Contacts of the helix formed by residues 216 - 229 (chain A) in PDB entry 2J0M
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 LYS 216 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A VAL* 1.3 81.0 - - + +
217A ALA* 1.3 55.2 + - - +
218A LYS* 3.3 3.4 - - + +
219A THR* 3.2 20.0 + - - +
220A LEU* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TYR* 4.5 2.4 + - - -
198A GLU* 4.4 17.7 - - - +
215A VAL 3.7 1.9 + - - -
216A LYS* 1.3 73.5 - - - +
218A LYS* 1.3 61.6 + - + +
220A LEU* 3.3 16.3 + - + +
221A ARG* 2.9 27.2 + - - +
----------------------------------------------------------
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 LYS* 3.3 3.7 - - + +
217A ALA* 1.3 77.6 - - + +
219A THR* 1.3 63.1 + - - +
221A ARG* 3.5 34.8 + - - +
222A LYS* 3.2 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A VAL* 3.7 24.6 - - + +
216A LYS* 3.2 23.2 + - - +
218A LYS* 1.3 76.8 - - - +
220A LEU* 1.3 59.0 + - - +
222A LYS* 3.2 9.8 + - + +
223A LEU* 2.9 46.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
194A TYR* 3.6 8.7 - - - +
198A GLU* 5.7 4.3 - - + +
203A LEU* 3.7 22.9 - - + -
211A LEU* 3.9 36.1 - - + +
212A LEU* 4.0 27.4 - - + +
215A VAL* 3.8 13.2 - - + +
216A LYS 2.8 13.4 + - - +
217A ALA* 3.3 18.4 - - + +
219A THR* 1.3 74.6 - - - +
221A ARG* 1.3 65.1 + - - +
223A LEU* 3.3 7.8 + - + +
224A ILE* 3.0 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LYS* 5.0 27.6 - - - +
194A TYR* 3.2 46.9 + - + +
217A ALA 2.9 11.1 + - - +
218A LYS* 3.5 55.9 + - - +
219A THR 3.3 0.4 - - - -
220A LEU* 1.3 77.0 - - - +
222A LYS* 1.3 72.8 + - - +
224A ILE* 3.9 1.6 - - - +
225A GLN* 2.9 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 3.2 21.9 + - - +
219A THR* 3.2 11.4 + - + +
221A ARG* 1.3 87.9 - - - +
223A LEU* 1.3 64.2 + - + +
225A GLN* 3.5 11.8 + - - +
226A GLN* 3.1 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.3 27.4 - - + -
211A LEU* 5.9 3.4 - - + -
215A VAL* 4.3 23.1 - - + -
219A THR* 2.9 33.4 + - + +
220A LEU* 3.6 9.4 - - + +
222A LYS* 1.3 76.3 - - + +
224A ILE* 1.3 61.6 + - - +
226A GLN* 3.3 10.0 + - - +
227A THR* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.3 10.1 - - + -
173A CYS* 3.8 18.9 - - - -
176A ILE* 4.6 9.4 - - + -
188A LEU* 4.1 20.0 - - + -
194A TYR* 3.3 39.9 - - + +
197A LEU* 6.0 0.2 - - + -
203A LEU* 3.8 17.9 - - + -
207A PHE* 3.7 30.1 - - + -
220A LEU* 3.0 25.4 + - + +
223A LEU* 1.3 71.8 - - - +
225A GLN* 1.3 67.7 + - - +
228A PHE* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.0 41.3 + - + +
189A GLU* 3.4 42.2 + - - +
190A LYS 4.9 0.6 + - - -
191A LYS* 5.8 1.0 - - - +
194A TYR* 4.7 7.5 - - + +
221A ARG* 2.9 50.3 + - - +
222A LYS* 3.6 10.9 - - - +
224A ILE* 1.3 76.2 - - - +
226A GLN* 1.3 64.8 + - + +
228A PHE* 3.2 19.5 - - - +
229A ARG* 3.5 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 3.1 32.4 + - - +
223A LEU* 3.8 10.5 - - - +
224A ILE 3.2 0.2 - - - -
225A GLN* 1.3 76.2 - - + +
227A THR* 1.3 58.2 + - + +
228A PHE 3.0 4.0 - - - -
229A ARG* 2.9 61.7 + - - +
230A GLN* 4.5 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLU* 6.3 1.1 - - + -
169A LEU* 3.8 40.7 + - + +
170A LYS* 4.2 11.4 + - - +
173A CYS* 4.1 11.7 - - - -
223A LEU* 2.8 22.8 + - + +
224A ILE* 4.7 0.9 - - - +
226A GLN* 1.3 74.2 - - + +
228A PHE* 1.3 60.4 + - - +
229A ARG* 5.3 0.7 - - - +
230A GLN* 3.2 33.9 - - - +
231A PHE* 3.8 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A CYS* 3.7 39.9 - - + -
176A ILE* 4.1 10.3 - - + -
177A ARG* 4.1 22.4 - - + -
183A MET* 3.8 22.0 - - + -
185A GLY* 3.0 34.5 - - - -
188A LEU* 4.0 27.8 - - + -
224A ILE 3.1 20.3 + - - +
225A GLN* 3.2 12.1 - - - +
227A THR* 1.3 77.7 - - - +
229A ARG* 1.3 62.2 + - - +
231A PHE* 2.9 17.6 + - + +
232A ALA* 3.1 20.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLY 5.7 0.2 - - - -
189A GLU* 5.8 2.7 - - - +
225A GLN 3.5 6.0 + - - +
226A GLN* 2.9 49.0 + - - +
227A THR* 5.3 0.4 - - - +
228A PHE* 1.3 79.3 - - - +
230A GLN* 1.3 60.7 + - + +
231A PHE 3.5 0.3 + - - -
232A ALA* 3.7 18.5 + - - +
233A ASN* 4.8 1.7 - - - +
----------------------------------------------------------
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