Contacts of the helix formed by residues 232 - 244 (chain A) in PDB entry 2IHU
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 ALA 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ALA 3.1 16.7 + - - +
228A ILE 4.3 0.2 + - - -
230A SER* 4.3 1.1 - - - -
231A GLY* 1.3 75.5 - - - +
233A VAL* 1.3 59.2 + - - +
234A PRO 3.5 2.2 - - - -
235A ALA 3.4 2.6 + - - -
236A ILE* 2.9 40.4 + - + +
339A VAL* 3.8 24.5 - - + -
340A LEU* 4.0 27.8 - - + +
343A VAL* 4.7 2.2 - - + -
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Residues in contact with VAL 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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227A ALA* 4.2 1.5 + - + +
228A ILE* 3.8 39.0 - - + +
231A GLY 3.5 0.6 - - - -
232A ALA* 1.3 76.5 - - - +
234A PRO* 1.4 74.4 - - + +
236A ILE* 3.8 6.8 - - + +
237A ARG* 3.0 24.3 + - + +
256A VAL* 3.4 39.4 - - + +
426A PRO* 3.9 24.9 - - + -
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Residues in contact with PRO 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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231A GLY 4.2 10.3 - - - +
232A ALA 3.9 1.1 - - - -
233A VAL* 1.4 96.8 - - + +
235A ALA* 1.3 56.7 + - - +
237A ARG* 3.5 7.3 + - + +
238A ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 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 GLY 5.4 0.2 + - - -
232A ALA 3.4 5.1 + - - +
233A VAL 3.3 0.6 - - - -
234A PRO* 1.3 77.3 - - - +
236A ILE* 1.3 65.4 - - - +
238A ALA* 3.6 6.0 + - - +
239A LEU* 3.1 17.7 + - - +
340A LEU* 3.7 31.0 - - + -
343A VAL* 3.5 25.7 - - + +
344A GLU* 5.3 4.0 - - + -
347A GLU* 4.1 3.5 - - + +
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Residues in contact with ILE 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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221A LEU* 4.1 20.6 - - + +
223A VAL* 4.2 21.5 - - + -
227A ALA* 3.7 30.1 - - + -
232A ALA* 2.9 29.3 + - + +
233A VAL* 3.8 7.0 - - + +
235A ALA* 1.3 74.1 - - - +
237A ARG* 1.3 60.8 + - - +
239A LEU* 3.3 6.0 + - + +
240A ALA* 2.9 28.2 + - - +
247A VAL* 4.8 7.9 - - + -
256A VAL* 6.0 5.4 - - + -
257A LEU* 6.2 0.9 - - + -
294A VAL* 3.8 18.8 - - + -
339A VAL* 4.4 0.2 - - + -
343A VAL* 3.8 22.4 - - + -
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Residues in contact with ARG 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 VAL* 3.0 18.2 + - + +
234A PRO* 3.7 7.9 - - + +
236A ILE* 1.3 77.5 - - - +
238A ALA* 1.3 56.6 + - - +
240A ALA* 3.3 3.1 + - - +
241A GLU* 2.9 62.5 + - - +
256A VAL 4.6 7.1 + - - +
257A LEU* 3.5 32.5 - - + +
258A PRO* 3.4 34.4 - - - +
261A HIS* 4.2 6.5 - - - -
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Residues in contact with ALA 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 PRO 3.0 18.0 + - - +
235A ALA* 3.9 7.2 - - - +
237A ARG* 1.3 76.2 - - - +
239A LEU* 1.3 58.2 + - - +
241A GLU* 4.0 9.7 - - - +
242A ARG* 3.1 29.6 + - - +
347A GLU* 4.0 8.6 - - - +
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Residues in contact with LEU 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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221A LEU* 4.5 23.1 - - + -
235A ALA 3.1 18.3 + - - +
236A ILE* 3.6 5.6 - - + +
237A ARG 3.3 0.2 - - - -
238A ALA* 1.3 74.3 - - - +
240A ALA* 1.3 66.1 + - - +
242A ARG* 3.4 30.4 + - - +
243A LEU* 3.1 41.9 + - + +
245A ILE* 5.1 3.8 - - + -
342A PHE* 5.7 2.2 - - + -
343A VAL* 4.5 15.3 - - + -
346A PHE* 3.8 30.3 - - + -
347A GLU* 3.5 21.7 + - + +
350A THR* 4.0 5.6 - - - +
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Residues in contact with ALA 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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221A LEU* 4.1 7.2 - - + -
236A ILE 2.9 16.6 + - - +
237A ARG* 3.8 4.9 - - - +
239A LEU* 1.3 77.6 - - - +
241A GLU* 1.3 54.9 + - - +
244A ASN* 2.7 31.7 + - - -
245A ILE* 3.0 35.5 + - - +
247A VAL* 3.8 20.9 - - + -
257A LEU* 5.5 1.8 - - + -
263A LEU* 3.3 8.0 - - + +
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Residues in contact with GLU 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 ARG* 2.9 48.8 + - + +
238A ALA* 4.0 7.5 - - - +
240A ALA* 1.3 77.6 - - + +
242A ARG* 1.3 63.3 + - - +
244A ASN* 3.6 7.8 + - - +
257A LEU* 5.6 0.2 - - + -
261A HIS* 2.7 39.9 + - + +
263A LEU* 3.8 6.6 - - + +
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Residues in contact with ARG 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 ALA 3.1 18.1 + - - +
239A LEU* 3.7 11.5 - - - +
241A GLU* 1.3 78.0 - - - +
243A LEU* 1.3 76.2 + - + +
347A GLU* 2.9 31.8 + - - -
350A THR* 2.8 48.1 + - - -
351A ALA* 3.5 19.6 + - - -
353A PHE 4.2 4.4 + - - +
355A ALA* 3.6 15.6 + - - +
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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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213A LEU* 3.7 28.7 - - + -
239A LEU* 3.1 38.7 + - + +
242A ARG* 1.3 101.1 - - + +
244A ASN* 1.3 65.3 + - - +
245A ILE* 3.3 15.4 + - + -
350A THR* 3.9 12.1 - - - +
353A PHE* 3.7 29.8 - - + +
354A GLY 4.0 10.3 - - - +
355A ALA* 4.0 1.8 - - - +
356A LYS* 2.8 36.3 + - + +
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Residues in contact with ASN 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 ALA 2.7 10.9 + - - -
241A GLU 3.6 6.5 + - - +
242A ARG 3.4 3.2 - - - -
243A LEU* 1.3 81.1 - - - +
245A ILE* 1.3 57.9 + - - +
246A PRO* 3.7 7.8 - - - +
262A GLU* 4.3 8.7 - - - +
263A LEU* 3.6 11.0 - - - +
355A ALA* 4.2 8.7 - - + -
356A LYS* 3.0 27.9 + - - +
357A GLN* 4.5 1.0 - - - +
358A ARG* 3.1 47.6 + - - +
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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