Contacts of the helix formed by residues 229 - 250 (chain A) in PDB entry 3FZF
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 GLY 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A LEU* 4.1 10.8 - - - -
201A GLY 4.0 5.2 - - - -
202A GLY 3.5 16.4 - - - -
203A GLY 4.3 0.2 - - - -
204A THR 4.7 0.2 - - - -
228A LEU* 1.3 76.9 - - - +
230A GLY* 1.3 66.2 + - - -
231A GLU 3.2 2.7 - - - -
232A ASP* 2.9 25.0 + - - +
233A PHE* 3.5 16.3 + - - -
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Residues in contact with GLY 230 (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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201A GLY 3.2 12.7 + - - -
202A GLY 3.2 1.8 + - - -
229A GLY* 1.3 68.9 - - - -
231A GLU* 1.3 66.7 + - - +
233A PHE* 3.0 26.4 + - - -
234A ASP* 3.1 9.7 + - - +
271A LYS* 3.1 18.3 + - - -
340A SER* 3.6 7.5 + - - -
401A ATP 3.6 15.7 - - - -
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Residues in contact with GLU 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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202A GLY* 3.2 27.8 + - - +
203A GLY* 5.2 0.7 - - - -
230A GLY* 1.3 76.4 - - - +
232A ASP* 1.3 60.4 + - - +
234A ASP* 3.3 17.4 + - + +
235A ASN* 3.0 37.8 + - - +
264A ARG* 5.7 8.8 - - - -
268A GLU* 5.3 3.6 - - - +
401A ATP 4.1 7.5 + - - -
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Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A HIS 3.6 9.3 - - - +
228A LEU* 3.3 16.0 + - + -
229A GLY* 2.9 30.2 + - - +
230A GLY 3.1 0.2 - - - -
231A GLU* 1.3 78.0 - - - +
233A PHE* 1.3 66.4 + - - +
235A ASN* 3.5 17.9 + - - +
236A ARG* 3.4 26.9 + - - +
306A ASN* 3.9 0.2 + - - -
309A LEU* 3.9 17.2 - - + +
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Residues in contact with PHE 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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200A LEU* 4.0 27.8 - - + -
228A LEU* 3.9 21.1 - - + -
229A GLY* 3.8 16.6 - - - -
230A GLY* 3.0 22.5 + - - +
232A ASP* 1.3 74.0 - - - +
234A ASP* 1.3 63.2 + - - +
236A ARG 3.6 1.0 + - - -
237A MET* 3.4 21.1 + - - +
271A LYS* 4.3 5.4 - - + -
302A PHE* 4.2 13.2 - - + -
306A ASN* 3.2 35.4 - - - +
309A LEU* 4.0 10.1 - - + -
310A PHE* 3.8 26.2 - + - -
313A THR* 5.0 2.2 - - + -
340A SER* 4.1 3.4 - - - -
343A ILE* 3.6 30.1 - - + -
346A ILE* 4.2 0.7 - - + -
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Residues in contact with ASP 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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230A GLY 3.1 4.3 + - - -
231A GLU* 3.4 19.0 - - + +
233A PHE* 1.3 74.3 - - - +
235A ASN* 1.3 60.1 + - - +
237A MET* 3.0 11.9 + - - +
238A VAL* 2.9 31.8 + - - +
264A ARG* 4.5 18.7 - - + +
267A CYS* 4.5 1.5 - - + +
268A GLU* 2.8 42.6 + - - +
271A LYS* 2.6 40.3 + - - +
401A ATP 5.3 0.2 + - - -
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Residues in contact with ASN 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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231A GLU* 3.0 25.3 + - - +
232A ASP* 3.6 23.9 + - - +
233A PHE 3.4 0.4 - - - -
234A ASP* 1.3 74.5 - - - +
236A ARG* 1.3 59.7 + - + +
238A VAL* 3.2 3.3 + - - +
239A ASN* 2.9 41.7 + - - +
264A ARG* 2.9 28.5 + - - +
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Residues in contact with ARG 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 ASP 3.4 15.5 + - - +
233A PHE 3.9 1.6 - - - +
234A ASP 3.3 0.4 - - - -
235A ASN* 1.3 77.4 - - + +
237A MET* 1.3 57.5 + - - +
239A ASN* 3.6 13.8 + - - +
240A HIS* 3.1 27.5 + - - +
305A LEU* 2.9 44.0 + - + +
306A ASN* 3.5 20.8 - - - +
308A ASP* 2.7 44.3 + - - -
309A LEU* 3.3 25.6 - - + +
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Residues in contact with MET 237 (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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233A PHE 3.4 11.4 + - - +
234A ASP* 3.0 12.7 + - - +
236A ARG* 1.3 74.2 - - - +
238A VAL* 1.3 67.3 + - - +
240A HIS* 3.1 8.4 + - - +
241A PHE* 2.8 31.9 + - + -
267A CYS* 3.6 46.2 - - - +
270A ALA* 4.3 2.9 - - + -
271A LYS* 4.0 15.3 - - - +
274A LEU* 4.5 0.9 - - + -
297A ILE* 4.1 28.5 - - + -
302A PHE* 3.6 38.4 - - + -
305A LEU* 4.4 10.5 - - + -
306A ASN* 4.9 0.4 - - - +
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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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234A ASP 2.9 20.9 + - - +
235A ASN* 3.6 7.2 - - - +
237A MET* 1.3 72.1 - - - +
239A ASN* 1.3 59.1 + - - +
241A PHE* 3.2 0.9 + - - +
242A ILE* 2.7 57.2 + - + +
260A VAL* 4.8 9.4 - - + +
263A LEU* 4.5 11.0 - - + -
264A ARG* 3.9 57.7 - - + +
267A CYS* 4.0 10.3 - - + -
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Residues in contact with ASN 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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235A ASN* 2.9 30.9 + - - +
