Contacts of the helix formed by residues 229 - 245 (chain A) in PDB entry 3IKH
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 GLY 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN* 4.4 3.8 - - - +
227A THR 3.2 0.8 + - - -
228A THR* 1.3 76.8 - - - +
230A ALA* 1.3 59.1 + - - +
231A GLY 3.3 3.1 - - - -
232A ASP* 3.7 21.7 - - - +
233A THR* 2.8 34.6 + - - -
264A THR* 3.9 1.6 - - - -
274A PHE* 4.0 14.5 - - - -
900A ATP 4.6 8.5 + - - -
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A THR* 3.0 19.7 + - - +
228A THR 3.2 1.0 + - - -
229A GLY* 1.3 76.8 - - - +
231A GLY* 1.3 58.6 + - - +
233A THR* 3.3 4.7 + - - -
234A PHE* 3.0 28.4 + - - +
261A ALA* 3.8 6.4 - - - +
264A THR* 4.1 9.4 - - + -
265A VAL* 3.8 26.7 - - + -
900A ATP 4.0 23.7 + - + +
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 5.1 2.2 - - - -
43A GLN* 5.2 1.1 - - - -
161A ASN* 5.8 1.3 + - - -
180A VAL* 5.8 0.5 - - - +
200A THR* 6.4 0.2 - - - -
229A GLY 3.3 0.2 - - - -
230A ALA* 1.3 77.1 - - - +
232A ASP* 1.3 63.7 + - - +
234A PHE* 3.4 2.8 + - - +
235A LEU* 3.0 24.8 + - - +
900A ATP 3.6 50.3 + - - -
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Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 2.8 40.8 + - - +
42A ASN* 3.0 44.0 + - + +
43A GLN* 3.0 35.8 + - + +
46A ILE* 4.4 2.2 - - + -
229A GLY* 3.3 13.8 + - - +
230A ALA 3.3 0.6 - - - -
231A GLY* 1.3 76.3 - - - +
233A THR* 1.3 57.8 + - - +
235A LEU 3.5 0.2 + - - -
236A ALA* 3.0 31.2 + - - +
900A ATP 5.2 1.1 + - - -
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Residues in contact with THR 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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46A ILE* 3.3 21.3 - - + +
229A GLY 2.8 20.3 + - - -
230A ALA 3.5 5.4 - - - -
232A ASP* 1.3 75.3 - - - +
234A PHE* 1.3 64.3 + - - +
236A ALA 3.4 0.2 + - - -
237A VAL* 3.0 28.7 + - + +
260A ALA* 3.6 36.1 - - + +
261A ALA* 3.7 2.9 - - - +
264A THR* 2.8 27.7 + - - +
274A PHE* 3.8 1.4 - - - -
275A PRO* 4.1 11.0 - - + -
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Residues in contact with PHE 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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180A VAL* 5.3 2.5 - - + -
198A VAL* 4.1 15.0 - - + -
200A THR* 3.9 22.9 - - + -
206A ALA* 3.7 20.6 - - + -
230A ALA 3.0 16.7 + - - +
231A GLY 3.6 4.9 - - - +
233A THR* 1.3 76.5 - - - +
235A LEU* 1.3 67.2 + - + +
238A MSE 3.0 33.5 + - + +
254A LEU* 3.8 20.9 - - + -
257A ALA* 3.2 36.9 - - + +
258A SER* 3.5 22.4 - - - -
261A ALA* 4.3 1.3 - - + +
900A ATP 3.5 37.9 - - - +
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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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43A GLN* 3.7 24.5 - - + +
134A LEU* 4.0 26.0 - - + -
159A VAL* 5.0 3.6 - - + -
161A ASN* 3.5 37.0 - - + +
180A VAL* 3.8 32.5 - - + -
231A GLY 3.0 17.8 + - - +
232A ASP 3.9 3.1 - - - +
234A PHE* 1.3 80.2 - - - +
236A ALA* 1.3 69.1 + - - +
238A MSE 3.7 8.4 - - + +
239A LEU* 3.1 29.8 + - + +
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Residues in contact with ALA 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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43A GLN* 3.6 23.8 - - - +
46A ILE* 3.5 26.7 - - + -
47A LEU* 3.4 18.4 - - + +
50A CYS* 5.1 0.9 - - - -
232A ASP 3.0 18.8 + - - +
235A LEU* 1.3 83.4 - - - +
237A VAL* 1.3 58.8 + - - +
239A LEU 3.4 0.2 + - - -
240A ALA* 2.9 29.1 + - - +
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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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46A ILE* 4.0 12.8 - - + -
50A CYS* 4.2 3.1 - - - -
233A THR* 3.0 17.9 + - + +
236A ALA* 1.3 72.1 - - - +
238A MSE 1.3 60.5 + - - +
240A ALA* 4.3 4.7 - - - -
241A SER* 2.8 29.8 + - - -
256A HIS* 3.8 28.3 - - + +
257A ALA* 3.9 7.4 - - - -
260A ALA* 3.4 21.3 - - + -
