Contacts of the helix formed by residues 862 - 873 (chain G) in PDB entry 5WUA
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 VAL 862 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861G ASP* 1.3 72.2 - - - +
863G HIS* 1.3 56.4 + - - +
865G SER* 2.7 26.3 + - - -
866G ASP* 2.9 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 863 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861G ASP* 3.3 6.8 - - + +
862G VAL* 1.3 76.3 - - - +
864G LEU* 1.3 50.5 + - - +
866G ASP* 4.7 2.0 - - - +
867G HIS* 2.4 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 864 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856G PRO 5.6 0.2 - - - +
857G PHE* 6.1 0.3 - - - -
860G LEU* 4.6 10.6 - - + +
861G ASP* 3.0 26.4 + - + +
863G HIS* 1.3 77.8 - - - +
865G SER* 1.3 52.2 + - - +
867G HIS* 3.6 7.6 - - - -
868G LEU* 2.6 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 865 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857G PHE* 5.4 12.6 - - - -
861G ASP 2.5 15.9 + - - -
862G VAL* 2.7 15.9 + - - -
864G LEU* 1.3 72.6 - - - +
866G ASP* 1.3 55.3 + - - -
867G HIS 3.2 0.4 - - - -
868G LEU* 2.9 8.9 + - - +
869G MET* 2.6 31.6 + - - +
893G TYR* 6.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 866 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862G VAL 2.9 14.1 + - - +
863G HIS* 4.7 1.6 - - - +
865G SER* 1.3 73.6 - - - +
867G HIS* 1.3 51.6 + - - +
869G MET* 2.9 13.0 + - + +
870G GLN* 2.5 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 867 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805G ALA 5.2 0.3 - - - +
807G SER* 5.6 10.3 - - - -
863G HIS 2.4 34.5 + - - +
864G LEU* 3.6 6.3 - - - -
866G ASP* 1.3 76.0 - - - +
868G LEU* 1.3 53.4 + - - +
870G GLN* 3.4 11.4 - - + +
871G ALA* 2.7 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 868 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856G PRO* 5.3 16.4 - - + +
857G PHE* 6.3 1.8 - - + -
864G LEU 2.6 26.1 + - - +
865G SER* 2.9 10.5 + - - +
867G HIS* 1.3 75.0 - - - +
869G MET* 1.3 55.2 + - - +
871G ALA* 5.1 2.0 - - - -
872G GLY* 2.9 27.4 + - - +
873G ILE 4.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 869 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865G SER 2.6 14.5 + - - +
866G ASP* 3.1 14.8 - - - +
868G LEU* 1.3 72.7 - - - +
870G GLN* 1.3 57.9 + - - +
872G GLY 3.9 0.4 - - - +
873G ILE* 3.4 7.4 + - + +
874G LEU* 2.8 30.8 + - - +
893G TYR* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 870 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805G ALA 5.1 1.1 - - - +
866G ASP 2.5 16.3 + - - +
867G HIS* 2.9 14.3 + - + +
869G MET* 1.3 74.9 - - - +
871G ALA* 1.3 56.9 + - - +
874G LEU* 3.0 23.9 - - - +
876G LEU* 4.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 871 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805G ALA* 3.0 40.1 + - + +
806G CYS* 4.3 5.6 - - - +
867G HIS 2.7 17.3 + - - +
868G LEU* 5.0 2.0 - - - +
870G GLN* 1.3 73.8 - - - +
872G GLY* 1.3 62.6 + - - +
873G ILE 3.5 0.8 + - - -
876G LEU* 3.8 13.0 - - - +
878G ARG* 3.1 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 872 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868G LEU* 2.9 22.8 + - - +
870G GLN 3.7 0.2 - - - -
871G ALA* 1.3 77.7 - - - +
873G ILE* 1.3 59.7 + - - +
878G ARG* 2.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 873 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868G LEU 4.1 0.4 + - - -
869G MET* 3.4 8.3 + - + +
871G ALA 4.2 0.7 - - - -
872G GLY* 1.3 77.8 - - - +
874G LEU* 1.3 76.7 + - - +
876G LEU* 2.9 22.0 + - - +
878G ARG 4.8 0.4 - - - -
879G ASP* 3.5 18.3 + - + +
896G HIS* 5.8 10.3 - - + +
----------------------------------------------------------
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