Contacts of the helix formed by residues 918 - 922 (chain C) in PDB entry 5UHE
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 918 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C ILE* 5.1 0.4 - - - -
724C MET 4.2 0.4 - - - -
725C PRO* 4.3 3.6 - - - +
730C ASN* 3.0 49.7 + - - +
731C TYR* 3.5 4.0 - - - +
732C GLU 4.3 2.7 - - - +
733C ASP* 5.1 7.0 - - - +
734C ALA 4.9 2.7 + - - +
916C ILE 4.0 0.2 + - - -
917C LEU* 1.3 72.6 - - - +
919C THR* 1.3 68.5 + - - +
920C HIS* 2.8 44.6 + - - +
921C GLY* 3.3 13.1 + - - +
922C VAL* 3.6 11.8 - - - +
579D LEU* 6.2 0.2 - - - +
580D ASP* 2.6 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 919 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C ILE* 3.2 29.5 + - + +
724C MET* 3.2 9.1 + - - +
725C PRO* 4.1 5.8 - - - -
917C LEU 3.5 2.6 + - - -
918C ASN* 1.3 75.3 + - - +
920C HIS* 1.3 65.1 + - - +
922C VAL* 3.3 8.9 - - - +
923C PRO* 3.3 17.2 - - - +
729D VAL* 3.1 40.0 + - + +
730D THR* 3.6 10.1 - - - +
731D VAL* 3.6 24.9 - - + +
802D ILE* 4.6 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 920 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C PRO* 3.6 24.3 - - + +
918C ASN* 2.8 26.8 + - - +
919C THR* 1.3 77.8 - - - +
921C GLY* 1.3 56.8 + - - +
922C VAL 3.0 6.4 + - - -
923C PRO* 3.4 5.5 - - - +
924C ARG* 3.2 25.2 - - - +
579D LEU* 4.1 15.5 - - + -
580D ASP* 3.4 33.2 + - - +
583D THR* 3.5 36.3 + - + +
729D VAL* 4.6 4.3 - - + -
802D ILE* 3.7 27.4 - - + +
807D ALA* 4.8 0.9 - - + -
808D THR* 4.4 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 921 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733C ASP* 3.9 20.6 - - - +
891C ASN* 5.8 2.1 - - - +
918C ASN* 3.3 12.1 + - - +
920C HIS* 1.3 76.9 - - - +
922C VAL* 1.3 63.4 + - - +
924C ARG* 4.4 7.2 - - - -
925C ARG* 3.4 27.7 + - - +
927C ASN* 5.3 0.2 + - - -
930C GLN* 4.5 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 922 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C ILE* 5.0 11.0 - - + -
917C LEU* 6.1 2.2 - - + -
918C ASN 3.6 11.7 - - - +
919C THR* 3.3 18.8 - - - +
920C HIS 3.0 6.5 + - - -
921C GLY* 1.3 83.3 - - - +
923C PRO* 1.3 67.8 - - + +
924C ARG 3.1 1.7 + - - +
925C ARG 3.6 7.1 + - - -
926C MET* 3.6 4.5 + - - -
927C ASN* 3.6 15.5 + - - +
928C ILE* 4.4 10.0 - - + +
930C GLN* 4.1 24.0 - - + +
931C ILE* 4.0 28.3 - - + -
731D VAL* 4.3 13.5 - - + -
----------------------------------------------------------
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