Contacts of the helix formed by residues 211 - 218 (chain E) in PDB entry 5X6E
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 LEU 211 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E LEU* 5.0 2.2 - - + -
151E THR* 4.2 25.8 - - + -
152E TYR* 3.4 41.5 - - + +
162E ILE* 6.0 4.0 - - + -
208E VAL* 5.2 6.9 - - + +
209E GLN 3.9 2.6 + - - -
210E ASN* 1.3 68.3 - - - +
212E ASP* 1.3 56.7 + - - +
213E TYR 3.0 5.4 - - - -
214E LEU* 2.8 44.2 + - + +
215E LYS* 3.3 23.1 + - + +
236E LEU* 4.8 10.8 - - + +
237E ASN* 3.5 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E ASN* 3.7 2.5 - - + +
211E LEU* 1.3 79.3 + - - +
213E TYR* 1.3 61.9 + - - +
215E LYS* 2.4 45.2 + - - +
216E ARG* 3.3 22.5 + - - +
237E ASN* 5.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E LEU* 5.0 5.4 - - - +
144E CYS* 4.5 3.6 - - - -
192E LYS* 5.8 4.3 - - - +
193E LEU* 3.6 28.5 - - + +
196E GLU* 4.8 23.7 - - + +
198E VAL* 4.1 19.5 - - + -
210E ASN* 3.6 34.5 + - - +
211E LEU 2.8 1.4 + - - -
212E ASP* 1.3 79.9 - - - +
214E LEU* 1.3 63.8 + - + +
216E ARG* 3.3 7.2 + - - +
217E TYR* 3.0 67.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E CYS* 3.7 38.9 - - + +
147E LEU* 4.1 15.7 - - + -
148E LEU* 3.8 35.9 - - + +
151E THR* 4.1 13.9 - - - +
193E LEU* 4.9 2.0 - - + -
198E VAL* 4.3 19.1 - - + -
199E ILE* 5.3 0.9 - - + -
208E VAL* 5.0 11.2 - - + -
210E ASN 4.9 0.7 - - - +
211E LEU* 2.8 24.0 + - + +
213E TYR* 1.3 82.5 - - + +
215E LYS* 1.3 56.0 + - - +
217E TYR* 3.1 7.5 + - - +
218E ALA* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E LEU* 3.7 17.0 - - + +
152E TYR* 3.7 21.5 + - + +
211E LEU* 3.3 23.3 + - + +
212E ASP* 2.4 44.6 + - - +
213E TYR 3.3 0.6 - - - -
214E LEU* 1.3 78.8 - - - +
216E ARG* 1.3 59.7 + - - +
218E ALA 3.2 17.0 - - - +
219E PRO* 3.6 2.4 - - - +
222E ASP* 3.2 30.1 - - + +
233E TRP* 5.5 4.1 - - - +
237E ASN* 4.1 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E ASP 3.3 11.9 + - - +
213E TYR* 3.6 11.0 - - - +
214E LEU 3.2 0.6 - - - -
215E LYS* 1.3 78.1 - - - +
217E TYR* 1.3 75.5 + - + +
219E PRO* 3.2 23.2 - - - +
52F SER* 5.8 0.6 + - - -
53F GLU* 4.8 13.6 + - - -
54F ASN* 3.8 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ASP* 4.0 13.9 - - - +
136E ILE* 5.2 2.1 - - - +
137E ASN* 4.9 13.3 + - + +
140E LEU* 3.7 28.9 - - + +
141E GLY* 4.2 11.6 - - - -
144E CYS* 3.7 24.9 - - + -
213E TYR* 3.0 74.8 + + - -
214E LEU 3.1 2.7 + - - +
216E ARG* 1.3 96.5 - - + +
218E ALA* 1.3 58.2 + - - +
219E PRO* 3.1 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ASP* 3.1 21.1 - - + +
144E CYS 4.4 0.2 - - - +
145E GLY* 3.9 17.9 - - - +
148E LEU* 4.1 12.1 - - + +
214E LEU 3.0 13.0 + - - +
215E LYS* 3.2 10.1 - - - +
217E TYR* 1.3 76.8 - - - +
219E PRO* 1.3 50.7 - - - +
220E LYS 3.3 0.3 + - - -
221E LEU* 3.5 21.8 + - + -
222E ASP* 2.6 24.3 + - - +
----------------------------------------------------------
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