Contacts of the helix formed by residues 229 - 244 (chain A) in PDB entry 1IC8
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 ARG 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A PRO* 2.9 33.8 + - - +
225A SER 3.0 8.4 + - - +
226A LYS* 3.2 38.2 - - - +
227A GLU 2.8 0.2 - - - -
228A GLU* 1.3 77.7 - - - +
230A GLU* 1.3 55.3 + - + +
231A THR 3.0 1.1 - - - -
232A LEU* 2.8 12.5 + - - +
233A VAL* 2.7 32.3 + - + +
261A GLU* 3.3 37.3 - - + +
264A VAL* 3.7 31.6 - - + +
265A TYR* 4.1 29.6 - - - +
268A PHE* 4.9 7.2 - - - -
301E C 5.9 4.8 + - - -
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Residues in contact with GLU 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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226A LYS* 3.8 28.7 + - - +
227A GLU* 3.7 11.4 - - - +
229A ARG* 1.3 71.7 + - + +
231A THR* 1.3 54.9 + - - +
232A LEU 2.6 16.0 + - - -
233A VAL* 3.0 21.2 + - - +
234A GLU* 3.3 23.5 + - + +
235A GLU 4.4 0.2 + - - -
261A GLU* 3.5 31.2 - - - +
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Residues in contact with THR 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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227A GLU* 3.0 17.8 + - - -
228A GLU* 3.1 32.3 + - - +
230A GLU* 1.3 77.9 - - - +
232A LEU* 1.3 60.3 + - + +
235A GLU* 3.2 28.1 - - - +
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Residues in contact with LEU 232 (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 ILE* 4.0 24.0 - - + +
214A LEU* 5.1 4.9 - - + -
217A ALA* 3.4 36.1 - - + +
220A ARG* 5.4 4.7 - - - +
228A GLU 3.9 15.0 - - - +
229A ARG* 2.8 8.8 + - - +
230A GLU 2.7 1.0 - - - -
231A THR* 1.3 86.2 - - + +
233A VAL* 1.3 53.7 + - - +
234A GLU 3.2 2.2 - - - -
235A GLU* 2.6 29.3 + - - +
236A CYS* 2.5 47.2 + - - +
264A VAL* 5.4 5.4 - - + -
268A PHE* 4.2 13.9 - - + -
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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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229A ARG* 2.7 31.4 + - + +
230A GLU* 3.2 22.7 - - - +
232A LEU* 1.3 71.6 - - - +
234A GLU* 1.3 61.3 + - + +
236A CYS 3.4 0.2 + - - -
237A ASN* 3.1 29.4 + - - +
259A VAL* 3.3 37.1 - - + +
261A GLU* 2.6 45.8 - - + +
264A VAL* 4.1 3.8 - - + +
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Residues in contact with GLU 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 GLU* 3.3 18.3 + - + +
232A LEU 3.2 0.2 - - - -
233A VAL* 1.3 79.8 - - + +
235A GLU* 1.3 60.1 + - - +
236A CYS 3.2 2.0 - - - -
237A ASN* 4.0 9.6 - - + +
238A ARG* 2.8 70.9 + - + +
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Residues in contact with GLU 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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213A ILE* 4.1 26.8 - - + +
230A GLU 4.4 0.8 + - - -
231A THR* 3.2 23.8 - - - +
232A LEU* 2.6 33.0 + - - +
234A GLU* 1.3 78.7 - - - +
236A CYS* 1.3 60.4 + - - +
238A ARG* 4.1 9.2 - - - +
239A ALA* 3.7 14.6 + - - +
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Residues in contact with CYS 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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206A TRP* 4.1 2.9 - - - -
210A SER* 3.2 33.0 + - - +
213A ILE* 3.4 28.3 - - - -
214A LEU* 4.0 17.5 - - - -
232A LEU* 2.5 23.3 + - - +
233A VAL* 3.6 2.2 - - - +
235A GLU* 1.3 73.7 - - - +
237A ASN* 1.3 53.4 + - - +
238A ARG 3.1 0.9 - - - -
239A ALA* 2.6 11.9 + - - +
240A GLU 2.6 32.1 + - - -
259A VAL* 3.4 16.2 - - + -
264A VAL* 5.7 0.2 - - - -
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Residues in contact with ASN 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* 3.1 17.7 + - - +
