Contacts of the helix formed by residues 857 - 876 (chain 4) in PDB entry 5U8T
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 ILE 857 (chain 4).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8514 GLN* 3.2 36.1 - - + +
8524 THR* 6.0 1.1 - - - -
8544 LYS* 3.4 55.9 - - + +
8554 SER 3.3 15.0 - - - +
8564 VAL* 1.3 77.2 - - + +
8584 GLN* 1.3 85.8 + - + +
8594 ARG 2.9 2.1 + - - -
8604 LYS* 3.1 25.8 - - - +
8614 LEU* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 858 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8514 GLN* 5.2 6.6 - - + +
8564 VAL 2.9 1.5 + - - +
8574 ILE* 1.3 94.5 - - + +
8594 ARG* 1.3 57.1 + - - +
8614 LEU* 3.4 16.4 - - - +
8624 GLN* 2.9 38.3 + - - +
8984 VAL* 5.6 4.2 - - - +
9024 ASP* 3.4 20.7 + - - +
9054 GLU* 5.3 5.9 - - - +
9064 ALA* 3.1 33.9 - - + +
9094 ARG* 5.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 859 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8564 VAL* 2.7 32.7 + - + +
8574 ILE 2.9 0.2 - - - -
8584 GLN* 1.3 76.5 - - - +
8604 LYS* 1.3 59.8 + - - +
8614 LEU 3.2 0.7 - - - -
8624 GLN* 2.7 29.7 + - - +
8634 GLU* 2.8 37.0 + - - +
9094 ARG* 4.8 6.3 - - - +
9104 LEU* 4.8 2.2 - - - +
9134 GLU* 2.5 36.0 + - - -
6906 ASN* 3.0 25.6 - - - +
6926 LYS* 5.5 18.2 - - + +
6936 LEU* 4.6 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 860 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8544 LYS* 4.5 9.1 - - - +
8564 VAL* 3.7 28.2 - - + +
8574 ILE* 3.1 38.9 + - - +
8594 ARG* 1.3 74.5 - - - +
8614 LEU* 1.3 78.3 + - + +
8634 GLU* 3.1 14.4 + - - +
8644 ASP* 3.0 31.1 + - - +
8964 ASP* 4.6 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 861 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8574 ILE 3.0 12.5 + - - +
8584 GLN* 3.4 28.5 - - - +
8604 LYS* 1.3 85.6 - - + +
8624 GLN* 1.3 50.1 + - - +
8644 ASP* 3.5 6.8 + - + +
8654 LEU* 2.8 51.3 + - + +
8904 ILE* 4.2 23.8 - - + -
8964 ASP 4.3 18.4 - - - +
8974 ARG* 4.5 5.8 - - - -
8984 VAL* 3.5 27.6 - - + -
9024 ASP 4.3 2.0 - - - +
9034 ILE* 4.4 3.6 - - + -
9064 ALA* 3.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 862 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8584 GLN* 2.9 23.5 + - - +
8594 ARG* 2.7 52.9 + - - +
8614 LEU* 1.3 75.0 - - - +
8634 GLU* 1.3 52.2 + - - +
8644 ASP 3.3 0.2 - - - -
8654 LEU* 3.5 23.1 - - + +
8664 SER* 2.7 37.2 + - - -
9064 ALA* 2.5 29.1 + - + +
9094 ARG* 3.2 30.5 - - - +
9104 LEU* 3.7 15.6 - - + +
9134 GLU* 4.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 863 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8564 VAL* 5.6 4.4 - - - +
8594 ARG* 2.8 23.9 + - - +
8604 LYS* 3.1 15.9 + - - +
8624 GLN* 1.3 77.3 - - - +
8644 ASP* 1.3 65.6 + - - +
8664 SER* 3.2 6.7 + - - -
8674 ARG* 2.9 30.4 + - - +
8704 MET* 5.5 0.2 - - - +
6926 LYS* 5.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 864 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8604 LYS* 3.0 17.3 + - - +
8614 LEU* 3.6 7.3 - - + +
8634 GLU* 1.3 83.9 - - - +
8654 LEU* 1.3 58.3 + - - +
8674 ARG* 3.8 8.2 - - - +
8684 GLU* 2.9 29.3 + - - +
8904 ILE* 5.2 3.9 - - + +
8964 ASP* 6.2 0.3 - - - +
8974 ARG* 4.4 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 865 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8614 LEU* 2.8 26.8 + - + +
8624 GLN* 3.5 19.5 - - + +
8634 GLU 3.2 0.4 - - - -
8644 ASP* 1.3 74.4 - - - +
8664 SER* 1.3 57.3 + - - +
8674 ARG 3.0 0.7 - - - -
8684 GLU* 2.9 5.7 + - - +
8694 ILE* 2.8 41.9 + - + +
8864 LEU* 4.7 4.7 - - + -
8904 ILE* 3.6 28.7 - - + -
9034 ILE* 3.6 17.3 - - + +
9064 ALA* 3.6 31.4 - - + -
9074 LEU* 3.7 27.1 - - + -
9104 LEU* 3.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 866 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8624 GLN 2.7 24.7 + - - -
8634 GLU* 3.2 8.8 + - - -
8654 LEU* 1.3 75.5 - - - +
8674 ARG* 1.3 58.7 + - - +
