Contacts of the helix formed by residues 1802 - 1807 (chain C) in PDB entry 5Y3R
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 TYR1802 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1605C PHE* 5.1 12.1 - + - -
1609C ALA 5.4 8.1 - - - -
1798C LEU* 3.0 54.7 - - - +
1799C GLU 3.5 1.8 - - - +
1801C VAL* 1.3 82.4 - - - +
1803C GLU* 1.3 62.1 + - - +
1804C MET 2.9 1.9 + - - -
1805C PHE* 3.0 27.0 + + + +
1806C ARG* 3.6 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1803 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C GLN* 4.2 4.7 + - + +
488C ILE* 5.5 3.5 - - - +
559C SER 4.1 2.6 - - - +
562C HIS* 3.0 24.9 - - - +
563C LEU* 3.0 32.0 + - - +
566C ASP* 2.7 18.4 - - - +
1799C GLU 3.0 7.5 + - - +
1800C SER 2.9 13.7 - - - +
1801C VAL 3.0 0.8 + - - -
1802C TYR* 1.3 75.3 - - - +
1804C MET* 1.3 67.4 + - + +
1805C PHE 3.2 0.2 - - - -
1806C ARG* 2.9 53.8 + - + +
1807C LYS* 3.9 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1804 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C VAL* 5.4 1.6 - - + -
482C VAL* 4.5 8.3 - - + +
485C GLN* 2.8 47.0 + - + +
486C GLY* 3.4 33.0 - - - +
489C ARG* 3.4 48.7 - - + +
1801C VAL* 2.9 7.9 + - - +
1802C TYR 2.9 0.8 + - - -
1803C GLU* 1.3 81.0 - - + +
1805C PHE* 1.3 60.3 + - - +
1808C ASP* 2.8 20.5 - - - +
1814C PHE* 4.9 14.8 - - + -
1818C SER* 4.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1805 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ARG* 5.1 2.3 - - - +
1802C TYR* 3.0 21.0 + + + +
1804C MET* 1.3 78.8 - - - +
1806C ARG* 1.3 70.3 + - + +
1808C ASP* 2.6 41.9 + - - +
1809C ASP* 2.9 58.9 + - + -
1815C THR* 4.2 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1806 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C HIS* 4.3 3.0 + - - +
566C ASP* 2.3 35.5 + - - -
1602C ASP* 3.3 14.5 - - - +
1605C PHE* 6.4 1.3 - - + -
1606C ARG* 5.0 25.4 + - + +
1609C ALA 5.3 10.2 - - - +
1798C LEU 5.0 1.2 + - - -
1799C GLU* 3.9 14.5 + - - +
1802C TYR* 3.7 32.2 - - + +
1803C GLU* 2.9 45.9 + - - +
1805C PHE* 1.3 83.9 - - + +
1807C LYS* 1.3 65.6 + - + +
1809C ASP* 3.2 18.2 - - - +
1810C PRO* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1807 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C THR* 6.4 1.8 - - + -
485C GLN* 4.8 10.5 - - - +
558C GLU* 5.6 0.2 + - - -
562C HIS* 3.1 44.7 + - + +
1606C ARG* 4.4 29.2 - - - +
1803C GLU 3.9 4.5 + - - +
1804C MET 4.4 0.8 + - - -
1805C PHE 3.3 0.2 - - - -
1806C ARG* 1.3 83.3 - - + +
1808C ASP* 1.3 49.3 - - - +
1809C ASP 3.3 3.1 - - - -
1810C PRO* 4.6 3.8 - - - +
1811C ARG* 2.2 34.2 + - - +
----------------------------------------------------------
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