234A GLU* 4.0 8.3 - - - +
236A CYS* 1.3 76.9 - - - +
238A ARG* 1.3 60.3 + - + +
240A GLU* 4.0 4.2 - - - +
241A CYS* 2.8 38.1 + - - -
249A SER 5.7 4.5 - - - +
254A LEU* 3.6 10.8 - - + +
258A LEU* 2.8 30.4 - - + +
259A VAL* 2.7 48.0 - - - +
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Residues in contact with ARG 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 GLU* 2.8 75.8 + - + +
235A GLU* 4.2 8.5 - - - +
236A CYS 3.1 0.2 - - - -
237A ASN* 1.3 76.0 - - - +
239A ALA* 1.3 53.3 + - - +
241A CYS* 3.7 5.3 - - - +
242A ILE* 2.8 46.3 + - + +
247A SER 5.3 0.8 - - - +
249A SER* 3.9 35.9 + - - +
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Residues in contact with ALA 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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209A ALA* 4.0 25.7 - - + +
213A ILE* 6.1 0.7 - - + -
235A GLU 3.7 12.9 + - - +
236A CYS* 2.6 15.9 + - - +
238A ARG* 1.3 77.5 - - - +
240A GLU* 1.3 55.2 + - - +
242A ILE* 3.1 11.4 + - - +
243A GLN* 2.7 36.4 + - - +
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Residues in contact with GLU 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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207A GLY* 3.7 20.7 - - - +
209A ALA* 3.3 8.0 - - - +
210A SER* 2.3 53.5 + - - +
236A CYS 2.6 16.0 + - - +
237A ASN* 3.8 2.0 - - - +
239A ALA* 1.3 72.9 - - - +
241A CYS* 1.3 60.7 + - - +
243A GLN* 3.7 8.2 - - - +
244A ARG* 2.3 70.9 + - - +
254A LEU* 3.8 19.3 - - + -
257A ASN 5.0 5.6 - - - +
259A VAL* 4.2 11.2 - - + -
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Residues in contact with CYS 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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176A GLN* 4.8 3.6 - - - -
237A ASN* 2.8 29.3 + - - +
238A ARG* 3.7 5.2 - - - +
240A GLU* 1.3 75.7 - - - +
242A ILE* 1.3 60.3 + - - +
244A ARG* 3.2 18.2 - - - +
246A VAL* 2.5 27.7 - - + +
247A SER* 4.1 18.6 - - - +
248A PRO 4.0 9.9 - - - +
249A SER 4.9 6.3 - - - -
251A ALA* 3.5 26.5 - - - -
254A LEU* 3.8 16.8 - - - -
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Residues in contact with ILE 242 (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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238A ARG* 2.8 38.7 + - + +
239A ALA* 3.4 8.5 - - - +
241A CYS* 1.3 77.0 - - - +
243A GLN* 1.3 69.5 + - - +
244A ARG 2.9 1.6 + - - -
245A GLY* 3.3 11.8 + - - +
246A VAL 3.4 9.0 - - - +
247A SER* 3.6 18.3 + - - +
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Residues in contact with GLN 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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124A GLN 4.0 4.0 + - - -
125A GLN* 2.7 51.7 + - + +
127A ASN* 6.1 0.4 - - - +
207A GLY* 5.6 0.4 - - - -
208A PRO* 3.6 25.3 - - - +
209A ALA* 3.3 27.8 + - + +
239A ALA 2.7 19.1 + - - +
240A GLU* 3.7 9.6 + - - +
242A ILE* 1.3 75.6 - - - +
244A ARG* 1.3 63.3 + - - +
245A GLY 3.2 4.9 + - - -
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Residues in contact with ARG 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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125A GLN* 3.1 41.2 + - + +
126A HIS* 3.3 53.8 + - + +
127A ASN* 4.8 8.3 - - - +
176A GLN* 4.3 5.4 - - - +
207A GLY* 5.2 0.4 - - - -
240A GLU* 2.3 55.4 + - - +
241A CYS* 3.2 9.9 - - - +
242A ILE 2.9 1.2 + - - -
243A GLN* 1.3 79.8 - - - +
245A GLY* 1.3 50.5 + - - +
246A VAL* 2.7 26.1 + - + +
254A LEU* 3.2 30.5 - - - +
257A ASN* 4.2 16.6 - - - +
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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