8694 ILE* 4.0 12.5 - - - +
8704 MET* 2.9 41.8 + - - +
9104 LEU* 4.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 867 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8634 GLU 2.9 21.7 + - - +
8644 ASP* 4.0 8.5 - - - +
8654 LEU 3.0 0.2 - - - -
8664 SER* 1.3 77.0 + - - +
8684 GLU* 1.3 57.8 + - - +
8704 MET* 3.4 32.3 - - + +
8714 ASN* 2.7 72.6 + - - +
8744 LYS* 3.1 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 868 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8644 ASP 2.9 20.1 + - - +
8654 LEU* 2.9 5.7 + - - +
8674 ARG* 1.3 73.3 - - - +
8694 ILE* 1.3 61.6 + - - +
8714 ASN* 3.8 6.9 - - - +
8724 VAL* 2.9 46.7 + - + +
8814 MET* 5.1 0.4 - - - -
8864 LEU* 3.7 27.8 - - + -
8894 GLN* 3.1 55.1 - - + +
8904 ILE* 5.1 2.5 - - + -
8934 HIS* 5.4 0.7 + - - -
8974 ARG* 4.3 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 869 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8654 LEU* 2.8 26.3 + - + +
8664 SER* 4.0 7.0 - - - +
8684 GLU* 1.3 73.4 - - - +
8704 MET* 1.3 60.6 + - - +
8724 VAL* 3.9 5.6 - - + +
8734 LEU* 2.9 28.1 + - - +
8794 ASP 5.1 0.9 - - - +
8814 MET* 4.9 10.1 - - + -
8864 LEU* 4.9 12.3 - - + -
9074 LEU* 3.7 29.8 - - + -
9104 LEU* 4.0 12.6 - - + -
9154 LYS 5.2 2.2 - - - +
9164 VAL* 4.3 8.5 - - + -
9254 ARG 5.4 1.1 - - - +
9264 SER* 3.3 37.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 870 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8634 GLU 5.5 0.2 - - - +
8664 SER* 2.9 34.9 + - - +
8674 ARG* 3.4 45.8 - - + +
8694 ILE* 1.3 77.5 - - - +
8714 ASN* 1.3 58.6 + - - +
8734 LEU* 3.0 10.6 + - + +
8744 LYS* 2.9 33.3 + - - +
9426 LEU* 3.9 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 871 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8674 ARG* 2.7 76.5 + - - +
8684 GLU* 4.1 9.0 - - - +
8704 MET* 1.3 75.8 - - - +
8724 VAL* 1.3 57.4 - - - +
8744 LYS* 3.8 12.5 + - - +
8754 ASP* 2.9 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 872 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8684 GLU* 2.9 37.0 + - - +
8694 ILE* 4.0 3.4 - - + +
8714 ASN* 1.3 75.9 - - - +
8734 LEU* 1.3 59.9 + - - +
8744 LYS 3.1 1.6 - - - -
8754 ASP* 4.2 3.1 - - + +
8764 GLN* 2.4 70.1 + - + +
8784 SER 5.2 0.7 - - - +
8794 ASP 6.1 0.7 - - - +
8804 SER 4.8 2.7 - - - +
8814 MET* 3.5 41.7 - - + +
8854 GLU* 5.9 0.4 - - + -
8894 GLN* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 873 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8694 ILE 2.9 18.3 + - - +
8704 MET* 3.0 8.7 + - + +
8724 VAL* 1.3 76.8 - - - +
8744 LYS* 1.3 56.9 + - - +
8764 GLN 2.9 17.3 - - - +
8784 SER 4.2 5.2 - - - -
8794 ASP* 3.3 27.6 - - - +
9264 SER* 3.2 31.2 - - - +
9274 VAL 4.5 6.7 - - - +
9416 LEU 5.5 0.5 - - - +
9426 LEU* 3.3 53.0 - - + +
9456 GLU* 3.4 19.5 - - - +
9466 ASN* 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 874 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8674 ARG* 3.1 40.0 - - - +
8704 MET* 2.9 17.5 + - - +
8714 ASN* 3.8 14.1 - - - +
8734 LEU* 1.3 77.8 - - - +
8754 ASP* 1.3 69.1 + - - +
8764 GLN 4.2 1.6 - - - +
9386 ASP 5.0 7.2 - - - +
9396 TRP* 4.7 18.6 - - - +
9426 LEU* 3.5 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 875 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8714 ASN* 2.9 23.7 + - - +
8724 VAL* 4.0 3.6 - - + +
8744 LYS* 1.3 84.8 - - - +
8764 GLN* 1.3 59.9 + - - +
8774 ALA* 3.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 876 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8724 VAL* 2.4 51.5 + - + +
8734 LEU 2.9 23.7 - - - +
8744 LYS 4.2 1.1 - - - +
8754 ASP* 1.3 70.7 - - + +
8774 ALA* 1.3 64.3 + - - +
8784 SER* 3.1 19.4 + - - +
8804 SER* 2.3 31.8 + - - +
8814 MET* 3.4 14.2 - - - +
8854 GLU* 5.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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