Contacts of the helix formed by residues 246 - 265 (chain A) in PDB entry 3N3B
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 TRP 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 3.7 33.2 - - + -
55A LEU* 3.8 18.8 - - + -
167A TRP* 3.5 37.0 - + + -
168A LEU* 4.1 9.6 - - + -
171A TYR* 3.5 41.5 + + - -
172A PHE* 4.8 1.8 - + - -
241A TYR* 4.2 5.4 - + + -
244A THR* 3.3 35.7 - - + +
245A PRO* 1.3 99.9 - - + +
247A ALA* 1.3 65.4 + - - +
248A ASP 3.3 2.7 - - - -
249A ASP* 3.0 19.9 + - + +
250A VAL* 3.2 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A THR* 3.8 13.2 - - + +
238A ASP* 4.4 18.2 - - - +
241A TYR* 4.4 20.2 - - + +
244A THR 4.6 2.9 + - - +
245A PRO 3.6 2.0 - - - -
246A TRP* 1.3 78.1 - - - +
248A ASP* 1.3 63.9 + - - +
250A VAL* 3.4 3.9 + - - +
251A LYS* 3.2 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO 5.3 0.6 + - - -
246A TRP 3.3 1.0 - - - -
247A ALA* 1.3 81.2 - - - +
249A ASP* 1.3 61.7 + - - +
251A LYS* 3.6 19.5 + - - +
252A ALA* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TRP* 3.7 26.3 + - + -
246A TRP* 3.0 14.9 + - + +
248A ASP* 1.3 76.5 - - - +
250A VAL* 1.3 64.0 + - - +
252A ALA* 3.7 5.0 + - - +
253A PHE* 3.3 20.3 + - - +
277A GLU 5.2 1.2 - - - +
278A VAL* 4.8 1.9 - - - +
279A ASN* 3.2 45.5 + - - +
282A ILE* 4.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR 4.6 0.2 - - - +
164A SER* 3.8 35.4 - - - +
167A TRP* 3.6 40.4 - - + -
237A THR* 3.8 19.7 - - + +
241A TYR* 3.8 19.1 - - + -
246A TRP 3.2 16.1 + - - +
247A ALA 3.7 5.4 - - - +
248A ASP 3.3 0.2 - - - -
249A ASP* 1.3 75.9 - - - +
251A LYS* 1.3 58.0 + - - +
253A PHE* 3.1 4.5 + - - +
254A LEU* 2.8 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TYR* 5.0 2.0 - - - +
234A LEU* 3.7 43.4 - - + +
237A THR* 4.2 16.2 - - + -
238A ASP* 2.8 34.3 + - - -
247A ALA* 3.2 23.3 + - - +
248A ASP* 3.9 18.7 + - - +
249A ASP 3.4 0.2 - - - -
250A VAL* 1.3 75.1 - - - +
252A ALA* 1.3 58.8 + - - +
254A LEU* 3.4 11.9 + - + +
255A CYS* 3.2 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASP 3.3 15.5 + - - +
249A ASP* 3.9 7.2 - - - +
250A VAL 3.3 0.2 - - - -
251A LYS* 1.3 76.8 - - - +
253A PHE* 1.3 57.9 + - - +
255A CYS 3.5 0.7 + - - -
256A TYR* 3.2 26.3 + - - +
275A MET 3.5 19.1 - - - +
276A ALA* 3.8 8.7 - - - -
277A GLU 3.6 26.7 - - - +
278A VAL* 3.8 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 3.4 48.0 - + - -
166A PHE* 4.6 1.6 - - + -
167A TRP* 3.7 33.0 - + + -
170A MET* 5.1 0.9 - - + -
249A ASP 3.3 12.5 + - - +
250A VAL 3.1 9.1 + - - +
252A ALA* 1.3 77.8 - - - +
254A LEU* 1.3 61.0 + - - +
256A TYR* 3.7 17.6 + + - +
257A ASN* 2.7 51.2 + - - -
278A VAL* 3.6 25.3 - - + +
282A ILE* 3.7 14.4 - - + -
283A LEU* 5.1 1.8 - - + -
286A LEU* 4.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.3 45.5 - - + +
161A LEU 4.3 0.4 - - - +
163A TYR* 4.5 1.6 - - - -
164A SER* 3.8 23.1 - - - +
230A TYR* 5.2 6.7 - - + -
233A GLU* 3.8 33.4 - - + +
234A LEU* 5.1 4.7 - - + -
237A THR* 3.5 24.2 - - - +
250A VAL* 2.8 17.5 + - + +
251A LYS* 3.5 20.0 - - + +
252A ALA 3.2 0.2 - - - -
253A PHE* 1.3 75.8 - - - +
255A CYS* 1.3 54.9 + - - +
257A ASN* 3.3 3.1 + - - +
258A ALA 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TYR* 3.7 26.0 - - - -
251A LYS 3.2 18.0 + - - +
252A ALA 3.9 0.7 - - - +
253A PHE 3.5 0.2 - - - -
254A LEU* 1.3 78.7 - - - +
256A TYR* 1.3 61.1 + - - +
258A ALA* 3.5 3.0 + - - +
259A ASN* 3.2 29.6 + - - +
271A PHE* 3.7 41.3 - - + -
275A MET* 3.5 31.4 - - - +
276A ALA* 4.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA 3.2 17.8 + - - +
253A PHE* 3.7 21.5 - + - +
255A CYS* 1.3 78.6 - - - +
257A ASN* 1.3 84.4 + - - +
259A ASN* 3.6 6.6 + - - +
260A LYS* 3.5 36.3 + - + +
