Contacts of the helix formed by residues 234 - 257 (chain A) in PDB entry 1PBW
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 234 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 4.1 23.1 - - + -
228A ARG* 5.7 3.0 - - + +
232A ILE 3.5 2.1 + - - -
233A PRO* 1.3 72.0 - - - +
235A GLN* 1.3 63.5 + - - +
236A TYR 3.3 0.7 + - - -
237A TRP* 3.3 34.3 + + - +
238A LEU* 3.2 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.8 16.6 - - + +
119A ALA* 3.1 26.0 + - + +
122A PHE* 2.8 62.0 + - + +
123A ALA* 3.6 12.5 - - - +
124A PRO* 3.9 11.9 - - + +
233A PRO* 3.1 9.9 + - - +
234A HIS* 1.3 81.1 + - - +
236A TYR* 1.3 60.0 + - + +
238A LEU* 4.0 1.3 - - - -
239A THR* 2.7 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 2.5 40.2 + - - -
118A LEU* 3.8 21.9 + - + -
119A ALA 4.3 9.2 - - - -
195A ASN* 3.6 19.8 + - + +
196A PRO 3.4 18.6 - - - -
197A VAL* 3.5 25.8 - - - +
199A PRO* 3.6 15.3 - - + -
227A ILE* 4.3 8.1 - - + -
232A ILE* 3.7 15.0 - - + -
233A PRO* 3.2 40.9 + - + +
235A GLN* 1.3 77.4 - - + +
237A TRP* 1.3 57.5 + - - +
239A THR* 3.8 1.9 - - - -
240A LEU* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU* 6.2 0.7 - - + -
224A LYS* 3.9 33.2 - - + -
227A ILE* 3.5 34.6 + - + +
228A ARG* 3.8 45.4 - - + +
233A PRO 4.3 0.8 + - - -
234A HIS* 3.3 36.3 + + - +
236A TYR* 1.3 78.7 - - - +
238A LEU* 1.3 60.2 + - + +
240A LEU* 3.1 24.1 + - + +
241A GLN* 2.8 65.7 + - + +
244A LEU* 5.4 3.4 - - + -
293A LEU* 5.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 3.9 22.0 - - + -
124A PRO* 4.0 15.0 - - + -
126A ASP 4.0 6.3 - - - +
127A ILE* 3.7 26.4 - - + +
234A HIS* 3.2 52.2 + - + +
235A GLN 4.0 3.8 - - - +
237A TRP* 1.3 79.3 - - + +
239A THR* 1.3 56.1 + - - +
241A GLN* 3.2 9.1 + - + +
242A TYR* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.7 31.1 - - + +
122A PHE* 3.6 17.7 - - - -
127A ILE 5.1 0.4 - - - -
129A PRO* 3.7 7.6 - - + +
132A LEU* 4.0 22.9 - - + -
189A TYR* 5.6 1.6 - - + -
190A LEU* 5.9 0.2 - - + -
197A VAL* 4.2 8.5 - - + -
235A GLN 2.7 22.6 + - - -
236A TYR 3.8 3.4 - - - -
238A LEU* 1.3 71.9 - - - +
240A LEU* 1.3 66.9 + - - +
242A TYR* 3.2 7.3 + - - +
243A LEU* 3.1 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 3.9 20.5 - - + +
198A ILE* 4.3 20.6 - - + -
223A LEU* 4.5 15.3 - - + -
227A ILE* 4.0 22.0 - - + -
236A TYR 3.0 17.8 + - - +
237A TRP* 3.1 24.9 + - + +
239A THR* 1.3 77.1 - - - +
241A GLN* 1.3 60.6 + - - +
243A LEU* 3.4 5.7 + - + +
244A LEU* 3.0 47.1 + - + +
272A LEU* 4.4 13.2 - - + -
290A ILE* 4.4 11.2 - - + -
293A LEU* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TRP* 2.8 61.9 + - + +
238A LEU* 3.5 13.2 - - + +
