Contacts of the helix formed by residues 4876 - 4892 (chain F) in PDB entry 6X34
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 ASP4876 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4854F PHE* 4.8 0.7 - - - -
4873F LYS 2.9 19.5 + - - +
4874F CYS 4.7 2.0 - - - -
4875F ASP* 1.3 80.0 - - + +
4877F MET* 1.3 64.2 + - - +
4878F MET* 4.2 4.5 - - + +
4879F THR* 3.3 28.9 + - - +
4880F CYS* 3.5 5.2 + - - -
4578H TYR 3.8 5.2 - - - +
4579H LYS* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET4877 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4850F THR* 4.6 5.0 - - - +
4854F PHE* 4.5 23.6 - - + -
4875F ASP 4.3 0.2 - - - -
4876F ASP* 1.3 73.0 - - - +
4878F MET* 1.3 59.0 + - - +
4880F CYS* 3.8 6.5 + - - +
4881F TYR* 3.8 15.6 + - - +
4575H LEU 3.6 16.8 - - - +
4576H LEU* 3.3 18.2 - - - +
4578H TYR* 2.9 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET4878 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4876F ASP* 3.2 3.9 - - + +
4877F MET* 1.3 76.8 - - - +
4879F THR* 1.3 64.5 + - - +
4880F CYS 3.3 0.4 - - - -
4881F TYR* 3.3 24.9 + - + +
4882F LEU* 3.3 22.7 + - + +
4573H PHE* 6.3 2.7 - - + -
4576H LEU* 2.9 34.7 + - - +
4577H PHE* 5.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR4879 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4873F LYS* 3.7 31.0 - - + -
4876F ASP* 3.3 19.7 + - - +
4878F MET* 1.3 76.3 - - - +
4880F CYS* 1.3 59.7 + - - +
4882F LEU* 3.4 7.7 + - + +
4883F PHE* 2.9 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS4880 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4850F THR* 3.9 18.6 - - + +
4853F ALA* 6.0 2.0 - - - -
4854F PHE* 4.9 16.4 - - + -
4861F TYR* 5.9 5.6 - - - -
4873F LYS* 3.1 37.7 - - - -
4874F CYS* 3.7 11.7 - - - -
4876F ASP 3.5 7.9 + - - -
4877F MET* 4.0 6.1 - - - +
4878F MET 3.3 0.8 - - - -
4879F THR* 1.3 78.1 - - - +
4881F TYR* 1.3 57.6 + - - +
4883F PHE* 4.3 1.8 - - - -
4884F HIS* 2.9 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR4881 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4843F ALA* 3.2 40.1 + - - +
4846F VAL* 4.1 15.1 - - + +
4847F TYR* 4.1 27.8 - + + -
4850F THR* 3.9 21.4 - - + +
4877F MET 3.8 9.4 + - - +
4878F MET* 3.3 30.6 + - + +
4879F THR 3.3 0.4 - - - -
4880F CYS* 1.3 80.1 - - - +
4882F LEU* 1.3 62.3 + - + +
4884F HIS* 4.1 1.0 - - + +
4885F MET* 3.1 42.2 + - + +
4576H LEU* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4882 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4908D GLU 6.3 0.2 - - - -
4909D LEU* 5.4 11.2 - - + -
4912D VAL* 3.8 39.9 - - + -
4878F MET* 3.3 14.1 + - + +
4879F THR* 3.9 9.6 - - + +
4880F CYS 3.3 0.2 - - - -
4881F TYR* 1.3 82.9 - - + +
4883F PHE* 1.3 61.5 + - - +
4885F MET* 4.8 5.2 - - + -
4886F TYR* 3.1 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4883 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4861F TYR* 4.2 21.1 - + + -
4863F LYS* 4.6 23.3 - - + -
4871F ASP 5.4 4.7 - - - -
4873F LYS* 4.3 17.3 - - + -
4879F THR* 2.9 20.0 + - + +
4880F CYS 3.8 3.8 - - - +
4881F TYR 3.3 0.2 - - - -
4882F LEU* 1.3 76.8 - - - +
4884F HIS* 1.3 75.7 + + + +
4886F TYR* 5.0 0.7 - - - -
4887F VAL* 3.2 43.6 + - + +
4895F ILE* 5.4 2.0 - - + +
4898F GLU* 4.1 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS4884 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4846F VAL* 5.2 11.1 + - + +
4849F TYR* 4.5 4.5 + - - +
4850F THR* 4.0 26.1 + - - +
4853F ALA* 3.7 20.2 - - + -
4861F TYR* 3.2 50.1 - + - -
4880F CYS* 2.9 34.4 + - + +
