Contacts of the helix formed by residues 901 - 915 (chain A) in PDB entry 4KXA
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 THR 901 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900A ASN* 1.3 95.6 - - - +
902A GLU* 1.3 64.9 + - - +
903A LEU* 3.6 10.8 + - - +
904A GLN* 3.0 32.5 + - - +
905A LEU 3.1 18.5 + - - -
932A VAL* 4.6 0.9 - - - +
936A ILE* 3.6 12.1 - - - +
939A LEU* 5.7 1.8 - - + -
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Residues in contact with GLU 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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901A THR* 1.3 73.7 - - - +
903A LEU* 1.3 57.1 + - - +
905A LEU* 3.5 14.7 + - - +
906A TRP* 3.0 28.9 + - - +
936A ILE* 3.6 36.0 - - + +
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Residues in contact with LEU 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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901A THR* 3.1 10.2 + - - +
902A GLU* 1.3 79.1 - - - +
904A GLN* 1.3 67.6 + - + +
906A TRP* 3.3 25.2 + - + +
907A GLN* 3.1 40.7 + - - +
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Residues in contact with GLN 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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864A LYS* 4.0 16.6 - - - +
865A ASN* 5.0 5.6 + - - +
899A PHE* 3.5 46.3 - - + +
900A ASN* 2.8 32.8 + - - +
901A THR* 3.0 24.8 + - - +
903A LEU* 1.3 79.9 - - + +
905A LEU* 1.3 66.4 + - - +
907A GLN* 3.1 20.2 + - - +
908A MET* 3.1 26.2 + - - +
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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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901A THR 3.1 15.9 + - - +
902A GLU* 3.8 16.2 - - - +
904A GLN* 1.3 76.9 - - - +
906A TRP* 1.3 56.9 + - - +
908A MET* 3.2 10.6 + - - +
909A GLU* 2.9 45.8 + - - +
929A LEU* 3.7 30.3 - - + +
932A VAL* 4.0 20.2 - - + +
933A LYS* 3.7 38.4 - - + -
936A ILE* 3.9 15.3 - - + -
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Residues in contact with TRP 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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902A GLU 3.0 19.6 + - - +
903A LEU* 3.5 24.0 - - + +
904A GLN 3.2 0.2 - - - -
905A LEU* 1.3 77.0 - - - +
907A GLN* 1.3 83.7 + - + +
909A GLU* 3.4 12.7 + - + +
910A SER* 2.9 53.2 + - - -
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Residues in contact with GLN 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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865A ASN* 5.3 2.8 - - - +
868A TRP* 3.4 30.5 + - - +
872A GLN* 4.7 5.3 - - - +
899A PHE* 4.9 2.1 - - - -
903A LEU* 3.1 39.7 + - - +
904A GLN* 3.1 20.5 + - - +
906A TRP* 1.3 92.3 - - + +
908A MET* 1.3 57.7 + - - +
910A SER* 3.3 4.8 + - - -
911A PHE* 2.9 30.8 + - - +
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Residues in contact with MET 908 (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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868A TRP* 3.7 28.0 - - + -
896A ALA* 4.2 3.4 - - + -
899A PHE* 3.9 17.3 - - + -
904A GLN 3.1 12.5 + - - +
905A LEU* 3.5 8.1 - - - +
907A GLN* 1.3 75.9 - - - +
909A GLU* 1.3 58.0 + - - +
911A PHE* 3.2 1.9 + - - +
912A PHE* 2.9 42.9 + - + -
928A VAL* 3.7 34.8 - - + +
929A LEU* 3.9 21.5 - - + -
932A VAL* 3.5 39.0 - - + -
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Residues in contact with GLU 909 (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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905A LEU* 2.9 31.9 + - - +
906A TRP* 3.9 13.1 - - + +
908A MET* 1.3 76.4 - - - +
910A SER* 1.3 57.6 + - - +
912A PHE* 3.8 7.3 - - - +
913A ALA* 2.9 30.5 + - - +
929A LEU* 3.9 19.3 - - + +
933A LYS* 4.0 24.3 + - - -
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Residues in contact with SER 910 (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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906A TRP* 2.9 52.7 + - - -
907A GLN* 3.6 6.5 - - - -
909A GLU* 1.3 74.3 - - - +
911A PHE* 1.3 63.8 + - - +
913A ALA* 3.4 6.8 + - - +
914A LYS* 3.1 22.7 + - - +
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Residues in contact with PHE 911 (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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868A TRP* 4.1 11.7 - + - -
871A ILE* 4.3 4.9 - - + -
872A GLN* 3.5 54.3 - - + +
875A TRP* 3.8 34.3 - + + -
893A VAL* 4.7 10.1 - - + -
907A GLN 2.9 16.4 + - - +
908A MET* 3.7 2.9 - - - +
910A SER* 1.3 73.2 - - - +
912A PHE* 1.3 97.9 + + - +
914A LYS* 3.0 14.9 + - + +
915A TYR* 3.0 44.3 + + + +
925A ARG* 5.0 3.8 - - - -
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Residues in contact with PHE 912 (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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868A TRP* 4.5 5.6 - + - -
893A VAL* 3.8 29.2 - - + -
908A MET* 2.9 36.6 + - + +
909A GLU* 3.9 6.1 - - - +
911A PHE* 1.3 98.0 - + - +
913A ALA* 1.3 58.8 + - - +
915A TYR 3.2 20.6 - - - +
916A PRO* 3.2 7.8 - - - +
925A ARG* 3.5 53.3 + - + +
928A VAL* 4.3 7.0 - - + -
929A LEU* 3.9 38.4 - - + -
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Residues in contact with ALA 913 (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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909A GLU 2.9 19.4 + - - +
910A SER* 3.8 7.0 - - - +
911A PHE 3.2 0.2 - - - -
912A PHE* 1.3 76.3 - - - +
914A LYS* 1.3 62.3 + - - +
916A PRO* 3.8 14.8 - - - +
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Residues in contact with LYS 914 (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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910A SER 3.1 13.0 + - - +
911A PHE* 3.0 12.6 + - + +
913A ALA* 1.3 79.5 - - - +
915A TYR* 1.3 98.3 + - + +
916A PRO* 3.2 8.1 - - - +
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Residues in contact with TYR 915 (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 GLN 4.4 8.8 + - - -
873A LEU 5.8 0.3 + - - -
875A TRP* 3.5 35.8 - + + +
876A ASP* 3.4 34.2 + - - -
911A PHE* 3.0 43.2 + + + +
912A PHE 3.2 2.6 - - - +
914A LYS* 1.3 120.0 + - + +
916A PRO* 1.4 57.3 - - - +
917A GLN 3.3 5.5 + - - +
925A ARG* 2.7 34.7 + - - +
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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