Contacts of the helix formed by residues 236 - 249 (chain A) in PDB entry 3RIE
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE 4.8 1.8 + - - -
50A MET* 3.1 32.4 + - + -
52A PRO* 4.7 12.7 - - + +
231A GLU* 3.0 38.7 + - - +
232A SER 4.6 0.4 - - - -
235A ILE* 1.3 98.4 + - + +
237A VAL* 1.3 64.3 + - - +
238A GLY* 3.1 1.6 - - - +
239A THR* 3.1 30.0 + - - +
240A ILE* 3.3 3.3 + - - +
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Residues in contact with VAL 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 LEU 3.4 25.8 - - - +
235A ILE 3.8 2.6 + - - -
236A HIS* 1.3 71.7 - - - +
238A GLY* 1.3 63.6 + - - +
240A ILE* 3.1 10.1 + - + +
241A LYS* 2.9 27.1 + - + +
313A PHE* 4.2 16.8 - - + -
314A LEU* 4.5 16.6 - - + -
317A GLU* 3.7 41.3 - - + +
318A ILE* 5.1 0.7 - - + -
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Residues in contact with GLY 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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236A HIS* 3.1 3.5 - - - +
237A VAL* 1.3 79.0 - - - +
239A THR* 1.3 54.4 + - - +
241A LYS* 3.4 14.2 + - - +
242A ASN* 2.9 37.2 + - - +
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Residues in contact with THR 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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200A PRO* 6.1 4.0 - - + -
208A PHE* 5.6 7.0 - - + -
231A GLU* 4.2 17.2 + - + +
236A HIS* 3.1 30.1 + - - +
238A GLY* 1.3 73.9 - - - +
240A ILE* 1.3 65.5 + - - +
242A ASN* 3.1 9.6 + - + +
243A MET* 2.9 39.5 + - + +
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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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230A CYS* 4.4 7.6 - - - -
231A GLU* 3.2 38.6 - - + +
232A SER 4.0 3.1 - - - +
233A LEU* 3.7 22.0 - - + -
236A HIS 3.3 5.8 + - - +
237A VAL* 3.1 14.7 + - + +
239A THR* 1.3 76.2 - - - +
241A LYS* 1.3 57.9 + - - +
243A MET* 3.2 1.9 + - - +
244A ILE* 2.8 45.5 + - + +
256A TYR* 3.6 37.9 - - + +
314A LEU* 4.4 10.1 - - + -
318A ILE* 4.5 9.4 - - + -
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Residues in contact with LYS 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 VAL* 2.9 21.0 + - + +
238A GLY* 3.5 15.3 - - - +
239A THR 3.2 0.2 - - - -
240A ILE* 1.3 76.3 - - - +
242A ASN* 1.3 66.2 + - - +
244A ILE* 4.0 0.7 - - - +
245A GLY* 3.0 19.6 + - - -
317A GLU* 3.2 51.2 + - - +
318A ILE* 4.2 9.0 - - + -
321A ILE* 4.0 31.7 - - + +
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Residues in contact with ASN 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 GLY 2.9 22.3 + - - +
239A THR* 3.1 11.6 + - + +
241A LYS* 1.3 80.7 - - - +
243A MET* 1.3 66.4 + - + +
245A GLY* 3.3 2.6 + - - -
246A TYR* 3.0 49.5 + - + +
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Residues in contact with MET 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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208A PHE* 3.4 45.1 - - + +
213A TYR* 4.4 15.7 - - - +
230A CYS* 4.1 19.7 - - - -
239A THR* 2.9 29.4 + - + +
240A ILE 3.7 2.9 - - - +
242A ASN* 1.3 81.1 - - + +
244A ILE* 1.3 60.3 + - - +
246A TYR* 3.0 49.4 + - + +
247A ALA* 2.9 28.4 + - - +
272A LEU* 3.9 19.2 - - + +
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Residues in contact with ILE 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 ILE* 2.8 42.4 + - + +
241A LYS 4.0 2.7 - - - +
243A MET* 1.3 72.7 - - - +
245A GLY* 1.3 57.4 + - - +
247A ALA* 3.3 1.9 + - - +
248A LYS* 2.9 50.6 + - + +
254A VAL* 4.1 12.5 - - + +
255A GLU 5.7 0.7 - - - -
256A TYR* 4.3 12.8 - - + +
272A LEU* 3.7 24.7 - - + +
318A ILE* 3.8 34.1 - - + +
321A ILE* 3.9 16.2 - - + -
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Residues in contact with GLY 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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210A GLN* 4.4 1.6 + - - -
241A LYS 3.0 13.3 + - - -
242A ASN* 3.7 3.8 - - - -
244A ILE* 1.3 76.7 - - - +
246A TYR* 1.3 64.5 + - - +
248A LYS* 4.1 4.2 - - - +
249A LYS* 3.4 26.0 + - - +
321A ILE* 3.6 21.3 - - - +
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Residues in contact with TYR 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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208A PHE 3.9 1.7 + - - -
209A ASN* 3.9 22.5 - - - +
210A GLN* 3.0 55.6 - - + +
213A TYR* 4.2 15.7 - + + -
242A ASN* 3.0 31.8 + - + +
243A MET* 3.0 46.6 + - + +
245A GLY* 1.3 79.2 - - - +
247A ALA* 1.3 62.7 + - - +
249A LYS* 3.4 7.8 + - - +
250A LEU* 4.0 5.4 - - - +
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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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213A TYR* 4.6 9.6 - - + -
243A MET 2.9 14.1 + - - +
244A ILE 3.8 2.5 - - - +
246A TYR* 1.3 76.0 - - - +
248A LYS* 1.3 52.2 + - - +
250A LEU* 3.1 4.7 + - - +
251A PHE* 2.8 43.9 + - + +
254A VAL* 3.6 24.5 - - + -
272A LEU* 4.4 7.0 - - + -
274A CYS* 3.8 23.8 - - - -
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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 ILE* 2.9 37.8 + - + +
245A GLY* 4.1 6.1 - - - +
246A TYR 3.3 0.4 - - - -
247A ALA* 1.3 71.1 - - - +
249A LYS* 1.3 63.8 + - - +
250A LEU 3.1 2.8 + - - -
251A PHE 3.7 12.9 - - - +
252A LYS 6.1 0.7 - - - +
254A VAL* 3.6 27.3 + - + +
318A ILE 5.7 3.0 + - - -
319A GLU 5.7 2.2 + - - -
321A ILE* 3.3 30.3 + - + +
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Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLN* 3.9 27.2 - - + +
245A GLY 3.4 12.6 + - - +
246A TYR 3.6 12.6 - - - +
247A ALA 3.2 1.0 - - - -
248A LYS* 1.3 74.8 - - - +
250A LEU* 1.3 62.3 + - + +
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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