3.7 23.7 - - + +
887A CYS* 3.7 22.0 - - - -
896A PRO* 3.7 31.2 - - + +
897A PRO 3.0 12.2 + - - +
898A PHE* 3.3 30.5 + - + +
900A GLN* 1.3 74.8 - - - +
902A HIS* 1.3 60.9 + - - +
904A PHE* 3.8 4.5 - - - +
905A LEU* 3.0 29.3 + - - +
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Residues in contact with HIS 902 (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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748A ALA* 3.2 28.5 - - + -
751A ALA* 3.8 15.1 - - + +
752A SER* 3.7 17.6 - - - +
755A ARG* 5.4 7.7 + - + -
898A PHE 2.8 17.9 + - - +
899A SER* 3.8 5.7 + - - +
901A LEU* 1.3 75.7 - - - +
903A ARG* 1.3 64.8 + - - +
905A LEU* 3.2 2.5 + - - +
906A ALA* 2.8 39.6 + - + +
1005A EDO 3.0 31.8 + - - -
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Residues in contact with ARG 903 (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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899A SER 3.0 19.4 + - - +
900A GLN* 3.8 11.0 - - - +
902A HIS* 1.3 81.4 + - - +
904A PHE* 1.3 58.9 + - - +
906A ALA* 4.7 1.6 - - - +
907A GLU* 2.8 64.8 + - - +
908A ASP* 3.7 5.6 - - - +
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Residues in contact with PHE 904 (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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879A GLY* 3.9 25.4 - - - -
880A LEU* 3.8 25.4 - - + -
883A LEU* 3.6 31.2 - - + -
886A ARG* 4.7 11.4 - - - -
900A GLN* 2.9 21.2 + - + +
901A LEU 3.8 3.4 - - - +
903A ARG* 1.3 77.1 - - - +
905A LEU* 1.3 60.6 + - - +
908A ASP* 3.2 33.0 + - + +
909A ALA* 2.8 41.6 + - + -
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Residues in contact with LEU 905 (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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744A LEU* 4.0 22.3 - - + +
747A ALA* 3.6 13.0 - - + +
748A ALA* 3.6 31.9 - - + +
751A ALA* 4.4 1.6 - - + -
829A PHE* 3.6 34.3 - - + -
833A LEU* 4.6 5.4 - - + -
880A LEU* 3.6 31.4 - - + -
883A LEU* 4.9 2.7 - - + -
901A LEU* 3.0 21.8 + - + +
902A HIS 3.9 0.9 - - - +
904A PHE* 1.3 80.7 - - + +
906A ALA* 1.3 60.3 + - - +
907A GLU 3.6 0.2 + - - -
909A ALA* 3.9 4.1 - - + +
910A LEU* 3.4 27.0 + - - +
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Residues in contact with ALA 906 (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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748A ALA* 4.2 4.0 - - + +
902A HIS* 2.8 42.8 + - + +
903A ARG* 4.4 1.8 - - - +
905A LEU* 1.3 73.6 - - - +
907A GLU* 1.3 66.0 + - + +
910A LEU* 3.4 22.4 - - - +
911A ASN* 4.9 1.2 - - - +
1005A EDO 4.2 9.6 - - - +
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Residues in contact with GLU 907 (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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903A ARG* 2.8 49.7 + - - +
906A ALA* 1.3 80.4 - - + +
908A ASP* 1.3 61.8 + - - +
909A ALA 3.4 1.8 - - - -
910A LEU* 3.1 2.8 + - - +
911A ASN* 2.7 54.3 + - - +
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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