Contacts of the helix formed by residues 233 - 247 (chain A) in PDB entry 3RC3
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 LEU 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A GLY 3.2 2.4 + - - -
232A PRO* 1.4 95.5 - - + +
234A LYS* 1.3 66.4 + - - +
235A LEU* 4.0 15.5 - - + +
236A LEU* 3.0 24.1 + - + +
237A ALA* 3.0 10.6 + - - +
275A THR* 3.8 8.9 - - - +
301A ARG* 5.0 4.0 - - - +
426A ALA 5.6 0.4 - - - +
429A MSE 3.3 41.5 - - + +
430A GLY* 4.1 6.7 - - - +
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Residues in contact with LYS 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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233A LEU* 1.3 70.8 - - - +
235A LEU* 1.3 65.2 + - + +
236A LEU 3.1 0.3 + - - -
237A ALA* 3.2 3.7 + - - +
238A HIS* 3.0 41.9 + - + +
255A THR* 3.8 11.7 - - + +
257A GLU* 2.6 46.9 + - - +
258A GLU* 3.4 21.2 + - - +
275A THR* 3.6 15.7 - - + +
401A PRO* 5.3 16.2 - - + +
636A ASP* 4.0 16.2 + - - -
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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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233A LEU* 3.2 12.9 - - + +
234A LYS* 1.3 79.5 - - + +
236A LEU* 1.3 58.4 + - - +
238A HIS* 3.5 7.8 + - + +
239A GLU* 2.9 29.2 + - - +
401A PRO* 4.0 28.3 - - + +
404A LYS* 3.9 31.2 - - + +
405A LEU* 4.1 29.6 - - + -
429A MSE 5.3 1.1 - - - +
430A GLY* 3.7 26.5 - - - +
431A LEU* 4.3 13.2 - - + -
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Residues in contact with LEU 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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229A TYR* 3.5 22.9 - - + +
231A GLY* 4.8 0.9 - - - -
232A PRO* 3.8 15.9 - - + -
233A LEU* 3.0 17.5 + - + +
235A LEU* 1.3 76.2 - - - +
237A ALA* 1.3 65.7 + - - +
239A GLU* 3.7 19.2 - - + +
240A ILE* 3.0 33.9 + - + +
291A ASP* 4.6 3.1 - - - +
429A MSE 3.4 32.3 - - + -
430A GLY* 3.7 31.4 - - - +
801A ANP 5.8 4.3 - - - +
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Residues in contact with ALA 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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229A TYR* 4.2 5.4 - - - -
233A LEU 3.0 11.4 + - - +
234A LYS 3.2 7.2 + - - +
236A LEU* 1.3 77.6 - - - +
238A HIS* 1.3 59.8 + - - +
241A PHE* 3.1 14.0 + - - +
253A LEU* 3.5 16.8 - - + +
255A THR* 4.0 8.3 - - + -
273A SER* 2.5 25.6 + - - +
274A CYS 3.8 28.9 - - - +
275A THR* 4.0 4.3 - - + +
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Residues in contact with HIS 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 LYS* 3.0 32.4 + - + +
235A LEU* 3.5 13.0 - - + +
237A ALA* 1.3 70.8 - - - +
239A GLU* 1.3 62.5 + - - +
241A PHE* 3.3 8.3 + + - +
242A GLU* 2.8 52.3 + - - +
253A LEU* 3.4 26.5 - - + +
255A THR* 4.4 2.1 - - + +
258A GLU* 2.8 42.5 + - - -
401A PRO* 6.3 2.9 - - + -
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Residues in contact with GLU 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 LEU 2.9 17.3 + - - +
236A LEU* 3.3 24.7 + - - +
238A HIS* 1.3 77.8 - - - +
240A ILE* 1.4 64.3 + - + +
242A GLU* 3.4 10.9 + - - +
243A LYS* 2.7 66.1 + - + +
430A GLY 4.1 14.0 - - - +
431A LEU* 5.2 0.2 - - - -
432A ASN* 3.0 27.6 + - - +
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Residues in contact with ILE 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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214A THR* 6.0 1.6 - - + -
218A ILE* 4.1 28.5 - - + -
221A TYR* 3.7 32.5 - - + +
222A PHE* 4.7 2.9 - - + -
229A TYR* 3.8 38.6 - - + -
236A LEU* 3.0 17.4 + - + +
239A GLU* 1.4 90.3 - - + +
241A PHE* 1.3 58.3 + - - +
243A LYS* 4.1 11.6 - - + +
244A SER* 2.9 28.9 + - - -
273A SER* 3.5 11.4 - - - +
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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 ALA 3.1 18.8 + - - +
238A HIS* 3.5 12.8 - + - +
240A ILE* 1.3 76.6 - - - +
242A GLU* 1.3 73.1 + - + +
244A SER* 3.9 0.7 - - - -
245A ASN* 2.8 43.0 + - - -
251A CYS* 3.2 32.8 - - - -
252A ASP 3.8 4.7 - - - -
253A LEU* 3.6 42.2 - - + -
260A VAL* 3.9 25.4 - - + -
262A VAL* 3.7 11.2 - - + -
273A SER* 3.6 10.9 + - - -
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Residues in contact with GLU 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 HIS* 2.8 42.5 + - - +
239A GLU* 3.7 10.1 - - - +
241A PHE* 1.3 86.6 - - + +
243A LYS* 1.3 60.4 + - + +
245A ASN* 3.4 3.6 + - - +
246A ALA* 2.9 31.3 + - - +
405A LEU* 5.8 3.8 - - - +
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Residues in contact with LYS 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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218A ILE* 6.2 0.9 - - + -
222A PHE* 3.9 19.0 - - + -
239A GLU* 2.7 59.7 + - + +
240A ILE* 4.1 10.6 - - + +
242A GLU* 1.3 72.0 - - + +
244A SER* 1.3 65.3 + - - +
246A ALA* 3.7 5.5 - - - +
247A ALA* 2.9 26.2 + - - +
432A ASN* 4.2 9.3 + - - +
801A ANP 4.8 14.1 + - - -
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Residues in contact with SER 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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221A TYR* 4.3 5.5 - - - -
222A PHE* 3.3 25.1 - - - -
240A ILE 2.9 19.1 + - - -
243A LYS* 1.3 76.7 - - - +
245A ASN* 1.3 61.4 + - - +
247A ALA* 3.1 8.2 + - - +
248A GLY 3.3 0.2 + - - -
249A VAL* 2.9 51.7 + - - +
251A CYS* 3.4 24.3 - - - +
271A HIS* 4.5 0.3 - - - +
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Residues in contact with ASN 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 40.9 + - - +
242A GLU* 4.0 3.6 - - - +
244A SER* 1.3 79.0 - - - +
246A ALA* 1.3 58.8 + - - +
248A GLY* 2.9 19.4 + - - -
249A VAL 3.6 4.0 - - - -
250A PRO* 3.5 8.3 - - - +
251A CYS* 3.0 44.0 + - - +
262A VAL* 4.0 12.7 - - - +
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Residues in contact with ALA 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 GLU 2.9 19.1 + - - +
243A LYS* 4.0 5.6 - - - +
245A ASN* 1.3 76.0 - - - +
247A ALA* 1.3 58.2 + - - +
248A GLY 3.2 1.7 + - - -
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Residues in contact with ALA 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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222A PHE* 4.6 19.1 - - + -
243A LYS 2.9 18.4 + - - +
244A SER* 3.1 7.8 + - - +
246A ALA* 1.3 74.5 - - - +
248A GLY* 1.3 61.2 + - - +
249A VAL* 3.3 10.6 + - + +
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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