4881F TYR* 4.3 2.0 - - + +
4883F PHE* 1.3 87.8 - + + +
4885F MET* 1.3 60.8 + - - +
4888F GLY* 3.0 27.3 + - - +
4889F VAL* 4.1 1.9 + - - +
4895F ILE* 4.8 11.8 - - + +
4914F PHE* 6.2 0.7 - + - -
4918F PHE* 5.3 10.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET4885 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4916D ILE* 4.1 16.8 - - + +
4920D PHE* 4.2 24.9 - - + -
4839F VAL* 6.5 0.4 - - + -
4842F LEU* 3.7 28.0 - - + -
4843F ALA* 6.0 1.3 - - + -
4846F VAL* 4.8 17.9 - - + +
4881F TYR* 3.1 34.6 + - + +
4882F LEU* 4.4 5.8 - - + +
4884F HIS* 1.3 76.8 - - - +
4886F TYR* 1.3 65.6 + - - +
4889F VAL* 3.3 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR4886 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4896D GLY* 4.0 13.4 - - - -
4899D ILE* 3.8 22.2 - - - +
4902D PRO* 5.1 15.2 - - + +
4911D ARG 4.8 1.2 + - - -
4912D VAL* 3.5 56.5 - - + -
4915D ASP* 3.6 26.0 - - + +
4916D ILE* 3.7 17.0 - - + +
4882F LEU* 3.1 20.7 + - + +
4883F PHE* 4.6 0.7 - - - +
4885F MET* 1.3 80.5 - - - +
4887F VAL* 1.3 78.4 + - + +
4890F ARG* 3.2 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4887 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4883F PHE* 3.2 41.8 + - + +
4886F TYR* 1.3 94.0 - - + +
4888F GLY* 1.3 66.4 + - - +
4890F ARG* 5.0 0.9 - - - -
4891F ALA* 3.1 32.0 + - + +
4894F GLY 5.4 0.2 - - - +
4895F ILE* 5.5 2.9 - - + -
4897F ASP* 6.5 0.4 - - + -
4898F GLU* 4.1 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4888 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4884F HIS* 3.0 19.7 + - - +
4887F VAL* 1.3 82.1 - - - +
4889F VAL* 1.3 61.6 + - - +
4891F ALA* 4.5 0.9 - - - +
4892F GLY* 3.6 15.2 + - - -
4894F GLY* 4.9 13.2 + - - -
4895F ILE* 4.8 15.1 - - - +
4918F PHE* 5.3 10.5 - - - -
4922F VAL* 6.4 1.3 - - - -
4923F ILE* 5.1 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4889 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4916D ILE* 5.5 2.2 - - + -
4919D PHE* 3.2 23.1 - - + -
4920D PHE* 3.7 33.2 - - + -
4842F LEU* 5.0 10.8 - - + -
4846F VAL* 5.4 8.7 - - + -
4884F HIS 4.7 1.3 - - - +
4885F MET* 3.3 42.6 + - + +
4888F GLY* 1.3 75.7 - - - +
4890F ARG* 1.3 65.0 + - - +
4891F ALA 3.6 0.2 + - - -
4892F GLY* 3.8 7.6 + - - -
4922F VAL* 6.3 4.0 - - + -
4923F ILE* 6.3 1.1 - - - -
4927F LEU* 4.4 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4890 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4893D GLY* 3.6 21.4 - - - +
4894D GLY* 5.9 0.2 - - - -
4896D GLY* 6.2 4.0 - - - +
4915D ASP* 5.5 2.5 - - + +
4916D ILE* 5.0 7.1 - - + +
4919D PHE* 3.5 41.5 - - + -
4886F TYR* 3.2 26.3 + - + +
4887F VAL* 4.5 1.1 - - - +
4889F VAL* 1.3 78.1 - - - +
4891F ALA* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4891 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4893D GLY* 4.7 10.7 - - - -
4887F VAL* 3.1 26.3 + - + +
4888F GLY 4.5 1.1 - - - +
4890F ARG* 1.3 81.3 - - - +
4892F GLY* 1.3 57.0 + - - +
4893F GLY* 3.2 10.9 + - - +
4894F GLY 4.9 8.1 - - - +
4897F ASP* 5.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4892 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4919D PHE* 5.8 2.5 - - - -
4888F GLY 3.6 11.8 + - - -
4889F VAL 3.8 7.1 + - - -
4890F ARG 3.4 2.2 - - - -
4891F ALA* 1.3 76.5 - - - +
4893F GLY* 1.3 55.0 + - - +
4894F GLY 3.2 8.6 + - - -
4919F PHE* 4.2 5.2 - - - -
4923F ILE* 3.7 29.9 - - - +
4927F LEU* 6.0 3.8 - - - -
----------------------------------------------------------
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