Contacts of the helix formed by residues 845 - 855 (chain D) in PDB entry 4G7Z
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 ASN 845 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 5.7 1.4 - - - +
84B GLU* 3.4 34.4 + - - +
175B ARG* 3.9 16.3 + - - +
843D PHE* 4.0 2.9 - - - +
844D ALA* 1.3 81.9 - - - +
846D PRO* 1.3 78.0 - - + +
847D ASP* 3.0 32.3 - - + +
848D GLU* 3.0 19.9 + - - +
849D ALA* 3.2 18.7 + - - +
866D VAL* 4.2 4.7 - - - -
867D ARG 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 846 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845D ASN* 1.3 86.4 - - + +
847D ASP* 1.3 71.1 + - - +
849D ALA* 3.0 20.6 + - + +
850D LEU* 3.2 19.3 + - + +
866D VAL* 4.1 5.1 - - + -
867D ARG 3.8 12.8 - - - +
868D TYR* 4.4 24.7 - - + -
880D ILE* 3.6 28.7 - - + -
884D ARG* 5.9 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 847 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 3.5 55.3 - - - +
176B ARG* 5.5 2.1 - - - +
200B TRP* 5.5 2.1 - - - +
845D ASN* 3.0 17.0 + - - +
846D PRO* 1.3 83.8 - - - +
848D GLU* 1.3 54.9 + - - +
850D LEU* 3.6 5.5 + - - +
851D LEU* 3.2 23.0 + - - +
884D ARG* 4.6 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 848 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 3.4 24.8 - - - +
150B TYR* 3.0 37.0 + - + -
170B VAL* 3.7 16.2 - - + +
175B ARG* 5.1 4.0 - - - +
843D PHE* 3.5 14.3 - - + -
844D ALA* 2.7 38.2 + - - +
845D ASN* 3.0 22.1 + - - +
846D PRO 3.1 0.4 - - - -
847D ASP* 1.3 71.9 - - - +
849D ALA* 1.3 68.0 + - - +
850D LEU 3.1 2.0 - - - -
851D LEU* 3.0 20.3 + - - +
852D ALA* 3.0 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 849 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843D PHE* 3.6 18.0 - - + -
845D ASN 3.2 6.4 + - - +
846D PRO* 3.0 13.9 + - + +
848D GLU* 1.3 77.7 - - - +
850D LEU* 1.3 66.8 + - + +
852D ALA* 3.2 16.3 - - - +
853D VAL* 3.1 17.6 - - - +
858D VAL* 4.2 2.1 - - - +
866D VAL* 3.8 29.8 - - + -
877D PRO* 5.0 6.9 - - + +
880D ILE* 5.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 850 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846D PRO* 3.2 14.6 + - + +
847D ASP 4.1 4.3 - - - +
848D GLU 3.1 0.6 - - - -
849D ALA* 1.3 76.5 - - + +
851D LEU* 1.3 66.0 + - - +
852D ALA 3.1 1.1 - - - -
853D VAL* 3.2 10.0 + - + +
854D ALA* 2.9 23.9 + - - +
860D LEU* 4.6 6.1 - - + -
877D PRO* 3.6 40.6 - - + +
880D ILE* 5.4 4.3 - - + -
881D LEU* 4.2 27.8 - - + +
884D ARG* 3.9 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 851 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.9 30.3 - - + +
149B GLY 4.4 7.0 - - - +
150B TYR* 4.0 24.7 - - + -
170B VAL* 4.2 19.5 - - + -
172B SER* 4.7 7.2 - - - +
174B VAL 4.7 13.7 - - - +
175B ARG* 5.6 5.2 - - - +
847D ASP 3.2 14.0 + - - +
848D GLU* 3.0 14.3 + - - +
850D LEU* 1.3 76.3 - - - +
852D ALA* 1.3 62.4 + - - +
854D ALA* 3.2 11.1 + - + +
855D HIS* 2.9 51.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 852 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR* 4.4 9.8 - - + -
843D PHE* 3.6 26.2 - - + -
848D GLU 3.0 6.2 + - - +
849D ALA 3.2 11.9 - - - +
851D LEU* 1.3 76.2 - - - +
853D VAL* 1.3 54.4 + - - +
855D HIS 2.7 23.2 + - - -
856D GLY 3.2 2.6 + - - -
857D ILE* 3.1 37.2 + - + +
858D VAL* 3.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 853 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849D ALA 3.1 17.3 - - - +
850D LEU* 3.2 14.5 + - + +
852D ALA* 1.3 73.6 - - - +
854D ALA* 1.3 61.9 + - - +
856D GLY* 3.1 11.6 + - - -
858D VAL* 3.5 32.2 - - + +
859D ASP* 4.3 1.3 - - - -
860D LEU* 3.8 33.0 - - + +
877D PRO* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 854 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 4.8 20.2 - - - +
45B LEU* 5.0 11.4 - - + -
850D LEU 2.9 12.8 + - - +
851D LEU* 3.5 13.5 - - + +
852D ALA 3.1 0.4 + - - -
853D VAL* 1.3 76.2 - - - +
855D HIS* 1.3 65.3 + - + +
856D GLY 3.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 855 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 3.8 39.9 + - - +
45B LEU* 3.5 19.1 + - + -
46B SER* 4.2 13.2 - - - -
149B GLY* 4.1 3.2 - - - -
150B TYR* 3.7 34.8 + - + +
851D LEU* 2.9 45.4 + - + +
852D ALA 2.7 16.3 + - - +
854D ALA* 1.3 78.1 - - + +
856D GLY* 1.3 56.8 + - - -
857D ILE* 3.1 24.9 + - + +
----------------------------------------------------------
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