Contacts of the helix formed by residues 228 - 247 (chain A) in PDB entry 3PMM
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 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 4.9 0.6 - - - +
213A HIS* 3.3 42.8 - + + +
226A ALA* 3.2 10.5 + - + +
227A ARG* 1.3 73.6 - - - +
229A ALA* 1.3 67.6 + - - +
230A ARG* 3.6 44.6 - - + +
231A GLY* 3.2 30.1 + - - -
232A ASN* 3.0 26.8 + - - +
234A TRP* 5.2 4.7 - + - -
281A THR* 3.2 34.3 + - - -
282A LEU* 4.3 2.5 - - + -
291A GLU* 5.8 0.6 + - - -
340A SER* 5.0 3.8 + - - -
343A THR* 3.4 38.3 + - + +
352A TYR* 3.6 34.0 + + + -
355A ILE* 6.0 1.4 - - - +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ARG 3.7 2.0 + - - -
228A TRP* 1.3 71.0 - - - +
230A ARG* 1.3 66.1 + - - +
232A ASN 3.1 2.3 + - - -
233A SER* 2.9 18.4 + - - -
279A TRP* 4.8 4.3 - - + +
280A HIS 3.4 23.8 - - - +
281A THR* 2.8 19.8 + - - +
283A LEU* 3.7 20.2 - - + -
291A GLU* 5.0 1.6 - - + +
294A ALA* 3.4 18.8 - - + -
298A PHE* 3.2 10.9 - - + -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 5.2 2.8 - - - -
228A TRP* 3.6 26.7 - - + +
229A ALA* 1.3 77.4 - - - +
231A GLY* 1.3 62.6 + - - +
233A SER* 2.7 24.5 + - - +
234A TRP* 3.4 29.8 + - + +
291A GLU* 3.4 9.2 + - - +
293A SER* 2.9 27.8 + - - -
294A ALA* 3.3 14.2 - - + +
340A SER* 2.8 27.0 + - - -
341A PHE 3.0 26.9 + - - -
342A GLY* 4.4 0.4 - - - -
343A THR* 3.6 14.3 + - - +
362A TYR* 3.2 31.8 + - - -
366A MSE 4.1 12.1 - - + -
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 3.2 36.3 - - - +
213A HIS* 4.9 0.2 - - - -
228A TRP* 3.2 32.0 + - - -
229A ALA 3.2 0.4 - - - -
230A ARG* 1.3 75.9 - - - +
232A ASN* 1.3 60.6 + - - +
234A TRP* 3.3 19.8 + - - +
235A LEU* 3.4 4.5 - - - +
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Residues in contact with ASN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 4.4 1.6 + - - -
210A LEU* 3.7 5.5 - - - +
211A TRP* 2.8 49.7 + - - +
227A ARG* 3.8 1.4 - - - +
228A TRP 3.0 34.3 + - - +
229A ALA 3.5 4.5 - - - +
231A GLY* 1.3 75.9 - - - +
233A SER* 1.3 63.3 + - - +
235A LEU* 3.0 16.3 + - - +
236A THR* 3.2 2.8 + - - -
265A GLN* 3.0 37.7 + - - +
283A LEU* 3.7 21.9 - - + +
298A PHE* 3.7 4.5 - - + -
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA 2.9 9.4 + - - -
230A ARG* 2.7 20.3 + - - -
232A ASN* 1.3 77.3 - - - +
234A TRP* 1.3 61.9 + - - +
236A THR* 3.2 3.8 + - - -
237A MSE 3.0 28.6 + - - +
294A ALA* 3.5 23.3 + - - -
297A GLY* 4.0 2.2 - - - -
298A PHE* 3.3 24.9 - - - -
366A MSE 3.3 23.2 - - - +
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Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TRP* 3.6 37.0 - + - -
69A VAL* 4.4 8.3 - - + -
166A ASP* 4.2 3.6 - - + +
