Contacts of the helix formed by residues 200 - 212 (chain A) in PDB entry 4USE
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 ALA 200 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP 3.8 2.2 + - - -
199A MET* 1.3 78.0 - - - +
201A PRO* 1.3 73.7 - - + +
202A GLU* 3.4 24.5 - - - +
203A VAL* 3.0 23.8 + - + +
204A VAL* 3.0 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A MET 3.9 2.4 - - - +
200A ALA* 1.3 86.5 - - + +
202A GLU* 1.3 64.3 + - - +
204A VAL* 3.1 10.8 + - + +
205A MET* 3.0 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 3.4 24.0 - - - +
201A PRO* 1.3 82.1 - - - +
203A VAL* 1.3 68.3 + - + +
205A MET* 4.1 7.8 - - - +
206A CYS* 3.2 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A MET* 3.7 26.2 - - + -
200A ALA* 3.0 25.1 + - + +
202A GLU* 1.3 85.5 - - + +
204A VAL* 1.3 67.2 + - - +
206A CYS* 3.3 4.3 + - - -
207A GLU* 3.2 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PRO* 5.7 0.7 - - + +
199A MET* 3.8 32.1 - - + +
200A ALA 3.0 19.1 + - - +
201A PRO* 3.1 9.6 + - + +
203A VAL* 1.3 75.4 - - - +
205A MET* 1.3 65.3 + - + +
207A GLU* 3.0 21.5 + - - +
208A THR* 3.2 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO* 3.0 18.0 + - + +
202A GLU* 4.4 7.0 - - - +
203A VAL 3.3 0.2 - - - -
204A VAL* 1.3 84.5 - - + +
206A CYS* 1.3 58.3 + - - +
207A GLU 3.2 0.7 - - - -
208A THR* 4.0 10.4 + - - -
209A MET* 2.8 60.4 + - + +
214A TYR* 6.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 3.2 21.2 + - - +
203A VAL* 3.3 7.0 + - - +
204A VAL 3.2 0.8 - - - -
205A MET* 1.3 77.6 - - - +
207A GLU* 1.3 71.0 + - - +
209A MET* 4.3 6.1 - - - -
210A LYS* 3.2 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A MET* 4.8 8.7 - - + -
203A VAL* 3.2 32.4 - - + +
204A VAL* 3.0 9.2 + - - +
206A CYS* 1.3 88.5 - - - +
208A THR* 1.3 62.5 + - + +
209A MET 3.3 0.7 - - - -
210A LYS* 3.3 2.2 + - - +
211A ASP* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.2 24.9 + - + +
205A MET* 4.0 15.4 + - - -
207A GLU* 1.3 75.8 - - + +
209A MET* 1.3 68.6 + - - +
211A ASP* 4.5 4.0 - - - -
212A THR* 3.6 14.5 + - - +
213A PRO* 4.6 2.5 - - - +
214A TYR* 3.3 40.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A MET* 2.8 57.6 + - + +
206A CYS* 4.3 5.6 - - - -
208A THR* 1.3 80.7 + - - +
210A LYS* 1.3 57.3 + - - +
211A ASP 3.6 0.2 + - - -
214A TYR* 3.6 28.5 - - + -
215A ASP* 2.8 42.6 + - - +
279A PRO* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 5.7 0.7 - - - +
156A ARG* 5.8 2.6 + - - +
185A THR* 5.5 6.2 - - - +
206A CYS* 3.2 21.4 + - + +
207A GLU* 3.3 4.0 + - - +
209A MET* 1.3 78.3 - - + +
211A ASP* 1.3 62.7 + - - +
215A ASP* 4.0 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 5.5 4.2 - - - +
207A GLU* 2.8 20.2 + - + +
208A THR* 3.7 4.2 + - - +
209A MET 3.3 0.6 - - - -
210A LYS* 1.3 80.2 - - - +
212A THR* 1.3 75.2 + - + +
215A ASP* 5.0 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG* 6.0 3.5 - - - -
208A THR* 3.6 6.3 + - - +
211A ASP* 1.3 88.6 - - + +
213A PRO* 1.4 83.0 - - + +
214A TYR* 2.1 22.7 + - - -
215A ASP* 2.8 15.0 + - - +
216A TYR* 4.9 16.4 + - - -
----------------------------------------------------------
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