240A LEU* 1.3 68.9 - - - +
242A TYR* 1.3 66.9 + - - +
244A LEU* 3.2 10.7 + - - +
245A LYS* 3.1 51.7 + - - +
293A LEU* 5.9 1.6 - - - +
297A GLU* 3.0 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.9 23.3 - - + +
128A ALA* 3.6 20.9 - - + -
132A LEU* 3.9 25.1 - - + -
133A ILE* 3.4 40.7 + - + +
136A VAL* 3.6 41.5 - - + +
137A GLU* 4.2 6.8 + - - +
238A LEU 2.9 17.0 + - - +
239A THR* 3.2 4.9 + - - +
241A GLN* 1.3 78.5 - - - +
243A LEU* 1.3 61.0 + - - +
245A LYS* 3.4 12.3 + - + +
246A HIS* 3.2 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 3.9 19.5 - - + -
136A VAL* 4.9 2.9 - - + -
186A PHE* 3.6 37.0 - - + -
190A LEU* 4.3 8.5 - - + -
197A VAL* 4.2 11.4 - - + -
239A THR* 3.1 28.3 + - + +
240A LEU* 3.8 7.9 - - + +
242A TYR* 1.3 74.3 - - + +
244A LEU* 1.3 67.0 + - + +
246A HIS* 3.1 6.8 + - + +
247A PHE* 3.0 43.4 + - + -
272A LEU* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TRP* 5.4 1.6 - - + -
240A LEU* 3.0 43.6 + - + +
241A GLN* 3.2 15.7 + - - +
243A LEU* 1.3 76.7 - - - +
245A LYS* 1.3 56.7 + - - +
247A PHE* 3.3 10.3 + - + +
248A PHE* 2.8 28.9 + - - +
272A LEU* 5.9 0.2 - - + -
290A ILE* 4.3 15.5 - - + +
293A LEU* 3.9 38.1 - - + +
294A ILE* 3.7 26.6 - - + +
297A GLU* 3.5 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 6.2 2.6 - - - +
241A GLN* 3.1 36.6 + - - +
242A TYR* 3.6 15.1 - - + +
244A LEU* 1.3 73.5 - - - +
246A HIS* 1.3 59.3 + - - +
248A PHE* 3.4 8.4 + - - +
249A LYS* 3.0 28.8 + - - +
297A GLU* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 3.6 26.1 - - + +
139A ILE* 4.1 10.5 - - + -
140A GLU* 2.7 43.2 + - + +
150A TYR* 2.7 28.8 + - - -
186A PHE* 4.2 10.8 - + - -
242A TYR* 3.2 11.8 + - + +
243A LEU* 3.1 10.6 + - + +
245A LYS* 1.3 73.7 - - - +
247A PHE* 1.3 79.8 + + - +
249A LYS* 3.2 4.4 + - - +
250A LEU* 3.0 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TYR* 5.2 0.2 - + - -
186A PHE* 4.2 11.2 - + - -
190A LEU* 5.6 0.7 - - + -
243A LEU* 3.0 41.2 + - + +
244A LEU* 3.7 7.9 - - + +
246A HIS* 1.3 94.8 - + - +
248A PHE* 1.3 64.9 + - - +
250A LEU* 3.3 4.1 + - + +
251A SER* 3.1 20.6 + - - -
264A LEU* 3.4 37.1 - - + +
268A PHE* 3.7 49.6 - + + -
272A LEU* 4.6 14.4 - - + -
290A ILE* 5.4 1.6 - - + -
294A ILE* 3.9 31.2 - - + -
----------------------------------------------------------
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 LEU 2.8 17.3 + - - +
245A LYS* 3.6 5.6 - - - +
247A PHE* 1.3 74.3 - - - +
249A LYS* 1.3 67.4 + - + +
251A SER* 2.7 25.4 + - - -
252A GLN* 3.1 48.1 + - + -
294A ILE* 3.2 23.8 - - + +
295A SER* 3.7 20.9 - - - -
297A GLU* 3.6 24.5 - - + -
