Contacts of the helix formed by residues 245 - 251 (chain B) in PDB entry 4RE1
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 ARG 245 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ASP* 2.6 34.2 + - - +
244B ILE* 1.3 80.1 - - + +
246B GLN* 1.3 59.4 - - + +
247B ILE 3.2 1.4 + - - -
248B TYR* 3.7 33.6 + - + +
249B ASP* 5.1 1.6 - - - +
410B LYS 3.7 15.1 + - - +
411B ASP* 4.0 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ASP* 3.0 33.2 + - + +
245B ARG* 1.3 78.2 - - - +
247B ILE* 1.3 60.0 + - + +
249B ASP* 4.5 0.4 - - - -
86C MET* 5.3 0.2 - - - +
89C ARG* 2.8 43.9 + - - +
90C LYS* 3.4 63.5 + - - +
91C LEU* 3.9 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B VAL* 4.8 4.5 - - + -
244B ILE* 2.9 21.6 + - + +
246B GLN* 1.3 88.4 - - + +
248B TYR* 1.3 66.6 + - - +
249B ASP* 3.1 6.3 - - - -
250B LYS* 2.9 21.7 + - + +
251B PHE* 3.5 17.5 - - + -
258B LEU* 4.2 8.1 - - + -
272B LEU* 4.1 25.6 - - + -
389B ALA* 4.0 25.4 - - + -
391B VAL* 6.0 1.6 - - + -
408B LEU* 3.8 26.9 - - + -
86C MET* 4.4 18.6 - - + -
89C ARG* 4.1 2.2 - - - +
91C LEU* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 3.2 52.8 + - + +
245B ARG* 3.7 32.4 + - + +
247B ILE* 1.3 76.7 - - - +
249B ASP* 1.3 58.8 + - - +
250B LYS 3.1 0.7 + - - -
251B PHE* 2.8 27.2 + - - +
253B GLU* 5.8 1.2 - - - +
258B LEU* 4.2 11.0 - - + +
259B LYS* 3.4 74.3 + - + +
262B PHE* 3.6 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ARG 5.1 1.2 + - - +
246B GLN 3.9 1.9 - - - +
247B ILE 3.8 3.5 - - - -
248B TYR* 1.3 78.8 + - - +
250B LYS* 1.3 63.2 + - - +
251B PHE 3.2 4.2 + - - +
314B PHE 5.0 1.7 - - - +
315B GLY* 4.1 10.0 + - - -
83C THR* 3.4 21.0 + - - -
84C VAL 5.3 0.3 + - - -
89C ARG* 2.4 34.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ILE* 2.9 17.1 + - + +
249B ASP* 1.3 81.1 + - - +
251B PHE* 1.3 64.6 + - + +
312B CYS* 4.3 0.3 - - - +
314B PHE* 6.2 1.2 - - - +
315B GLY* 3.5 17.6 + - - +
368B GLU* 2.9 29.1 + - - +
369B ASN* 3.8 8.2 + - - +
371B THR* 2.8 47.4 + - + +
391B VAL* 5.4 2.2 - - + -
83C THR* 3.0 41.9 + - - +
84C VAL 4.6 0.4 - - - -
86C MET* 3.8 22.4 - - + -
89C ARG* 3.5 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ILE* 3.5 23.8 - - + -
248B TYR 2.8 18.6 + - - +
249B ASP* 3.2 3.4 - - - +
250B LYS* 1.3 89.8 - - + +
252B PRO* 1.3 73.3 - - + +
253B GLU* 3.6 3.1 + - - +
258B LEU* 3.9 31.4 - - + +
312B CYS* 4.5 6.5 - - - -
315B GLY* 3.6 6.0 - - - +
371B THR* 3.2 35.0 - - + -
372B ILE 3.6 20.0 - - - -
373B LEU* 3.8 20.6 - - + -
389B ALA* 3.5 29.2 - - + -
390B CYS 4.0 5.6 - - - -
391B VAL* 4.5 5.6 - - + -
----------------------------------------------------------
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