Contacts of the helix formed by residues 207 - 217 (chain E) in PDB entry 3LUE
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 GLU 207 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E SER 5.7 0.6 - - - +
59E GLN* 4.9 14.1 - - + +
203E THR 3.7 0.8 + - - +
204E ALA* 2.6 12.6 + - - +
206E ARG* 1.3 90.8 + - - +
208E ILE* 1.3 62.6 + - + +
209E VAL 3.4 1.3 - - - -
210E ARG* 3.1 52.9 + - - +
211E ASP* 3.4 13.2 - - - +
288G ASP* 3.9 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E PHE* 3.7 24.0 - - + -
204E ALA* 3.5 6.7 + - + +
205E GLU* 3.1 36.8 + - + +
207E GLU* 1.3 78.8 - - + +
209E VAL* 1.3 64.0 + - - +
211E ASP* 3.6 13.8 + - - +
212E ILE* 3.2 29.4 + - + +
240E TYR* 4.8 13.4 - - + +
242E LEU* 4.2 11.7 - - + -
243E PRO* 4.3 28.5 - - + -
248E ILE* 5.1 1.3 - - + -
291G LYS* 5.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E THR* 3.4 24.7 - - + +
189E LEU* 3.2 17.6 - - + +
190E MET* 3.8 36.3 - - + +
193E LEU* 4.6 2.7 - - + -
200E PHE* 4.0 32.8 - - + -
205E GLU 3.9 0.6 + - - +
206E ARG 2.9 24.7 - - - +
208E ILE* 1.3 77.5 - - - +
210E ARG* 1.4 62.7 + - - +
212E ILE* 3.0 11.2 + - + -
213E LYS* 2.9 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E SER 5.1 2.9 - - - -
15E GLY* 3.9 34.8 + - - -
16E MET* 4.8 9.9 - - - +
186E THR* 4.0 22.2 - - + +
207E GLU* 3.1 46.1 + - - +
208E ILE 3.3 0.2 - - - -
209E VAL* 1.4 80.5 - - - +
211E ASP* 1.3 80.5 + - - +
213E LYS* 3.5 4.9 - - - +
214E GLU* 3.0 71.7 + - - +
215E LYS* 4.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E GLU* 3.4 16.5 - - - +
208E ILE* 3.6 12.9 + - - +
209E VAL 3.2 0.4 - - - -
210E ARG* 1.3 93.7 + - - +
212E ILE* 1.3 60.1 + - - +
214E GLU* 4.3 2.0 - - - +
215E LYS* 2.6 64.8 + - - +
240E TYR* 3.3 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E LEU* 4.1 13.0 - - + -
193E LEU* 3.9 19.7 - - + -
200E PHE* 4.4 5.4 - - + -
208E ILE* 3.2 21.3 + - + +
209E VAL* 3.0 14.2 + - - +
211E ASP* 1.3 73.1 - - - +
213E LYS* 1.3 58.8 + - - +
215E LYS* 2.8 0.6 + - - -
216E LEU* 2.7 60.4 + - + +
217E CYS* 3.7 1.9 + - - -
240E TYR* 3.8 24.9 - - + -
248E ILE* 3.9 22.7 - - + -
250E ILE* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E ASP* 5.9 0.4 + - - -
182E GLY* 3.2 18.9 + - - -
185E LEU* 3.6 5.4 - - + +
186E THR* 2.6 44.7 + - - +
189E LEU* 3.6 11.1 - - + +
209E VAL 2.9 16.4 + - - +
210E ARG* 3.5 8.1 - - - +
212E ILE* 1.3 77.5 - - - +
214E GLU* 1.3 89.0 + - - +
217E CYS* 3.2 30.1 + - - +
257E CYS* 4.0 17.3 - - - -
306E TYR* 3.8 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E GLY* 5.1 2.6 - - - -
210E ARG* 3.0 70.6 + - - +
211E ASP* 4.3 2.5 - - - +
213E LYS* 1.3 99.4 + - - +
215E LYS* 1.3 66.0 + - + +
216E LEU 3.9 0.2 + - - -
217E CYS 4.8 2.8 + - - +
306E TYR* 5.4 5.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
210E ARG* 4.7 5.1 - - - +
211E ASP* 2.6 65.1 + - + +
212E ILE* 2.8 3.5 + - - +
214E GLU* 1.3 81.5 + - + +
216E LEU* 1.3 71.6 + - + +
217E CYS 5.1 1.0 - - - +
218E TYR* 5.7 1.7 - - - -
240E TYR* 4.5 15.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E ILE* 2.7 43.6 + - + +
215E LYS* 1.3 85.8 - - + +
217E CYS* 1.4 66.3 + - - +
218E TYR* 3.1 10.5 - - - -
238E LYS* 3.9 30.1 - - + +
239E SER 5.2 6.1 - - - +
240E TYR* 4.3 15.0 - - + -
250E ILE* 3.7 21.3 - - + -
254E ARG* 2.8 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E LEU* 4.5 6.3 - - - -
212E ILE* 4.6 1.6 - - - -
213E LYS* 3.2 33.8 + - - +
214E GLU 5.1 2.3 - - - +
215E LYS 3.9 1.4 - - - -
216E LEU* 1.4 77.4 - - - +
218E TYR* 1.3 68.7 + - - +
253E GLU 4.4 0.2 - - - -
254E ARG* 3.0 27.6 - - - +
257E CYS* 3.7 22.7 - - - -
258E PRO* 3.8 4.3 - - + -
306E TYR* 3.8 22.6 - - + -
307E PRO* 3.8 14.4 - - - +
----------------------------------------------------------
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