236A ARG* 3.7 15.2 - - - +
238A VAL* 1.3 77.5 - - - +
240A HIS* 1.3 63.8 + - - +
242A ILE* 3.5 9.5 + - - +
243A ALA* 3.1 26.2 + - - +
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Residues in contact with HIS 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 ARG 3.1 16.9 + - - +
237A MET 3.1 2.4 + - - +
239A ASN* 1.3 79.2 - - - +
241A PHE* 1.3 96.4 + + - +
243A ALA* 3.4 5.5 + - - +
244A GLU* 3.1 35.4 + - - +
247A ARG* 4.7 5.8 + - - -
296A SER 5.2 2.0 + - - -
297A ILE* 4.1 9.1 - - + +
301A ARG* 3.3 52.4 + - + +
305A LEU* 3.7 25.5 - - + +
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Residues in contact with PHE 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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237A MET* 2.8 33.8 + - + +
240A HIS* 1.3 94.6 - + - +
242A ILE* 1.3 58.7 + - - +
244A GLU* 3.0 14.8 + - - +
245A PHE* 2.8 28.9 + - - +
263A LEU* 3.9 21.3 - - + -
267A CYS* 3.4 31.4 - - - -
282A ILE* 3.8 13.7 - - + -
293A PHE* 3.7 13.5 - + + -
295A THR* 3.5 34.3 - - + -
296A SER 4.1 6.1 - - - -
297A ILE* 3.7 27.6 - - + -
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Residues in contact with ILE 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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238A VAL* 2.7 44.6 + - + +
239A ASN* 4.0 9.0 - - - +
241A PHE* 1.3 71.5 - - - +
243A ALA* 1.3 57.8 + - - +
245A PHE* 3.4 8.7 + - - +
246A LYS* 3.2 43.9 + - + +
252A ASP* 4.5 1.8 - - - +
253A ILE* 4.0 31.4 - - + +
254A SER* 3.1 30.7 - - - +
260A VAL* 4.9 6.3 - - + -
263A LEU* 4.2 3.3 - - + +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ASN 3.1 18.3 + - - +
240A HIS* 3.7 6.1 - - - +
242A ILE* 1.3 76.5 - - - +
244A GLU* 1.3 60.9 + - - +
246A LYS* 3.7 9.5 - - - +
247A ARG* 3.0 40.5 + - - +
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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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240A HIS* 3.1 26.6 + - - +
241A PHE* 3.0 20.2 + - - +
243A ALA* 1.3 75.4 - - - +
245A PHE* 1.3 65.2 + - - +
247A ARG* 3.4 20.7 + - - +
248A LYS* 3.3 52.1 + - + +
293A PHE* 3.8 15.6 - - + -
294A TYR 4.8 0.2 - - - +
295A THR* 2.7 32.7 + - - -
296A SER 5.3 0.7 - - - +
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Residues in contact with PHE 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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241A PHE 2.8 15.5 + - - +
242A ILE* 3.7 9.4 - - - +
243A ALA 3.3 0.4 - - - -
244A GLU* 1.3 77.5 - - - +
246A LYS* 1.3 55.2 + - - +
249A HIS* 2.9 54.8 + + + +
251A LYS* 3.6 28.5 - - + +
253A ILE* 3.4 30.3 - - + -
263A LEU* 6.4 0.2 - - + -
287A LEU* 4.1 11.4 - - + -
288A TYR* 4.0 15.5 - + + -
291A ILE* 3.4 39.3 - - + -
293A PHE* 3.3 43.5 - + + -
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Residues in contact with LYS 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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242A ILE* 3.2 28.5 + - + +
243A ALA* 3.7 9.0 - - - +
244A GLU 3.3 0.2 - - - -
245A PHE* 1.3 74.0 - - - +
247A ARG* 1.3 64.9 + - - +
250A LYS* 2.7 35.5 + - - +
251A LYS 3.4 19.3 - - - +
252A ASP* 3.3 40.3 + - - +
254A SER* 5.2 0.6 + - - -
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Residues in contact with ARG 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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240A HIS* 4.7 5.5 + - - -
243A ALA* 3.0 22.7 + - - +
244A GLU* 3.4 34.6 + - - +
246A LYS* 1.3 77.2 - - - +
248A LYS* 1.3 72.4 + - + +
250A LYS* 4.6 8.3 - - - +
301A ARG* 5.1 11.3 - - - +
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Residues in contact with LYS 248 (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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244A GLU* 3.3 43.9 + - + +
246A LYS 3.2 0.4 - - - -
247A ARG* 1.3 91.2 - - + +
249A HIS* 1.3 80.3 + - + +
250A LYS* 3.9 0.7 - - - -
293A PHE* 5.6 3.3 - - + -
294A TYR 5.0 7.5 + - - -
295A THR* 5.8 0.4 - - - +
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Residues in contact with HIS 249 (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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245A PHE* 2.9 60.5 + + + +
248A LYS* 1.3 95.5 + - + +
250A LYS* 1.3 73.0 + - - +
251A LYS* 3.1 9.3 + - - +
291A ILE* 3.4 36.1 - - + +
292A ASP 4.0 10.3 + - - -
293A PHE* 4.7 5.6 - + - -
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Residues in contact with LYS 250 (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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246A LYS* 2.7 30.6 + - - +
247A ARG* 4.6 8.5 - - - +
248A LYS 5.5 0.2 - - - -
249A HIS* 1.3 74.8 - - - +
251A LYS* 1.3 68.2 + - - +
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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