Contacts of the helix formed by residues 216 - 227 (chain B) in PDB entry 3E61
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 ASN 216 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 4.2 7.6 + - - +
214B LEU 3.3 2.4 - - - +
215B ASP* 1.3 75.2 - - - +
217B ASP* 1.3 65.5 + - - +
218B LYS* 3.9 11.0 + - - +
219B LYS* 3.3 27.2 + - + +
220B PHE* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A HIS* 5.5 3.5 - - - -
214B LEU 4.1 4.5 - - - +
215B ASP 3.7 4.1 + - - +
216B ASN* 1.3 75.8 + - - +
218B LYS* 1.3 70.4 + - - +
220B PHE* 3.2 5.8 + - - +
221B ILE* 3.0 27.7 + - - +
246B ILE* 3.7 31.1 - - + +
249B ARG* 3.1 31.7 + - - -
250B TYR* 3.4 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A HIS 5.9 1.3 - - - +
328A HIS 5.6 6.7 - - - +
216B ASN* 3.4 8.6 + - - +
217B ASP* 1.3 81.2 + - - +
219B LYS* 1.3 57.6 + - - +
221B ILE* 3.4 8.4 + - + +
222B ASP* 3.0 46.5 + - - +
250B TYR* 4.1 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU 5.6 2.0 - - - +
216B ASN* 3.3 34.2 + - + +
218B LYS* 1.3 75.6 - - - +
220B PHE* 1.3 66.3 + - - +
222B ASP* 3.4 13.2 + - - +
223B LEU* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.6 17.9 - - + -
179B VAL* 4.4 2.9 - - + -
209B LEU* 3.4 35.0 - - + -
213B LEU 4.3 9.5 + - - +
214B LEU* 4.0 15.3 - - + +
216B ASN 3.2 10.2 + - - +
217B ASP* 3.2 11.1 + - - +
219B LYS* 1.3 78.1 - - - +
221B ILE* 1.3 61.5 + - + +
223B LEU* 3.1 10.8 + - + +
224B ILE* 2.9 46.8 + - + +
232B ILE* 4.2 11.0 - - + -
243B VAL* 4.2 20.0 - - + -
246B ILE* 3.7 27.6 - - + -
247B VAL* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ASP 3.0 17.9 + - - +
218B LYS* 3.6 10.3 - - + +
219B LYS 3.3 0.2 - - - -
220B PHE* 1.3 77.4 - - + +
222B ASP* 1.3 68.7 + - - +
224B ILE* 3.4 6.1 + - + +
225B LYS* 3.0 52.4 + - + +
246B ILE* 3.7 23.3 - - + +
247B VAL* 4.3 10.8 - - + -
250B TYR* 3.5 43.5 - - + -
252B PHE* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LYS* 3.0 36.4 + - - +
219B LYS* 3.5 15.2 - - - +
221B ILE* 1.3 78.7 - - - +
223B LEU* 1.3 58.1 + - - +
225B LYS* 3.5 9.8 + - - +
226B GLU* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 4.4 18.4 - - + -
209B LEU* 4.1 35.9 - - + -
219B LYS 3.2 9.5 + - - +
220B PHE* 3.1 12.4 + - + +
222B ASP* 1.3 77.3 - - - +
224B ILE* 1.3 65.1 + - + +
226B GLU* 3.2 7.4 + - + +
227B LEU* 3.0 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.4 33.4 - - + -
220B PHE* 2.9 39.3 + - + +
221B ILE* 3.5 12.3 - - + +
223B LEU* 1.3 76.3 - - + +
225B LYS* 1.3 58.3 + - - +
228B SER* 3.1 21.7 + - - -
229B ILE* 3.1 34.7 + - + +
232B ILE* 4.4 5.6 - - + -
247B VAL* 5.0 0.9 - - + -
252B PHE* 3.8 22.4 - - + -
258B ILE* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS* 5.3 12.7 + - - -
221B ILE* 3.0 40.1 + - + +
222B ASP* 3.8 9.4 - - - +
224B ILE* 1.3 72.7 - - - +
226B GLU* 1.3 67.5 + - - +
228B SER* 3.0 17.9 + - - +
250B TYR* 5.6 2.0 + - - -
252B PHE* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASP 3.0 18.2 + - - +
223B LEU* 3.2 8.7 + - + +
225B LYS* 1.3 76.2 - - - +
227B LEU* 1.3 71.3 + - + +
228B SER* 3.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ASN* 3.8 14.9 - - - +
177B LEU* 4.3 5.4 - - + -
207B LYS* 3.9 44.0 - - + +
223B LEU* 3.0 41.3 + - + +
226B GLU* 1.3 88.8 - - + +
228B SER* 1.3 70.8 + - - +
229B ILE* 3.2 24.6 + - + +
----------------------------------------------------------
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