Contacts of the helix formed by residues 797 - 805 (chain D) in PDB entry 5UHF
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 797 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735D ASP* 2.9 48.3 + - - +
793D TYR* 4.2 9.9 - - + -
794D PRO* 3.1 29.4 + - + +
795D ASP 4.2 0.2 - - - +
796D ASP* 1.3 75.3 - - - +
798D PRO* 1.3 57.8 - - - +
799D ILE* 3.2 12.7 - - - +
800D ILE* 2.9 40.9 + - + +
801D THR* 2.5 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 798 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919C THR* 5.3 0.9 - - + -
1007C LYS* 5.0 4.3 - - - +
728D GLY 4.0 10.3 - - - +
729D VAL* 3.9 10.8 - - + -
730D THR 3.3 46.2 - - - +
731D VAL* 5.4 1.3 - - + -
735D ASP* 4.2 14.4 - - - +
796D ASP 3.1 8.5 - - - +
797D ASN* 1.3 88.5 - - - +
799D ILE* 1.3 60.7 + - + +
801D THR* 3.6 10.7 - - - +
802D ILE* 2.9 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 799 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923C PRO* 4.6 18.0 - - + +
730D THR 4.5 0.9 - - - +
731D VAL* 3.8 29.8 - - + -
735D ASP* 3.7 30.1 - - + +
736D VAL* 3.8 25.8 - - + +
793D TYR* 5.6 3.4 - - + +
797D ASN* 3.2 11.6 - - - +
798D PRO* 1.3 76.2 - - - +
800D ILE* 1.3 61.1 + - + +
802D ILE* 3.8 5.1 + - - +
803D VAL* 3.2 24.6 + - - +
814D THR* 3.7 33.2 - - + +
817D LEU* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 800 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790D ARG* 5.6 4.5 - - + +
793D TYR* 3.8 28.5 - - + +
794D PRO 4.3 7.6 - - - +
795D ASP* 4.9 11.7 - - - +
797D ASN* 2.9 26.6 + - + +
799D ILE* 1.3 74.4 - - - +
801D THR* 1.3 59.9 + - - +
802D ILE 3.2 0.2 - - - -
803D VAL* 3.0 2.6 + - + -
804D ASP* 2.6 60.7 + - + +
811D PHE* 3.8 33.4 - - + -
814D THR* 3.8 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 801 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583D THR* 5.3 6.1 - - + +
586D TYR* 4.8 18.0 - - + -
587D TYR* 6.6 0.2 - - - -
729D VAL* 4.3 18.8 - - + -
795D ASP 3.0 20.5 + - - +
796D ASP 3.2 10.0 + - - -
797D ASN 2.5 25.4 + - - -
798D PRO* 3.6 10.5 - - - -
800D ILE* 1.3 73.1 - - - +
802D ILE* 1.3 52.6 + - - +
804D ASP* 4.1 2.2 - - - -
805D SER* 2.6 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 802 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919C THR* 4.2 7.0 - - + +
920C HIS* 3.6 39.9 - - + +
923C PRO* 4.9 15.0 - - + -
924C ARG* 5.8 0.4 - - + -
583D THR* 4.0 14.6 - - - +
729D VAL* 3.7 26.5 - - + -
731D VAL* 5.9 0.2 - - + -
798D PRO 2.9 19.1 + - - +
799D ILE* 4.0 5.2 - - - +
801D THR* 1.3 74.8 - - - +
803D VAL* 1.3 67.3 + - + +
805D SER* 3.1 13.5 + - - -
807D ALA* 3.4 10.5 + - + +
808D THR* 3.3 37.9 - - + +
809D GLY* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 803 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923C PRO* 6.2 2.5 - - + -
790D ARG* 5.3 1.3 - - - +
799D ILE* 3.2 19.7 + - + +
800D ILE* 3.0 7.0 + - + +
802D ILE* 1.3 80.4 - - + +
804D ASP* 1.3 70.2 + - - +
805D SER 3.1 6.0 + - - -
806D GLY* 3.1 14.9 + - - -
808D THR 3.6 10.2 - - - +
809D GLY* 4.2 12.0 - - - +
810D ASN 3.6 11.2 - - - +
811D PHE* 4.0 31.6 - - + +
814D THR* 3.3 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 804 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D TYR* 3.8 15.9 + - + +
689D HIS* 3.8 11.1 + - - -
790D ARG* 3.4 27.8 + - - -
795D ASP* 4.7 12.1 - - - +
800D ILE* 2.6 42.7 + - + +
801D THR* 4.1 2.5 - - - +
803D VAL* 1.3 84.0 - - - +
805D SER* 1.3 56.6 + - - +
806D GLY 3.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 805 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582D VAL* 3.7 6.2 - - - +
583D THR* 3.9 4.2 + - - -
586D TYR* 3.4 39.5 - - - -
689D HIS* 3.2 20.8 - - - -
690D LYS 3.5 11.3 + - - -
801D THR* 2.6 24.5 + - - -
802D ILE* 3.1 10.2 + - - -
803D VAL 3.1 0.2 + - - -
804D ASP* 1.3 76.9 - - - +
806D GLY* 1.3 60.4 + - - +
807D ALA* 3.0 14.6 + - - +
----------------------------------------------------------
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