Contacts of the helix formed by residues 203 - 207 (chain F) in PDB entry 1R4N
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 THR 203 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F ARG* 2.5 36.6 + - - -
198F ALA* 4.7 9.4 - - + +
199F CYS 3.4 6.1 + - - -
200F ILE 3.6 2.6 - - - +
202F CYS* 1.3 75.7 - - - +
204F LEU* 1.3 61.1 + - - +
205F GLU 3.3 3.2 + - - -
206F LEU* 3.4 35.0 + - + +
207F TYR* 4.5 5.2 - - - -
321F TYR* 4.7 2.7 - - + -
337F ALA* 3.5 32.1 - - + -
338F GLU 4.8 4.0 - - - +
149K GLN* 4.2 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F ILE* 4.6 8.3 - - + -
152F ARG* 4.2 21.1 - - + +
200F ILE* 3.4 10.5 + - + +
201F GLU* 3.3 39.0 - - - +
202F CYS 2.9 4.2 + - - +
203F THR* 1.3 78.1 - - - +
205F GLU* 1.3 61.0 + - + +
206F LEU 3.3 2.0 + - - -
207F TYR* 3.6 28.4 + - + +
372F ALA 4.9 1.8 - - - +
373F SER* 4.2 17.9 - - - +
374F LEU 4.1 19.3 - - - +
375F GLN* 3.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F CYS 4.6 0.8 + - - +
203F THR 3.3 1.0 - - - -
204F LEU* 1.3 76.5 - - + +
206F LEU* 1.3 62.6 + - - +
207F TYR 3.0 11.5 + - - +
340F LYS* 3.4 26.1 + - - +
372F ALA* 3.2 43.8 - - + +
373F SER* 4.5 3.6 - - - -
375F GLN* 5.0 3.8 - - - +
142K ARG* 3.2 30.6 + - - +
149K GLN* 4.4 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F THR* 3.6 31.6 - - + +
204F LEU 3.3 1.4 - - - -
205F GLU* 1.3 78.1 - - - +
207F TYR* 1.3 60.6 + - - +
208F PRO 3.7 1.2 - - - -
321F TYR* 3.6 34.8 - - + +
335F PHE* 4.1 13.0 - - + -
142K ARG* 4.0 18.2 - - + +
144K ILE* 4.3 6.7 - - + -
149K GLN* 3.6 26.0 + - + +
170K VAL* 3.8 21.5 - - + -
171K LEU* 3.8 9.9 - - - +
172K ALA* 3.1 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F ILE* 3.9 39.5 - - + -
151F ARG* 3.5 25.0 + - - -
179F ASP* 4.5 1.0 + - - -
188F ASN* 4.8 1.2 + - - -
190F ARG* 3.1 27.4 + - - -
200F ILE* 5.1 7.7 - - + +
203F THR 4.5 5.6 - - - -
204F LEU* 3.6 31.4 - - + +
205F GLU* 3.0 12.8 - - - +
206F LEU* 1.3 79.2 - - - +
208F PRO* 1.3 77.3 - - + +
375F GLN* 6.3 0.2 - - - +
142K ARG* 3.5 7.6 + - - -
172K ALA* 3.5 27.8 - - + -
173K LEU 3.2 27.7 + - - -
174K ARG* 4.1 6.5 - - + -
----------------------------------------------------------
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