Contacts of the helix formed by residues 216 - 230 (chain A) in PDB entry 2RD0
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 VAL 216 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ASP 3.1 6.4 + - - +
215A CYS* 1.3 76.3 - - - +
217A PRO* 1.4 76.7 - - + +
218A GLU* 4.0 10.3 - - + +
219A GLN* 3.1 35.7 + - + +
220A VAL* 3.1 15.2 + - - +
264A LYS* 4.5 16.4 - - + -
265A TYR 3.4 29.4 - - - +
266A PRO* 4.3 1.8 - - + -
267A LEU* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 1.4 90.3 - - + +
218A GLU* 1.3 57.1 + - - +
220A VAL* 3.0 11.3 + - + +
221A ILE* 2.8 38.5 + - + +
251A ILE* 5.7 2.7 - - + -
252A LEU* 4.1 16.6 - - + +
261A PHE* 4.0 27.8 - - + +
262A LEU* 6.1 0.2 - - - -
263A GLU 3.9 23.6 - - - +
264A LYS* 4.4 3.8 - - + -
265A TYR 3.6 9.6 - - - +
267A LEU* 5.1 6.5 - - + +
270A TYR* 4.3 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 3.3 10.0 - - + +
217A PRO* 1.3 80.4 - - + +
219A GLN* 1.3 62.6 + - + +
221A ILE* 3.4 10.8 + - + +
222A ALA* 3.1 18.7 + - - +
247A GLN* 3.4 25.6 + - + +
248A GLY* 5.2 11.4 - - - -
264A LYS* 3.3 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ASP 4.7 0.5 - - - +
215A CYS* 3.2 30.2 - - - -
216A VAL* 3.1 36.6 + - + +
218A GLU* 1.3 74.4 - - + +
220A VAL* 1.3 65.1 + - - +
222A ALA* 3.4 6.9 - - - +
223A GLU* 3.1 24.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
192A VAL* 5.4 9.0 - - + -
194A ILE* 4.5 11.2 - - + -
209A LEU* 3.9 16.5 - - + +
211A ILE* 4.6 12.6 - - + -
215A CYS* 3.6 22.7 - - - +
216A VAL 3.1 16.1 + - - +
217A PRO* 3.0 9.5 + - + +
219A GLN* 1.3 74.3 - - - +
221A ILE* 1.3 67.0 + - - +
223A GLU* 3.4 4.0 + - - -
224A ALA* 3.0 22.9 + - - +
252A LEU* 4.1 18.2 - - + -
267A LEU* 4.4 14.8 - - + -
285A LEU* 5.3 5.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
194A ILE* 4.8 0.7 - - - -
217A PRO* 2.8 24.7 + - + +
218A GLU* 3.4 11.2 + - + +
220A VAL* 1.3 74.4 - - - +
222A ALA* 1.3 55.9 + - - +
224A ALA* 3.3 8.2 + - - +
225A ILE* 2.9 41.6 + - + +
247A GLN* 3.6 24.0 - - - +
248A GLY* 6.0 0.4 - - - -
250A TYR* 3.4 27.4 - - + +
251A ILE* 3.6 25.1 - - + -
252A LEU* 4.1 10.5 - - + +
287A LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLU 3.1 12.0 + - - +
219A GLN* 3.4 13.2 - - - +
221A ILE* 1.3 70.6 - - - +
223A GLU* 1.3 56.3 + - - +
224A ALA 2.9 3.4 - - - -
225A ILE* 2.7 23.4 + - - -
226A ARG* 2.8 23.8 + - - +
243A VAL* 3.3 17.8 - - + +
247A GLN* 3.2 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.8 26.2 - - + +
211A ILE* 4.0 28.6 - - + +
219A GLN 3.1 13.8 + - - +
220A VAL* 4.0 1.3 - - - +
222A ALA* 1.3 78.4 - - - +
224A ALA* 1.3 59.8 + - - +
226A ARG* 3.1 36.8 + - - +
227A LYS* 3.4 20.8 + - + +
230A ARG* 4.2 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 3.6 39.7 - - + -
207A TYR* 4.8 6.7 - - + -
209A LEU* 3.7 9.8 - - + +
220A VAL 3.0 17.0 + - - +
221A ILE 3.4 6.1 - - - +
222A ALA 2.9 0.8 + - - -
223A GLU* 1.3 79.1 - - - +
225A ILE* 1.3 57.7 + - - +
227A LYS* 3.4 4.3 + - - +
228A LYS* 3.2 26.0 + - - +
287A LEU* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 2.9 36.2 + - + +
222A ALA 2.7 11.6 + - - +
224A ALA* 1.3 70.8 - - - +
226A ARG* 1.3 65.5 + - - +
228A LYS* 4.0 9.0 - - + +
229A THR* 3.2 26.1 + - + +
243A VAL* 3.9 25.2 - - + +
246A TYR* 3.5 49.8 - - + +
247A GLN* 4.2 7.2 - - - +
250A TYR* 4.4 10.5 - - + -
287A LEU* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA* 2.8 25.6 + - - +
223A GLU* 3.1 44.3 + - - +
225A ILE* 1.3 78.0 - - - +
227A LYS* 1.3 65.0 + - - +
229A THR* 4.1 0.3 - - - -
230A ARG* 2.9 54.5 + - - +
239A LEU* 4.2 15.5 - - + +
240A LYS* 4.6 16.2 - - - +
243A VAL* 3.6 30.8 + - + +
247A GLN* 4.8 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 4.3 23.0 - - + +
208A THR* 3.0 31.5 + - - +
209A LEU* 3.8 22.0 - - + -
223A GLU* 3.4 6.5 + - + +
224A ALA 3.4 9.5 + - - +
225A ILE 3.4 0.4 - - - -
226A ARG* 1.3 81.5 - - - +
228A LYS* 1.3 63.7 + - - +
229A THR 3.1 0.9 + - - -
230A ARG* 3.5 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL* 3.5 35.1 - - + +
198A VAL* 4.3 10.7 - - - +
205A GLN* 4.4 6.5 - - - +
207A TYR* 3.3 47.4 - - + +
224A ALA 3.2 13.0 + - - +
225A ILE* 4.3 10.5 - - + +
226A ARG 3.4 0.4 - - - -
227A LYS* 1.3 80.3 - - - +
229A THR* 1.3 63.8 + - - +
230A ARG 4.3 3.8 - - - +
246A TYR* 5.8 2.7 - - - +
287A LEU* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ILE* 3.2 21.9 + - - +
226A ARG 3.1 1.8 + - - -
228A LYS* 1.3 82.6 - - - +
230A ARG* 1.3 67.2 + - - +
231A SER* 3.4 10.7 + - - -
234A LEU* 3.9 19.3 - - + +
239A LEU* 3.6 18.6 - - + -
242A CYS* 4.4 15.7 - - + -
243A VAL* 5.3 0.2 - - + -
246A TYR* 3.2 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 4.2 10.5 + - - -
226A ARG* 2.9 59.0 + - - +
227A LYS* 3.5 21.8 + - - +
228A LYS 4.3 3.3 - - - +
229A THR* 1.3 77.6 - - - +
231A SER* 1.3 60.3 + - - +
234A LEU* 5.7 0.4 - - - -
239A LEU* 3.9 23.6 - - + +
----------------------------------------------------------
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