Contacts of the helix formed by residues 216 - 229 (chain A) in PDB entry 5EJC
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 216 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 1.3 88.5 - - + +
217A GLU* 1.3 65.6 + - - +
218A SER* 3.3 10.8 - - - +
219A SER* 3.1 11.4 + - - +
220A LEU 2.9 22.5 + - - -
268A GLN* 3.6 32.5 - - + +
271A SER* 3.1 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS 4.9 0.3 - - - +
140A ALA* 3.4 38.6 - - + +
143A GLU* 3.8 30.2 - - + +
144A MSE 3.7 19.2 - - + +
213A GLY* 5.0 5.9 + - - -
215A LEU 4.2 8.8 - - - +
216A PRO* 1.3 76.8 - - - +
218A SER* 1.3 61.9 + - - +
220A LEU* 4.0 8.7 - - + +
221A GLN* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 4.3 11.3 - - - +
217A GLU* 1.3 77.7 - - - +
219A SER* 1.3 65.1 + - - +
221A GLN* 3.4 28.4 + - - +
222A ARG* 4.1 9.9 + - - +
272A ASP* 5.1 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 5.1 1.8 - - - -
216A PRO* 3.1 8.7 + - - +
218A SER* 1.3 82.4 + - - +
220A LEU* 1.3 67.8 + - - +
221A GLN 3.2 0.4 - - - -
222A ARG* 3.0 26.1 + - - +
223A VAL 3.6 2.4 + - - -
271A SER* 3.6 28.8 + - - -
272A ASP* 3.1 35.2 + - - -
275A VAL* 3.9 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA* 4.4 4.5 - - + -
144A MSE 3.8 12.8 - - + -
210A CYS 3.4 20.6 - - - +
211A PHE* 3.7 30.1 - - + +
212A ALA* 3.9 7.4 - - - -
213A GLY 5.0 0.4 - - - +
215A LEU* 4.1 21.5 - - + +
216A PRO 2.9 16.2 + - - +
217A GLU* 3.4 8.3 + - + +
219A SER* 1.3 77.8 - - - +
221A GLN* 1.3 61.6 + - - +
223A VAL* 2.9 27.4 + - + +
224A TRP* 3.0 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 5.5 2.8 + - - -
56A ARG* 3.5 46.1 + - - +
60A TRP* 3.6 2.5 - - + -
144A MSE 3.8 38.8 - - - +
217A GLU 3.1 17.4 + - - +
218A SER* 3.4 29.0 + - - +
220A LEU* 1.3 76.8 - - - +
222A ARG* 1.3 59.3 + - - +
224A TRP* 3.1 5.5 + - - +
225A ASP* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PRO* 4.5 22.0 - - + +
56A ARG* 4.1 15.7 - - - +
218A SER 4.1 13.0 + - - +
219A SER* 3.0 13.2 + - - +
221A GLN* 1.3 76.4 - - + +
223A VAL* 1.3 59.9 + - - +
225A ASP* 3.5 23.0 - - - +
226A LYS* 3.6 16.3 + - - +
272A ASP* 3.1 41.2 + - - -
275A VAL* 3.7 25.3 - - + +
276A SER* 3.1 19.3 + - - +
279A ILE* 4.3 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 5.0 2.0 - - + -
215A LEU* 4.8 3.8 - - + -
219A SER 3.6 1.8 + - - +
220A LEU* 2.9 22.1 + - + +
222A ARG* 1.3 76.7 - - - +
224A TRP* 1.3 67.8 + - + +
225A ASP 3.2 0.2 - - - -
226A LYS* 3.0 24.5 + - - +
227A VAL* 3.3 9.2 + - + +
234A ILE* 4.5 9.2 - - + -
235A LEU* 3.9 28.0 - - + -
238A VAL* 4.0 24.2 - - + -
275A VAL* 3.7 33.9 - - + -
279A ILE* 5.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.8 15.3 - + + -
137A ILE* 3.8 18.4 - - + -
140A ALA* 3.8 20.4 - - + -
141A MSE 3.8 31.4 - - + -
144A MSE 3.7 28.0 - - + -
158A PHE* 3.7 32.5 - + + -
209A ARG 4.1 4.5 - - - -
210A CYS* 3.0 34.1 + - + +
212A ALA* 4.1 9.4 - - + -
220A LEU* 3.0 34.4 + - + +
221A GLN* 3.1 6.0 + - - +
223A VAL* 1.3 82.2 - - + +
225A ASP* 1.3 66.0 + - - +
226A LYS 3.1 0.2 - - - -
227A VAL* 3.7 10.8 - - + -
228A VAL* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 4.1 7.9 - - - +
50A PRO* 4.0 4.3 - - - +
51A LEU* 3.2 38.5 + - + +
56A ARG* 3.1 33.0 + - - -
60A TRP* 3.1 19.7 + - - +
63A LEU* 5.4 0.3 - - - +
221A GLN 2.8 16.0 + - - +
222A ARG* 3.5 16.9 - - - +
224A TRP* 1.3 77.1 - - - +
226A LYS* 1.3 66.6 + - + +
228A VAL* 3.9 2.9 - - - +
229A SER* 3.0 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER 2.9 24.3 + - - +
47A GLN* 3.3 14.4 + - - -
48A ARG 4.5 1.6 + - - -
49A PHE 3.1 24.9 + - - +
50A PRO* 3.9 8.5 - - - +
222A ARG 3.6 16.6 + - - +
223A VAL* 3.0 10.0 + - - +
225A ASP* 1.3 80.2 - - - +
227A VAL* 1.3 64.6 + - - +
229A SER* 2.9 17.6 + - - -
230A GLY 3.2 0.3 + - - -
231A SER 3.2 20.8 + - - +
234A ILE* 4.0 21.1 - - + -
279A ILE* 4.2 26.6 - - + +
282A TRP* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.5 28.7 - - + -
161A GLN* 3.7 4.8 - - - +
162A LEU* 4.5 8.7 - - + -
166A TYR* 2.8 41.4 + - + -
210A CYS* 5.2 2.7 - - + -
223A VAL 3.3 12.8 + - - +
224A TRP* 3.3 15.4 + - + +
226A LYS* 1.3 73.1 - - - +
228A VAL* 1.3 64.6 + - - +
230A GLY 3.4 0.7 + - - -
231A SER 3.3 8.5 - - - +
232A CYS* 5.1 3.1 - - + -
234A ILE* 3.9 9.0 - - + -
235A LEU* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A CYS* 5.6 0.2 - - - -
60A TRP* 4.2 34.8 - - + -
63A LEU* 3.8 34.8 - - + +
64A LEU* 4.1 23.8 - - + -
154A ILE* 6.0 0.2 - - + -
158A PHE* 4.0 22.7 - - + -
161A GLN* 3.5 20.5 + - - -
224A TRP* 2.9 20.2 + - + +
225A ASP 3.9 3.4 - - - +
227A VAL* 1.3 78.4 - - - +
229A SER* 1.3 58.1 + - - +
230A GLY* 3.0 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A CYS* 3.8 33.2 - - - +
46A SER* 3.6 23.7 - - - -
47A GLN* 2.5 36.5 + - - +
63A LEU* 4.2 10.1 - - - -
225A ASP 3.0 14.2 + - - -
226A LYS* 2.9 9.6 + - - -
228A VAL* 1.3 77.2 - - - +
230A GLY* 1.3 55.0 + - - +
----------------------------------------------------------
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