Contacts of the helix formed by residues 217 - 228 (chain A) in PDB entry 7ACN
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 PRO 217 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.8 16.4 - - + -
216A SER* 1.3 88.9 - - - +
218A LYS* 1.3 61.4 + - - +
220A VAL* 3.2 12.1 + - + +
221A ILE 3.7 0.3 + - - -
248A ILE* 3.9 13.7 - - + -
249A SER* 4.9 3.8 - - - +
252A GLY* 3.4 41.7 - - - +
255A THR* 4.4 4.9 - - + -
256A ILE* 3.2 29.2 - - + +
364A GLU* 5.2 5.6 - - - +
368A ARG* 5.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A SER* 3.2 12.5 + - - +
217A PRO* 1.3 76.6 - - - +
219A ASP* 1.3 56.4 + - - +
221A ILE* 3.2 15.8 + - + +
222A LEU* 2.9 42.1 + - + +
255A THR* 3.8 11.9 - - + +
259A MET* 3.8 15.9 - - - -
359A THR* 3.8 12.3 - - + +
360A ASN* 2.6 34.6 + - - +
444A SER 3.0 8.1 + - - -
445A TYR 2.8 28.0 + - - -
463A VAL* 4.9 0.4 - - - -
464A THR 2.7 39.6 + - - +
465A SER* 3.9 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP 4.2 1.9 - - - +
215A THR* 3.4 13.7 - - + -
216A SER* 3.0 33.2 + - - +
218A LYS* 1.3 72.3 - - - +
220A VAL* 1.3 60.1 + - - +
222A LEU* 3.8 7.5 - - - +
223A LYS* 2.9 32.1 + - - +
318A LEU* 3.7 20.1 - - + +
319A LYS 4.0 2.7 - - - +
320A PRO* 3.5 10.4 - - - +
321A HIS* 2.8 37.8 + - + +
465A SER* 5.0 7.3 + - - -
468A ILE* 6.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.0 24.0 - - + -
211A LEU* 4.4 6.1 - - + -
216A SER 4.3 7.0 - - - +
217A PRO* 3.2 14.6 + - + +
219A ASP* 1.3 76.5 - - - +
221A ILE* 1.3 57.9 + - - +
223A LYS* 3.6 3.0 - - - +
224A VAL* 3.0 35.8 + - + +
240A TYR* 4.5 6.5 - - + -
248A ILE* 5.1 3.1 - - + -
256A ILE* 4.0 28.0 - - + -
313A ILE* 4.3 5.7 - - + +
315A LEU* 3.9 17.9 - - + -
318A LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PRO 3.7 0.4 + - - +
218A LYS* 3.2 28.5 - - + +
220A VAL* 1.3 77.8 - - - +
222A LEU* 1.3 65.0 + - - +
224A VAL* 4.2 15.3 - - + -
225A ALA* 3.0 27.0 + - + +
240A TYR* 4.0 15.0 - - - +
255A THR 4.0 3.4 - - - +
256A ILE* 3.6 37.5 - - + +
259A MET* 3.5 39.6 - - + +
260A GLY* 3.8 19.7 - - - +
263A ILE* 5.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 2.9 34.8 + - + +
219A ASP* 3.8 11.9 - - - +
221A ILE* 1.3 75.1 - - - +
223A LYS* 1.3 60.7 + - - +
225A ALA* 4.7 0.9 - - - -
226A GLY 3.3 10.9 + - - -
259A MET* 4.2 12.6 - - + -
321A HIS* 3.4 40.2 - - + +
323A ASN* 3.1 51.9 + - + +
331A ALA* 3.8 5.5 - - - +
463A VAL* 3.9 19.1 - - + +
464A THR* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP 2.9 18.6 + - - +
220A VAL 3.6 4.0 - - - +
222A LEU* 1.3 73.1 - - - +
224A VAL* 1.3 65.1 + - - +
226A GLY* 3.2 4.4 + - - -
227A ILE* 3.0 48.0 + - + +
313A ILE* 3.9 18.6 - - + +
318A LEU* 4.0 20.9 - - + +
321A HIS* 4.0 27.9 - - + +
331A ALA* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 4.5 18.6 - - + -
220A VAL* 3.0 22.0 + - + +
221A ILE* 3.5 19.7 + - + +
223A LYS* 1.3 74.2 - - - +
225A ALA* 1.4 57.8 + - - +
227A ILE* 3.0 10.2 + - + +
228A LEU* 2.9 51.4 + - + +
238A VAL* 5.5 1.6 - - + -
240A TYR* 4.4 15.0 - - - +
263A ILE* 4.5 8.1 - - + -
311A ILE* 5.4 3.6 - - + -
313A ILE* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 3.0 20.9 + - + +
222A LEU* 3.9 5.2 - - - +
224A VAL* 1.4 71.7 - - - +
226A GLY* 1.3 65.0 + - - +
229A THR* 2.9 26.5 + - - -
259A MET* 5.1 9.4 - - + +
262A GLU* 5.5 5.6 - - + +
263A ILE* 3.7 23.3 - - + +
323A ASN* 4.4 0.9 - - - +
328A PRO 4.1 17.7 - - - +
329A ASP* 3.4 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU 3.3 6.5 + - - -
223A LYS 3.2 7.5 + - - -
225A ALA* 1.3 77.5 - - - +
227A ILE* 1.3 61.6 + - - +
229A THR* 4.2 7.6 + - - +
329A ASP* 3.5 22.8 + - - +
331A ALA* 4.1 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LYS* 3.0 46.4 + - + +
224A VAL* 3.0 12.7 + - - +
226A GLY* 1.3 77.5 - - - +
228A LEU* 1.3 65.3 + - + +
229A THR* 3.6 6.2 + - - +
309A GLN* 6.3 0.2 - - - +
311A ILE* 4.5 30.5 - - + -
312A GLU 6.0 0.2 - - - +
313A ILE* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 4.7 13.5 - - + -
205A VAL* 5.6 0.7 - - + -
224A VAL* 2.9 35.6 + - + +
227A ILE* 1.3 73.1 - - + +
229A THR* 1.3 82.9 + - - +
232A GLY* 3.0 38.9 - - - +
238A VAL* 5.5 1.3 - - + -
263A ILE* 3.8 19.5 - - + -
309A GLN* 4.2 20.4 - - - +
311A ILE* 3.6 34.1 - - + -
----------------------------------------------------------
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