298A TRP* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU* 3.3 36.5 + - + +
144A LEU* 4.4 22.2 - - + +
245A LYS 3.0 15.5 + - - +
246A HIS* 3.4 9.6 - - - +
248A PHE* 1.3 76.9 - - - +
250A LEU* 1.3 63.6 + - - +
252A GLN* 3.0 27.2 + - + +
253A THR* 3.9 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 5.5 0.9 - - + -
140A GLU* 4.8 2.0 - - + +
143A GLY 5.4 0.2 - - - -
144A LEU* 3.4 29.2 - - + -
149A LEU* 4.5 13.9 - - + -
150A TYR* 3.6 20.9 - - + -
246A HIS* 3.0 53.1 + - + +
247A PHE* 3.6 7.9 - - + +
248A PHE 3.3 0.2 - - - -
249A LYS* 1.3 76.2 - - - +
251A SER* 1.3 60.5 + - - +
253A THR 3.2 7.1 + - - -
257A ASN* 2.8 36.6 + - - +
259A LEU* 4.0 15.3 - - + -
264A LEU* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE 3.1 12.8 + - - -
248A PHE* 2.7 27.9 + - - -
250A LEU* 1.3 73.5 - - - +
252A GLN* 1.3 68.0 + - - +
254A SER* 2.9 23.0 - - - -
259A LEU 3.0 21.0 + - - -
260A ASN* 4.2 2.5 - - - -
261A ALA* 3.9 22.7 - - - -
264A LEU* 4.6 0.4 - - - -
294A ILE* 4.6 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 3.1 64.2 + - + +
249A LYS* 3.0 16.8 + - + +
251A SER* 1.3 86.5 + - - +
253A THR* 1.3 58.0 + - - +
254A SER* 3.4 1.4 + - - -
255A SER* 5.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.9 23.1 - - + +
145A GLU* 3.7 20.0 - - + -
249A LYS 3.9 4.0 + - - -
250A LEU* 3.2 3.3 + - - -
251A SER 3.2 0.8 - - - -
252A GLN* 1.3 78.0 + - - +
254A SER* 1.3 56.3 + - - +
255A SER* 3.2 7.2 - - - +
256A LYS* 3.0 37.2 + - + +
257A ASN* 2.9 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU 3.6 1.0 + - - -
251A SER 2.9 21.0 + - - -
252A GLN 3.4 1.4 + - - -
253A THR* 1.3 72.2 - - - +
255A SER* 1.3 65.8 + - - +
256A LYS 3.1 0.2 - - - -
257A ASN* 3.2 12.6 - - - -
258A LEU* 2.9 25.3 + - - +
259A LEU 3.2 23.4 + - - -
260A ASN* 3.3 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A GLN 5.3 1.4 + - - -
253A THR* 4.1 6.9 + - - -
254A SER* 1.3 81.0 - - - +
256A LYS* 1.3 76.5 + - - +
258A LEU* 3.4 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 3.3 48.5 + - + +
147A SER* 3.5 11.3 - - - -
253A THR* 3.0 23.3 + - + +
255A SER* 1.3 86.7 + - - +
257A ASN* 1.3 64.3 + - - +
258A LEU* 3.2 14.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
143A GLY 4.9 1.3 - - - +
144A LEU* 2.8 28.0 + - - +
145A GLU 4.3 0.4 + - - -
146A CYS 3.5 21.5 - - - +
147A SER* 3.4 6.2 - - - +
151A ARG* 2.6 33.3 + - - -
250A LEU* 2.8 34.5 + - - +
253A THR* 2.9 17.3 + - - -
254A SER* 3.2 10.0 - - - -
256A LYS* 1.3 72.0 - - - +
258A LEU* 1.3 55.3 + - - +
259A LEU* 2.7 42.2 + - + +
----------------------------------------------------------
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