Contacts of the helix formed by residues 596 - 600 (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 PHE 596 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C ILE 3.5 0.2 + - - -
595C PRO* 1.3 85.5 - - + +
597C LEU* 1.3 64.4 + - - +
598C GLU* 3.2 7.9 - - - +
599C HIS* 3.2 34.7 + + + +
600C ASP* 3.9 9.0 + - - +
626C VAL* 4.6 0.9 - - + -
929C GLY* 4.0 11.9 - - - -
932C LEU* 3.6 50.5 - - + -
933C GLU* 3.8 12.1 - - - -
936C LEU* 3.5 33.9 - - + -
974C THR* 4.1 25.5 + - + +
976C VAL* 6.1 1.0 - - - +
980C ALA* 4.1 25.1 - - + -
981C GLN 5.9 1.1 - - - -
985C LEU* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 597 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C ILE* 5.1 1.3 - - + -
586C MET* 6.3 0.4 - - + -
587C VAL* 4.5 8.1 - - + -
591C THR* 3.6 32.3 - - + +
594C ILE* 3.3 38.7 + - + +
595C PRO 4.4 0.2 - - - -
596C PHE* 1.3 71.7 - - - +
598C GLU* 1.3 59.4 + - - +
599C HIS 2.8 11.9 + - - -
600C ASP* 3.0 13.7 + - + -
605C ALA* 3.7 18.6 - - + -
976C VAL* 3.6 30.9 - - + +
977C PHE* 4.6 7.2 - - + -
849D TYR* 3.1 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 598 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C PHE* 5.1 2.5 - - - -
597C LEU* 1.3 79.2 + - - +
599C HIS* 1.3 74.8 + - + +
600C ASP 3.6 0.4 - - - -
975C PRO 4.9 0.2 - - - +
976C VAL* 4.5 1.7 - - - -
977C PHE* 2.9 46.7 + - + -
978C ASP 3.8 16.6 + - - +
980C ALA 5.1 1.9 - - - +
981C GLN* 4.3 12.8 + - - +
842D GLU 5.3 0.7 - - - +
843D GLY* 3.5 19.8 - - - -
844D LEU* 3.2 50.4 + - - +
849D TYR* 3.6 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 599 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C PHE* 3.3 31.7 - + + +
597C LEU 2.8 0.8 + - - -
598C GLU* 1.3 98.6 + - + +
600C ASP* 1.3 60.3 + - - +
926C MET 3.3 9.9 - - - +
928C ILE* 3.2 29.0 - - + +
929C GLY* 4.0 8.1 - - - -
932C LEU* 3.4 26.9 - - + +
980C ALA 5.1 5.1 + - - -
981C GLN* 5.8 1.8 + - - -
982C GLU* 4.8 8.0 + - + -
840D PHE* 2.6 34.4 + - - -
841D ARG 3.1 23.7 + - - -
842D GLU 3.7 5.8 + - - -
843D GLY* 3.6 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 600 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C ILE* 4.0 10.2 - - - +
596C PHE 4.0 8.2 - - - +
597C LEU* 3.0 6.7 + - - +
599C HIS* 1.3 80.5 - - - +
601C ASP* 1.3 63.9 - - - +
605C ALA* 4.2 13.5 - - + +
889C HIS* 2.6 33.4 + - + +
926C MET 3.6 2.7 - - - -
927C ASN* 3.2 18.6 - - + -
929C GLY* 2.8 30.5 + - - -
840D PHE* 3.5 5.7 - - - -
849D TYR* 2.6 32.2 + - - -
----------------------------------------------------------
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