276A ALA* 4.0 16.1 - - + +
278A VAL* 3.6 18.4 - - + -
283A LEU* 4.0 16.5 - - + +
286A LEU* 4.3 6.9 - - + +
84D ARG* 3.4 14.8 - - - +
110D GLU* 2.7 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER 3.0 22.2 - - - +
160A PHE* 4.1 5.6 - - - +
163A TYR* 3.3 55.1 - - + +
253A PHE* 2.7 40.9 + - - +
254A LEU 3.9 3.1 - - - +
256A TYR* 1.3 87.1 - - - +
258A ALA* 1.3 59.3 - - - +
259A ASN 3.3 0.7 - - - -
260A LYS* 3.2 16.8 + - - +
261A ALA* 2.9 24.1 + - - +
286A LEU* 5.6 0.2 - - - +
85D ASN* 5.0 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.6 27.3 - - + -
226A LEU* 4.1 10.8 - - + +
254A LEU 2.8 18.5 + - - +
255A CYS 3.6 6.3 - - - +
257A ASN* 1.3 76.3 - - - +
259A ASN* 1.3 61.0 + - - +
261A ALA* 3.4 3.7 + - - +
262A LEU* 3.1 28.8 + - - +
271A PHE* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A CYS 3.2 12.9 + - - -
256A TYR* 3.7 9.3 + - - +
258A ALA* 1.3 77.3 - - - +
260A LYS* 1.3 55.5 + - + +
262A LEU* 3.2 10.3 + - - +
263A MET* 2.9 34.4 + - + +
269A PRO* 3.6 22.6 - - + +
270A LEU 3.1 8.0 + - - -
271A PHE* 3.0 51.5 + - - +
276A ALA* 4.4 10.1 - - - +
114D THR* 4.9 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER* 4.9 2.0 - - - +
256A TYR* 3.5 39.9 + - + +
257A ASN* 3.2 17.4 + - - +
259A ASN* 1.3 74.1 - - + +
261A ALA* 1.3 60.4 + - - +
263A MET* 3.3 6.4 + - - -
264A ASN* 3.0 33.3 + - - -
322A PEO 3.5 17.3 - - - +
83D ASN* 2.8 32.2 + - - +
84D ARG* 4.3 1.2 - - - +
85D ASN* 3.3 19.1 + - - +
110D GLU* 2.9 28.7 + - + +
111D LEU* 3.6 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 3.4 22.1 - - + +
156A PHE* 4.0 17.7 - - + -
159A SER* 3.8 25.7 + - - -
160A PHE* 3.9 15.0 - - + -
257A ASN 2.9 12.9 + - - +
258A ALA* 3.6 9.0 - - - +
260A LYS* 1.3 75.1 - - - +
262A LEU* 1.3 61.6 + - - +
264A ASN* 3.5 1.5 + - - -
265A LEU* 3.5 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 4.3 17.5 - - + -
222A ALA* 5.3 1.6 - - + -
223A PHE* 3.9 27.8 - - + -
226A LEU* 3.7 27.8 - - + -
258A ALA 3.1 18.9 + - - +
259A ASN* 3.4 11.7 - - - +
261A ALA* 1.3 77.4 - - - +
263A MET* 1.3 53.9 + - - +
265A LEU* 3.2 6.4 + - - +
266A GLY 3.1 8.0 + - - -
267A TYR* 2.7 44.9 + - + +
268A GLU 3.7 14.8 - - - +
270A LEU* 3.7 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLN* 4.5 1.4 + - - -
259A ASN* 2.9 24.4 + - - +
260A LYS* 3.3 12.5 + - - +
262A LEU* 1.3 74.5 - - - +
264A ASN* 1.3 65.8 + - - +
266A GLY* 3.1 9.4 + - - -
267A TYR 3.7 11.7 - - - +
269A PRO* 3.6 23.1 - - + -
13D ASN* 3.8 10.2 - - - +
16D ARG* 4.6 0.2 + - - -
110D GLU* 4.1 6.3 - - - +
111D LEU* 3.7 32.1 - - + -
112D MET* 3.2 43.7 - - + +
113D GLY 3.2 31.4 - - - +
114D THR* 3.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 4.1 6.5 - - + -
159A SER* 3.3 23.4 + - - -
193A ALA 5.2 1.0 + - - -
196A GLY 3.5 24.0 - - - +
197A TYR* 3.9 18.5 + - - +
200A GLY* 3.2 17.0 - - - -
201A TYR 4.0 0.5 + - - -
204A GLN* 2.9 18.0 + - - -
260A LYS 3.0 14.1 + - - +
261A ALA 3.6 9.9 - - - +
262A LEU 3.3 0.4 - - - -
263A MET* 1.3 77.1 - - - +
265A LEU* 1.3 55.7 - - - +
266A GLY 3.2 0.2 - - - -
322A PEO 3.4 13.2 + - - -
13D ASN* 5.6 1.1 - - - +
83D ASN* 5.4 0.6 - - - +
111D LEU* 3.6 27.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS 4.4 0.7 - - - +
152A ILE* 4.3 21.5 - - + -
155A VAL* 3.9 30.5 - - + -
156A PHE* 3.8 29.8 - - + -
200A GLY* 4.2 2.2 - - - -
203A TYR* 3.7 41.5 - - + -
204A GLN* 3.3 20.6 - - - +
222A ALA* 5.1 0.4 - - + -
261A ALA 3.5 15.7 + - - +
262A LEU* 3.2 7.7 + - - +
263A MET 3.2 0.6 - - - -
264A ASN* 1.3 74.0 - - - +
266A GLY* 1.3 60.0 + - - +
267A TYR* 3.7 28.4 + - + -
----------------------------------------------------------
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