Contacts of the helix formed by residues 238 - 253 (chain A) in PDB entry 3N2Q
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 238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TYR* 3.7 25.7 - + - -
234A PHE* 2.8 20.3 + - + +
235A THR 3.8 2.0 - - - -
237A ALA* 1.3 88.3 + - + +
239A GLY* 1.3 65.1 + - - +
240A GLU 3.4 2.2 - - - -
241A ASP* 3.3 9.6 + - + -
242A ASN* 2.9 21.8 + - - +
269A TYR* 3.2 59.0 - + + +
272A ASP* 3.3 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR* 3.2 21.0 + - - -
236A GLN 4.7 1.6 + - - -
237A ALA 4.0 0.6 - - - -
238A HIS* 1.3 73.1 - - - +
240A GLU* 1.3 51.2 + - - +
242A ASN* 3.1 8.7 + - - +
243A THR* 2.8 39.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A HIS 3.4 0.6 - - - -
239A GLY* 1.3 73.7 - - - +
241A ASP* 1.3 60.1 + - - +
243A THR* 3.5 9.8 - - - -
244A LYS* 3.1 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PHE* 4.3 2.2 - - + -
238A HIS* 3.3 12.6 + - + +
239A GLY 3.3 0.4 - - - -
240A GLU* 1.3 76.6 - - - +
242A ASN* 1.3 62.2 + - - +
244A LYS* 3.0 34.9 + - - +
245A ILE* 3.0 19.5 + - - +
269A TYR* 2.8 40.6 + - - +
274A MSE 3.6 25.7 + - + +
307A PRO* 5.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR* 3.2 28.6 - - - -
230A PRO* 5.3 2.6 - - - +
234A PHE* 3.5 21.0 - - + -
235A THR* 3.3 33.6 + - - +
238A HIS 2.9 14.8 + - - +
239A GLY* 3.2 12.7 + - - +
241A ASP* 1.3 74.2 - - - +
243A THR* 1.3 59.9 + - - +
245A ILE* 3.1 5.0 + - - +
246A ASN* 2.8 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLY 2.8 16.4 + - - -
240A GLU* 3.5 14.1 - - - +
241A ASP 3.2 0.2 - - - -
242A ASN* 1.3 79.2 + - - +
244A LYS* 1.3 56.0 + - + +
246A ASN* 3.4 11.3 + - + +
247A ASN* 2.9 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU* 3.1 20.5 + - - +
241A ASP* 3.0 26.2 + - - +
243A THR* 1.3 75.8 - - + +
245A ILE* 1.3 58.2 + - + +
247A ASN* 3.1 13.3 + - - +
248A PHE* 2.8 26.7 + - - +
274A MSE 5.8 1.1 - - + -
305A LYS* 3.5 24.3 - - - +
306A LEU* 4.1 7.8 - - + +
307A PRO* 4.3 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR* 3.6 34.1 - - + -
234A PHE* 4.0 29.4 - - + -
241A ASP 3.0 10.8 + - - +
242A ASN 3.1 5.1 + - - +
244A LYS* 1.3 73.4 - - - +
246A ASN* 1.3 66.9 + - - +
248A PHE* 3.0 7.9 + - + +
249A ALA* 2.8 22.5 + - - +
263A VAL* 4.5 3.1 - - + -
265A ALA* 5.5 0.4 - - + -
267A VAL* 4.1 5.8 - - + -
274A MSE 4.5 7.2 - - + -
277A LEU* 3.8 36.8 - - + -
279A MSE 4.5 20.2 - - - -
306A LEU* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR* 2.5 39.4 + - - -
242A ASN* 2.8 38.7 + - - +
243A THR* 3.6 11.4 + - + +
245A ILE* 1.3 75.7 - - - +
247A ASN* 1.3 64.1 + - - +
249A ALA* 3.2 5.8 + - - +
250A LYS* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 2.9 35.1 + - - +
244A LYS* 3.3 11.7 - - - +
246A ASN* 1.3 71.7 - - - +
248A PHE* 1.3 69.0 + - - +
250A LYS* 3.1 25.7 + - - +
251A GLU* 3.2 16.2 + - - +
305A LYS* 3.5 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS 2.8 15.9 + - - +
245A ILE* 3.0 10.5 + - + +
247A ASN* 1.3 71.9 - - - +
249A ALA* 1.3 57.8 + - - +
251A GLU* 2.8 32.1 + - - +
252A ILE* 3.5 30.2 + - + +
263A VAL* 4.6 8.3 - - + -
279A MSE 3.4 38.6 - - + -
298A ALA* 3.3 28.3 - - + -
301A GLY* 3.5 21.3 - - - -
302A MSE 3.9 11.7 - - + -
305A LYS* 3.8 8.9 - - + +
306A LEU* 4.0 20.2 - - + -
314A LEU* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TYR* 4.7 2.0 - - - +
245A ILE 2.8 15.2 + - - +
246A ASN* 3.5 11.4 - - - +
248A PHE* 1.3 80.0 - - - +
250A LYS* 1.3 61.8 + - + +
252A ILE* 3.2 24.4 - - - +
253A LYS* 3.3 9.1 + - - +
260A PHE* 5.4 10.5 - - + -
261A ILE* 4.7 8.3 + - - +
263A VAL* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ASN* 3.0 26.3 + - - +
247A ASN* 3.1 20.3 + - - +
249A ALA* 1.3 76.1 - - + +
251A GLU* 1.3 68.2 + - - +
253A LYS* 3.2 43.7 + - + +
254A GLY 4.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ASN* 3.4 16.4 - - - +
248A PHE* 2.8 13.8 + - - +
250A LYS* 1.3 84.1 - - - +
252A ILE* 1.3 64.0 + - + +
254A GLY* 3.2 11.8 + - - -
297A LEU* 3.8 21.2 - - + +
301A GLY* 4.6 19.5 - - - -
304A ASP* 5.5 3.6 - - + +
305A LYS* 3.9 28.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 4.0 19.3 - - + +
249A ALA* 3.2 17.3 - - - +
251A GLU* 1.3 73.2 - - + +
253A LYS* 1.3 52.3 + - - +
254A GLY 2.9 5.6 - - - -
255A PHE* 2.8 33.8 + - - +
261A ILE* 3.7 29.7 - - + +
263A VAL* 3.8 27.8 - - + -
281A ILE* 4.4 15.5 - - + -
294A LEU* 4.3 11.2 - - + -
297A LEU* 4.1 8.7 - - - +
298A ALA* 3.8 37.9 - - + +
314A LEU* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA 3.3 8.8 + - - +
250A LYS* 3.2 48.0 + - + +
252A ILE* 1.3 77.3 - - - +
254A GLY* 1.3 57.7 + - - +
255A PHE* 3.0 2.5 + - - -
257A ASN 3.9 1.4 + - - -
258A GLY* 3.0 48.9 + - - +
259A ASP 3.5 25.9 - - - +
260A PHE* 3.9 20.2 - - + -
261A ILE* 4.7 4.5 - - - +
----------------------------------------------------------
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