Contacts of the helix formed by residues 232 - 247 (chain A) in PDB entry 4IX8
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 SER 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GLU* 4.2 9.8 + - - -
230A ASN 3.6 2.4 + - - -
231A PHE* 1.3 77.4 - - - +
233A ARG* 1.3 65.0 + - - +
234A ALA* 3.5 9.1 + - - +
235A HIS* 3.1 25.6 + - - +
236A VAL* 3.2 18.7 + - - +
267A THR* 4.3 0.2 - - - -
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Residues in contact with ARG 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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131A GLN* 3.6 12.1 - - - +
135A ARG* 3.4 20.6 - - - +
232A SER* 1.3 72.1 - - - +
234A ALA* 1.3 59.2 + - - +
236A VAL* 3.1 3.8 + - - +
237A SER* 2.9 28.2 + - - -
267A THR* 3.6 34.7 + - + +
271A ASP* 2.9 48.1 + - - -
272A PHE* 3.7 24.9 - - + -
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Residues in contact with ALA 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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232A SER* 3.1 8.8 + - - +
233A ARG* 1.3 81.3 - - - +
235A HIS* 1.3 58.8 + - - +
237A SER* 3.4 8.2 + - - -
238A ASP* 3.0 34.1 + - - +
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Residues in contact with HIS 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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201A GLU* 3.7 27.5 + - + +
202A CYS* 3.0 58.1 + - + +
204A LEU* 4.6 6.5 - - + +
231A PHE* 3.6 32.3 - + + -
232A SER* 3.1 24.1 + - - +
234A ALA* 1.3 75.4 - - - +
236A VAL* 1.3 59.5 + - - +
238A ASP* 3.2 13.3 + - - +
239A ILE* 2.9 46.4 + - + +
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Residues in contact with VAL 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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220A ILE* 5.3 4.3 - - + -
222A ASN* 4.3 3.6 - - - +
231A PHE* 3.7 27.1 - - + -
232A SER 3.2 13.6 + - - +
233A ARG 3.1 7.7 + - - +
235A HIS* 1.3 75.8 - - - +
237A SER* 1.3 62.9 + - - +
239A ILE* 3.1 10.9 + - + +
240A ILE* 3.0 24.1 + - + +
267A THR* 4.1 22.7 - - + +
269A VAL* 4.0 26.7 - - + -
272A PHE* 3.5 25.6 - - + -
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Residues in contact with SER 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 ARG* 2.9 13.9 + - - -
234A ALA* 3.4 13.5 - - - -
236A VAL* 1.3 76.0 - - - +
238A ASP* 1.3 58.8 + - - +
240A ILE* 3.3 7.7 + - - +
241A ASP* 2.9 37.4 + - - +
272A PHE* 3.8 23.7 - - - -
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Residues in contact with ASP 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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204A LEU* 3.8 18.1 - - + +
234A ALA* 3.0 22.2 + - - +
235A HIS* 3.2 14.3 + - - +
237A SER* 1.3 78.3 + - - +
239A ILE* 1.3 60.1 + - - +
241A ASP* 3.2 14.7 + - - +
242A PHE* 2.9 28.9 + - - +
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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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202A CYS* 3.9 17.3 - - - -
204A LEU* 4.1 15.9 - - + -
218A PHE* 4.0 15.3 - - + -
220A ILE* 4.1 12.3 - - + -
231A PHE* 4.0 12.8 - - + -
235A HIS* 2.9 46.8 + - + +
236A VAL* 3.1 14.8 + - + +
238A ASP* 1.3 75.3 - - - +
240A ILE* 1.3 63.8 + - - +
242A PHE* 3.1 7.0 + - - +
243A CYS* 3.0 21.0 + - - -
250A LEU* 3.8 32.3 - - + -
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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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236A VAL* 3.0 18.7 + - + +
237A SER* 3.5 7.9 - - - +
239A ILE* 1.3 73.5 - - - +
241A ASP* 1.3 69.4 + - - +
243A CYS* 3.0 10.5 + - - +
244A GLN* 3.0 19.6 + - + +
250A LEU* 3.8 20.6 - - + -
269A VAL* 4.2 11.2 - - + +
272A PHE* 3.6 44.4 - - + -
274A THR* 3.8 28.7 - - + +
276A VAL* 4.0 11.0 - - + +
278A ARG* 4.5 7.6 - - - -
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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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237A SER* 2.9 25.7 + - - +
238A ASP* 3.5 17.8 - - - +
240A ILE* 1.3 79.1 - - - +
242A PHE* 1.3 64.1 + - - +
244A GLN* 3.1 9.2 + - - +
245A GLN* 3.0 24.7 + - - +
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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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169A LEU* 4.4 4.0 - - + -
204A LEU* 3.5 41.5 - - + -
207A ALA* 3.8 21.3 - - + -
208A ALA* 3.7 12.1 - - + -
211A VAL* 4.1 5.2 - - + -
218A PHE* 3.6 32.1 - + - -
238A ASP 2.9 12.9 + - - +
239A ILE* 3.2 14.8 - - - +
241A ASP* 1.3 77.5 - - - +
243A CYS* 1.3 61.5 + - - +
245A GLN* 3.4 2.9 + - - -
246A HIS* 3.1 67.1 + + - +
248A ILE* 4.5 6.3 - - + -
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Residues in contact with CYS 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 PHE* 3.7 35.0 - - - -
239A ILE 3.0 14.5 + - - +
240A ILE* 3.0 9.9 + - - +
242A PHE* 1.3 79.4 - - - +
244A GLN* 1.3 59.0 + - - +
247A GLN* 2.8 24.4 + - - -
248A ILE* 3.2 31.6 + - - +
250A LEU* 3.9 24.2 - - + -
276A VAL* 3.9 13.7 - - + -
41B PHE* 3.6 3.4 - - - -
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Residues in contact with GLN 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* 3.0 8.1 + - + +
241A ASP* 3.4 12.8 - - - +
243A CYS* 1.3 75.6 - - - +
245A GLN* 1.3 68.3 + - - +
247A GLN* 3.2 15.8 + - - +
274A THR* 4.8 0.7 + - - -
275A ASN* 4.8 3.6 + - - +
276A VAL* 3.2 33.3 + - + +
40B SER 3.3 27.9 + - - +
41B PHE* 3.6 14.3 - - - +
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Residues in contact with GLN 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 ASP 3.0 16.1 + - - +
242A PHE* 3.8 6.7 - - - +
244A GLN* 1.3 77.8 - - - +
246A HIS* 1.3 72.6 + - + +
247A GLN* 4.5 7.6 + - - +
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Residues in contact with HIS 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 ALA* 4.0 30.5 - - + +
211A VAL* 3.9 28.6 - - + +
242A PHE* 3.1 55.6 + + - +
245A GLN* 1.3 85.3 + - + +
247A GLN* 1.3 71.6 + - - +
248A ILE* 3.3 20.4 + - + +
42B ARG* 3.8 9.5 + - - -
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Residues in contact with GLN 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 CYS 2.8 12.7 + - - -
244A GLN* 3.2 12.7 + - - +
245A GLN 4.5 6.0 + - - +
246A HIS* 1.3 79.2 - - - +
248A ILE* 1.3 56.5 + - - +
249A PRO* 4.6 1.0 - - - +
40B SER 4.5 12.0 + - - +
41B PHE* 3.5 23.6 - - + -
42B ARG* 2.8 75.3 + - + +
44B ILE* 5.7 1.4 - - - +
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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