Contacts of the helix formed by residues 210 - 217 (chain E) in PDB entry 3BVH
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 210 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E GLY 3.2 1.0 - - - -
209E LYS* 1.3 97.6 - - + +
211E CYS* 1.3 64.4 + - - +
212E GLU* 2.8 29.2 + - - +
213E GLU* 3.0 30.2 + - - +
214E ILE* 3.1 14.8 + - - +
227E ILE* 4.0 20.2 - - + -
250E THR* 3.9 9.9 - - - +
302E LEU* 4.4 14.8 - - + -
305E MET* 4.9 8.3 - - - +
456E PRO* 3.0 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E GLU* 1.3 74.8 - - - +
212E GLU* 1.3 62.5 + - - +
214E ILE* 3.7 4.2 - - - +
215E ILE* 3.1 19.8 + - - +
227E ILE* 4.4 0.2 - - - +
238E VAL* 4.0 11.7 - - - -
240E CYS* 2.0 59.0 - - + -
242E MET* 3.8 1.7 - - - +
248E GLY* 3.6 11.1 - - - +
249E TRP 3.5 19.3 - - - +
250E THR* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E GLU* 2.8 17.2 + - - +
211E CYS* 1.3 75.0 - - - +
213E GLU* 1.3 56.3 + - - +
215E ILE* 3.2 13.7 - - - +
216E ARG* 3.0 54.0 - - - +
247E GLY 3.9 2.1 - - - +
248E GLY* 3.3 16.2 + - - +
250E THR* 4.7 0.2 + - - -
455E ARG* 2.9 27.1 + - + -
456E PRO* 3.5 33.2 - - + +
458E PHE* 5.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E GLY* 3.7 6.8 - - - -
209E LYS* 2.9 52.6 + - - +
210E GLU* 3.0 22.9 + - - +
212E GLU* 1.3 76.9 - - - +
214E ILE* 1.3 59.0 + - - +
216E ARG* 3.5 25.1 + - - +
217E LYS* 3.1 60.8 + - + +
176F GLN* 5.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E VAL* 4.0 10.0 - - + +
207E SER* 3.7 9.0 - - - +
208E GLY* 3.7 18.8 - - - +
210E GLU 3.1 9.4 + - - +
211E CYS* 3.7 7.6 - - - +
212E GLU 3.3 0.2 - - - -
213E GLU* 1.3 74.5 - - - +
215E ILE* 1.3 63.0 + - - +
217E LYS* 3.0 15.4 + - - +
218E GLY 3.2 0.9 + - - -
219E GLY* 2.9 20.9 + - - -
225E TYR* 3.6 45.5 - - + -
226E LEU 3.9 8.7 - - - +
227E ILE* 3.8 23.1 - - + -
240E CYS* 4.4 3.6 - - - -
242E MET* 3.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E CYS 3.1 14.3 + - - +
212E GLU* 3.2 26.9 - - - +
214E ILE* 1.3 72.9 - - - +
216E ARG* 1.3 65.3 + - + +
217E LYS 3.0 4.9 - - - -
218E GLY* 2.9 18.2 + - - -
219E GLY 3.4 24.2 - - - +
220E GLU* 4.7 7.4 - - + -
242E MET* 3.9 23.1 - - + +
246E ASN 5.0 6.7 - - - +
247E GLY 4.9 2.2 - - - -
248E GLY* 4.1 15.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
209E LYS* 6.4 0.2 - - - +
212E GLU* 3.0 45.9 + - - +
213E GLU* 3.7 24.2 - - - +
214E ILE 3.3 0.4 - - - -
215E ILE* 1.3 84.5 - - + +
217E LYS* 1.3 59.5 + - + +
218E GLY 3.2 1.2 + - - -
458E PHE* 5.5 10.1 - - - -
209F ILE* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E VAL* 3.8 13.7 - - + +
207E SER 3.1 25.9 + - - +
208E GLY* 4.7 0.6 - - - -
213E GLU* 3.1 44.4 + - + +
214E ILE 3.0 11.2 + - - +
215E ILE 3.0 0.8 - - - -
216E ARG* 1.3 79.3 - - + +
218E GLY* 1.3 57.9 + - - +
219E GLY 3.6 0.2 - - - -
176F GLN* 6.0 0.4 + - - -
209F ILE* 3.2 21.9 - - - +
210F GLN* 4.2 6.4 - - - -
213F GLU* 3.4 54.5 + - + +
214F GLY 5.1 0.9 - - - +
232F LYS* 6.3 0.8 - - - +
----------------------------------------------------------
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