167A ASP* 3.6 37.5 - - + +
170A MSE 4.3 10.5 - - + +
171A MSE 3.7 21.5 - - + -
228A TRP* 5.2 4.8 - + - -
230A ARG* 3.4 38.2 + - + +
231A GLY* 3.3 17.4 + - - +
232A ASN 3.1 1.0 - - - -
233A SER* 1.3 79.3 + - - +
235A LEU* 1.3 58.6 + - - +
237A MSE 3.7 36.9 - - + +
238A VAL* 3.1 31.3 + - - +
366A MSE 3.5 28.5 - - + -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 3.8 27.4 - - + +
169A LEU* 3.5 31.9 - - + -
211A TRP* 3.5 48.2 - - + -
231A GLY 3.4 19.3 - - - +
232A ASN* 3.0 10.9 + - - +
234A TRP* 1.3 76.8 - - - +
236A THR* 1.3 66.1 + - - +
237A MSE 3.1 0.2 - - - -
238A VAL* 3.9 7.4 - - + -
239A ILE* 3.1 41.6 + - + +
265A GLN* 4.2 8.1 - - - +
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ASN 3.2 10.0 + - - -
233A SER 3.2 6.2 + - - -
235A LEU* 1.3 77.0 - - - +
237A MSE 1.3 58.1 + - - +
240A PRO* 2.9 26.7 - - - +
262A LEU* 4.1 6.7 - - + +
265A GLN* 2.7 24.7 + - - +
266A ILE* 4.2 20.4 - - + -
269A LEU* 4.4 1.3 - - + -
297A GLY 4.5 0.2 - - - -
298A PHE* 3.3 29.7 - - + +
301A GLY* 3.2 27.9 - - - -
302A ILE* 4.2 8.5 - - + +
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Residues in contact with MSE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 5.1 0.4 - - + -
72A TYR* 5.6 0.2 - - + -
170A MSE 3.7 33.4 - - + -
233A SER 3.0 16.8 + - - +
234A TRP* 3.7 36.3 - - + +
236A THR* 1.3 77.5 - - - +
238A VAL* 1.3 62.7 + - - +
240A PRO* 3.4 9.4 - - - +
241A ASP* 3.5 20.3 + - - +
297A GLY* 3.3 36.1 - - - +
300A TYR* 3.8 29.2 - - + -
301A GLY* 4.2 0.2 - - - -
366A MSE 4.3 7.9 - - - -
369A LEU* 4.3 20.2 - - + -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.7 44.0 - - + +
170A MSE 3.7 21.8 - - - +
174A LEU* 4.0 18.6 - - + -
196A PHE* 4.0 17.5 - - + -
234A TRP 3.1 22.0 + - - +
235A LEU* 3.8 11.9 - - + +
237A MSE 1.3 75.4 - - - +
239A ILE* 1.3 67.6 + - + +
241A ASP* 3.3 2.6 + - - -
242A PHE* 2.8 29.3 + - - +
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 5.7 0.2 - - + -
196A PHE* 4.0 24.0 - - + -
200A VAL* 5.9 1.1 - - + -
211A TRP* 4.6 7.2 - - + +
235A LEU* 3.1 29.5 + - + +
238A VAL* 1.3 79.7 - - + +
240A PRO* 1.3 71.8 - - + +
242A PHE* 3.7 1.2 - - - +
243A LEU* 2.9 43.5 + - + +
258A LEU* 3.8 26.2 - - + +
261A VAL* 4.4 23.6 - - + -
262A LEU* 4.0 22.0 - - + -
265A GLN* 5.8 2.5 - - + +
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Residues in contact with PRO 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A THR 2.9 30.1 - - - +
237A MSE 3.4 7.4 - - - +
239A ILE* 1.3 91.9 - - + +
241A ASP* 1.3 56.6 + - - +
243A LEU* 4.4 0.9 - - + -
244A GLU* 3.0 29.1 + - - +
262A LEU* 3.9 15.5 - - + -
301A GLY* 3.8 17.0 - - - +
304A LYS* 3.8 24.7 - - + -
305A ALA* 4.2 4.5 - - + +
310A TYR* 3.7 25.3 - - + -
