Contacts of the helix formed by residues 224 - 236 (chain A) in PDB entry 2NL9
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 HIS 224 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A VAL* 2.6 33.6 + - + +
221A GLN 2.8 6.1 + - - +
222A ARG 3.5 12.7 + - - -
223A ASN* 1.3 89.0 - - + +
225A GLU* 1.3 59.5 + - - +
226A THR 3.3 2.7 - - - -
227A ALA* 3.2 7.8 + - + +
228A PHE* 2.8 44.7 + - + -
64B ARG* 4.6 8.7 - - - -
65B ILE* 3.7 36.8 - - + +
68B GLU* 3.1 35.6 + - - -
69B PHE* 5.4 3.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLN* 3.2 18.8 + - + +
222A ARG* 3.3 14.0 - - - +
223A ASN* 3.0 29.4 + - - +
224A HIS* 1.3 78.0 - - - +
226A THR* 1.3 57.8 + - - +
228A PHE* 3.3 6.2 + - - +
229A GLN* 2.9 48.0 + - - +
273A PHE* 4.6 4.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ASN 5.0 3.0 + - - -
224A HIS 3.3 0.4 - - - -
225A GLU* 1.3 76.0 + - - +
227A ALA* 1.3 62.6 + - - +
229A GLN* 3.3 17.7 + - - +
230A GLY* 2.9 26.3 + - - -
233A ARG* 5.1 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A HIS* 3.2 14.4 + - + +
226A THR* 1.3 80.6 - - - +
228A PHE* 1.3 57.2 + - - +
230A GLY* 3.2 2.6 + - - -
231A MSE 2.9 36.1 + - + +
57B TRP* 4.6 4.2 - - - -
61B GLU* 4.2 17.7 - - + +
64B ARG* 4.7 4.5 - - - +
65B ILE* 3.9 25.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
220A VAL* 4.6 5.2 - - + -
221A GLN* 3.5 32.3 - - + -
224A HIS* 2.8 37.7 + - + +
225A GLU* 3.7 7.2 - - - +
227A ALA* 1.3 76.4 - - - +
229A GLN* 1.3 58.7 + - - +
231A MSE 3.3 25.4 + - + +
232A LEU* 2.9 25.1 + - - +
266A THR* 4.3 14.8 - - + -
269A SER* 3.7 7.0 - - - -
270A PHE* 3.6 37.2 - + + -
273A PHE* 3.4 43.5 - + + -
65B ILE* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 2.9 41.4 + - - +
226A THR* 3.5 15.3 + - - +
228A PHE* 1.3 78.4 - - - +
230A GLY* 1.3 57.2 + - - +
232A LEU* 3.4 4.9 + - - +
233A ARG* 3.0 47.1 + - + +
273A PHE* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR 2.9 13.9 + - - -
227A ALA 3.6 3.4 - - - -
229A GLN* 1.3 73.1 - - - +
231A MSE 1.3 64.0 + - - +
233A ARG* 3.4 27.3 + - - +
234A LYS* 3.1 27.7 + - - +
57B TRP* 4.1 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA 2.9 16.5 + - - +
228A PHE* 3.5 26.7 - - + -
230A GLY* 1.3 73.6 - - - +
232A LEU* 1.3 61.1 + - - +
234A LYS 3.2 1.2 + - - -
235A LEU* 2.8 30.3 + - - +
270A PHE* 3.5 30.3 - - + -
57B TRP* 3.4 24.9 - - + -
58B ILE* 3.6 18.0 - - + +
61B GLU* 3.7 21.3 - - + -
62B LEU* 3.4 43.3 - - + -
65B ILE* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE 2.9 17.2 + - - +
229A GLN* 3.5 5.8 - - - +
231A MSE 1.3 74.7 - - - +
233A ARG* 1.3 65.0 + - + +
235A LEU* 3.2 5.8 + - + +
236A ASP* 3.1 20.4 + - - -
237A ILE* 4.3 7.4 + - + -
270A PHE* 3.7 6.6 - - + -
273A PHE* 3.7 21.8 - - + -
274A VAL* 3.9 33.7 - - + -
277A HIS* 3.6 52.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 5.1 1.4 + - - +
229A GLN* 3.0 39.6 + - + +
230A GLY* 3.6 24.0 + - - +
231A MSE 3.2 0.2 - - - -
232A LEU* 1.3 79.2 - - + +
234A LYS* 1.3 61.3 + - + +
236A ASP* 3.5 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLY 3.1 15.5 + - - +
231A MSE 3.7 5.8 - - - +
233A ARG* 1.3 74.5 - - + +
235A LEU* 1.3 65.1 + - - +
236A ASP* 4.0 4.5 - - - +
54B PRO* 4.0 33.4 - - + +
57B TRP* 3.4 51.0 - - + +
58B ILE* 3.9 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A MSE 2.8 16.9 + - - +
232A LEU* 3.2 7.2 + - + +
234A LYS* 1.3 80.1 - - - +
236A ASP* 1.3 69.3 + - - +
237A ILE* 4.2 17.9 - - + +
238A LYS* 5.0 0.3 + - - -
242A ASP* 5.5 0.3 - - - +
245A SER* 3.7 32.7 + - - +
246A LEU* 3.9 34.5 - - + +
249A VAL* 4.7 1.6 - - + -
270A PHE* 4.2 9.0 - - + -
274A VAL* 3.8 37.9 - - + -
58B ILE* 3.5 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU 3.1 11.5 + - - -
233A ARG* 3.5 15.0 + - - +
234A LYS 3.3 5.6 - - - +
235A LEU* 1.3 78.0 - - - +
237A ILE* 1.3 64.8 + - - +
238A LYS* 2.6 56.1 + - - +
242A ASP* 4.0 1.4 - - - +
----------------------------------------------------------
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