280A LEU* 3.8 17.0 - - + -
283A LEU* 4.2 4.5 - - + -
284A LEU* 3.9 20.9 - - + -
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Residues in contact with MSE 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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159A VAL* 5.7 1.6 - - + -
178A ILE* 4.3 15.3 - - + -
180A VAL* 3.9 23.3 - - + -
198A VAL* 3.6 34.1 - - - -
234A PHE* 3.0 26.4 + - + +
235A LEU* 3.7 9.2 - - + +
237A VAL* 1.3 76.3 - - - +
239A LEU* 1.3 81.0 + - + +
242A ALA* 3.2 20.3 + - - +
249A PRO* 4.4 13.7 - - + -
253A ALA* 3.6 33.5 - - + +
254A LEU* 4.0 14.1 - - + -
257A ALA* 3.7 8.8 - - + +
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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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3A VAL* 4.8 3.4 - - + -
47A LEU* 4.2 20.9 - - + -
132A ILE* 3.7 36.8 - - + -
134A LEU* 4.6 11.9 - - + -
159A VAL* 4.4 25.4 - - + -
178A ILE* 4.6 12.8 - - + -
235A LEU* 3.1 20.3 + - + +
236A ALA 3.7 3.8 - - - +
238A MSE 1.3 86.2 - - + +
240A ALA* 1.3 65.3 + - - +
242A ALA* 3.3 8.7 + - + +
243A LEU* 2.9 35.9 + - + +
249A PRO* 5.7 2.0 - - + -
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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
----------------------------------------------------------
47A LEU* 4.0 3.7 - - + +
50A CYS* 3.5 36.8 - - + -
52A ILE* 3.8 21.8 - - + -
236A ALA 2.9 18.6 + - - +
237A VAL 3.8 2.0 - - - +
239A LEU* 1.3 75.6 - - - +
241A SER* 1.3 58.5 + - - +
243A LEU* 3.2 1.5 + - - +
244A LEU* 2.8 38.6 + - + +
284A LEU* 5.0 1.6 - - + -
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Residues in contact with SER 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 2.8 21.6 + - - -
238A MSE 3.7 4.3 - - - -
240A ALA* 1.3 74.4 - - - +
242A ALA* 1.3 61.7 + - - +
244A LEU* 3.4 3.9 + - - +
245A ARG* 2.9 43.6 + - - +
253A ALA* 3.6 9.8 - - - -
256A HIS* 2.8 37.0 - - - -
284A LEU* 3.7 12.9 - - - +
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Residues in contact with ALA 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 MSE 3.2 11.3 + - - +
239A LEU* 3.7 11.4 - - + +
241A SER* 1.3 79.4 - - - +
243A LEU* 1.3 63.5 + - + +
245A ARG* 3.3 10.1 + - - +
246A GLY 3.0 18.5 + - - -
247A VAL* 3.0 33.7 + - + +
248A ALA 4.2 0.7 - - - -
249A PRO* 3.9 28.0 - - + -
253A ALA* 4.6 1.1 - - + -
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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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-1A LEU* 4.0 34.8 - - + +
3A VAL* 3.8 27.8 - - + -
47A LEU* 4.8 0.9 - - + -
52A ILE* 3.8 29.6 - - + -
132A ILE* 3.7 24.7 - - + -
239A LEU* 2.9 30.4 + - + +
240A ALA 3.5 4.0 - - - +
242A ALA* 1.3 76.9 - - + +
244A LEU* 1.3 62.2 + - - +
246A GLY* 3.1 13.5 + - - -
247A VAL 5.1 0.4 - - - +
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Residues in contact with LEU 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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50A CYS 3.8 17.0 - - - +
51A GLY* 5.1 4.7 - - - +
52A ILE* 4.0 18.2 - - + -
240A ALA* 2.8 26.4 + - + +
241A SER* 3.9 3.6 - - - +
243A LEU* 1.3 71.5 - - - +
245A ARG* 1.3 62.6 + - + +
246A GLY 3.4 0.7 - - - -
284A LEU* 3.8 34.1 - - + -
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Residues in contact with ARG 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 SER* 2.9 41.3 + - - +
242A ALA* 4.1 4.1 - - - +
243A LEU 3.2 0.2 - - - -
244A LEU* 1.3 81.9 - - + +
246A GLY* 1.3 63.1 + - - +
247A VAL* 3.3 19.1 + - + +
250A ASP* 2.8 41.8 + - - -
252A LEU* 3.7 28.3 - - - +
253A ALA* 3.3 13.9 - - - +
256A HIS* 4.4 4.1 - - - -
284A LEU 5.4 4.3 - - - +
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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
------------------------------------------------------------
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