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Residues in contact with ASP 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A TYR* 2.6 35.1 + - - +
170A MSE 5.0 1.7 - - - +
174A LEU* 3.8 22.4 - - + +
237A MSE 3.5 12.4 + - - +
238A VAL 3.3 6.8 + - - +
239A ILE 3.3 0.6 - - - -
240A PRO* 1.3 76.9 - - - +
242A PHE* 1.3 62.9 + - - +
244A GLU* 3.4 9.7 + - - +
245A LEU* 3.0 22.7 + - - +
300A TYR* 2.9 24.6 + - - -
304A LYS* 2.7 30.9 + - - +
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Residues in contact with PHE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 4.0 16.0 - - + +
177A ALA* 3.8 27.6 - - + -
189A VAL 5.2 0.7 - - - -
192A ALA* 4.0 6.5 - - + -
193A THR* 3.5 36.6 - - + -
196A PHE* 3.5 37.5 - + + -
238A VAL 2.8 21.4 + - - +
239A ILE 3.7 2.7 - - - +
241A ASP* 1.3 71.4 - - - +
243A LEU* 1.3 60.7 + - - +
245A LEU* 3.1 4.7 + - + +
246A VAL* 2.9 56.4 + - + +
248A LEU* 6.2 0.2 - - + -
254A VAL* 5.6 1.6 - - + -
258A LEU* 3.9 29.8 - - + -
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ILE* 2.9 39.2 + - + +
240A PRO* 3.7 0.9 - - + +
242A PHE* 1.3 75.8 - - - +
244A GLU* 1.3 64.6 + - - +
246A VAL* 3.5 11.9 - - + +
247A ASP* 3.0 23.0 + - - -
248A LEU* 4.5 0.9 + - + -
255A ARG* 4.0 40.4 - - + +
258A LEU* 4.2 18.4 - - + -
259A ILE* 3.5 26.5 - - + +
262A LEU* 4.7 2.2 - - + -
310A TYR* 3.5 32.4 + - + +
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 5.4 0.9 + - - -
240A PRO 3.0 17.3 + - - +
241A ASP* 3.6 7.4 - - - +
243A LEU* 1.3 76.9 - - - +
245A LEU* 1.3 63.7 + - - +
247A ASP* 3.6 13.9 + - - +
304A LYS* 2.8 36.8 + - - -
307A ARG* 4.8 4.9 + - - -
308A LYS* 3.3 29.1 + - - +
310A TYR* 3.1 12.8 + - - +
382A FMT 3.8 20.3 - - - +
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 4.9 7.0 - - - +
174A LEU* 4.0 15.9 - - + -
177A ALA* 3.6 19.3 - - + -
178A LYS* 3.4 55.0 - - + +
181A LYS* 3.8 31.0 - - + +
189A VAL* 6.5 0.2 - - + -
241A ASP 3.0 14.3 + - - +
242A PHE* 3.1 9.8 + - + +
244A GLU* 1.3 80.2 - - - +
246A VAL* 1.3 63.6 + - + +
247A ASP* 3.4 4.2 + - - +
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LYS* 4.2 17.7 + - - +
189A VAL* 4.1 20.9 - - + -
193A THR* 4.8 2.2 - - - +
242A PHE* 2.9 61.9 + - + +
243A LEU* 3.5 16.4 - - + +
245A LEU* 1.3 77.2 - - + +
247A ASP* 1.3 72.1 + - - +
248A LEU* 3.2 37.7 + - + +
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Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU 3.0 15.8 + - - -
244A GLU 3.8 11.8 - - - +
245A LEU 3.3 3.8 - - - +
246A VAL* 1.3 80.2 - - - +
248A LEU* 1.3 64.4 + - - +
249A PRO* 4.0 2.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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