Contacts of the helix formed by residues 201 - 212 (chain A) in PDB entry 5EN4
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 ASP 201 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A MET* 3.2 1.9 - - - +
200A PRO* 1.3 80.3 - - + +
202A PRO* 1.3 67.5 - - - +
203A ARG* 3.2 19.6 + - - +
204A ALA* 3.2 25.9 + - + +
205A THR* 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ALA* 3.3 33.8 - - + +
197A ALA* 4.1 14.8 - - - +
199A MET 3.4 13.0 - - - +
200A PRO 3.7 4.0 - - - +
201A ASP* 1.3 85.3 - - - +
203A ARG* 1.3 63.7 + - - +
205A THR* 3.1 4.7 + - - -
206A ILE* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 3.2 10.6 + - - +
202A PRO* 1.3 79.1 - - - +
204A ALA* 1.3 58.2 + - - +
206A ILE* 3.3 9.9 + - - +
207A ARG* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 3.2 31.2 + - + +
203A ARG* 1.3 78.3 - - - +
205A THR* 1.3 58.7 + - - +
207A ARG* 3.7 5.3 - - - +
208A GLU* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TRP* 3.5 24.1 - - + -
196A ALA* 4.2 7.0 - - + -
199A MET* 3.3 35.0 - - + +
201A ASP 3.1 13.0 + - - -
202A PRO* 3.1 9.8 + - - -
204A ALA* 1.3 76.6 - - - +
206A ILE* 1.3 56.5 + - - +
208A GLU* 3.4 7.0 + - - +
209A GLY* 2.9 22.9 + - - -
302A 5Q6 4.8 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TRP* 4.0 27.1 - - + -
192A TRP* 4.0 11.0 - - + -
193A GLU* 5.9 2.0 - - + -
196A ALA* 3.9 22.0 - - + -
202A PRO* 2.9 26.4 + - + +
203A ARG* 3.8 7.6 - - - +
205A THR* 1.3 73.9 - - - +
207A ARG* 1.3 66.4 + - - +
209A GLY* 3.0 2.6 + - - -
210A MET* 2.9 35.2 + - + +
218A MET* 3.8 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ARG 3.0 17.2 + - - +
204A ALA* 3.7 7.0 - - - +
206A ILE* 1.3 77.7 - - - +
208A GLU* 1.3 61.8 + - - +
210A MET* 3.2 13.2 + - - +
211A LEU* 3.1 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA 2.8 18.0 + - - +
205A THR* 3.6 8.1 - - - +
207A ARG* 1.3 75.6 - - - +
209A GLY* 1.3 62.5 + - - +
211A LEU* 3.3 7.4 + - - +
212A ALA* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASN* 3.4 16.1 + - - -
192A TRP* 3.9 20.6 - - - -
205A THR 2.9 15.1 + - - -
206A ILE 3.0 5.3 + - - -
208A GLU* 1.3 78.4 - - - +
210A MET* 1.3 56.6 + - - +
212A ALA* 3.6 2.0 + - - -
213A GLN* 2.8 21.1 + - - +
218A MET* 4.0 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 2.9 29.5 + - + +
207A ARG* 3.2 12.1 + - - +
209A GLY* 1.3 75.8 - - - +
211A LEU* 1.3 65.8 + - + +
213A GLN* 3.1 17.6 + - - +
216A GLY* 3.4 37.5 - - - +
217A ARG* 4.4 7.4 - - + -
218A MET* 4.2 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 3.1 24.2 + - + +
208A GLU* 3.3 6.5 + - - +
210A MET* 1.3 79.2 - - + +
212A ALA* 1.3 60.5 + - - +
213A GLN 3.1 13.7 + - - +
216A GLY* 4.9 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASN* 3.9 9.4 - - - +
208A GLU 3.1 14.8 + - - +
209A GLY* 3.8 5.2 - - - +
210A MET 3.2 1.0 - - - -
211A LEU* 1.3 77.0 - - - +
213A GLN* 1.3 70.9 + - - +
214A PRO* 4.1 2.1 - - - +
249A ALA* 3.7 21.7 - - + +
----------------------------------------------------------
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