Contacts of the helix formed by residues 228 - 243 (chain D) in PDB entry 4IGM
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 228 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D PRO* 3.7 5.7 + - + +
197D ALA* 5.8 1.3 - - - -
200D THR* 3.0 17.5 + - + +
227D GLY* 1.3 70.6 - - - -
229D PHE* 1.3 67.9 + - - +
230D PRO* 3.2 5.6 - - - -
231D PHE* 2.8 18.7 + - + +
232D THR* 3.0 21.7 + - + +
196E PRO* 6.2 0.9 - - + -
228E ALA* 3.6 30.3 - - + -
231E PHE* 4.4 6.1 - - - -
232E THR* 4.7 1.3 - - + -
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Residues in contact with PHE 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D THR* 3.5 10.0 + - + -
203D ILE* 3.8 34.3 - - + -
204D CYS* 4.5 9.9 - - - -
207D ILE* 3.9 23.8 - - + -
226D GLY* 3.2 15.4 + - - +
228D ALA* 1.3 78.2 - - - +
230D PRO* 1.3 64.2 - - + +
232D THR* 3.7 5.6 - - - -
233D VAL* 2.8 57.5 + - + +
236D ILE* 3.8 31.9 - - + -
255D PRO* 4.9 3.6 - - + -
259D LEU* 3.9 25.6 - - + -
262D PHE* 4.0 13.2 - + - -
280D VAL* 5.8 0.4 - - + -
281D ILE* 4.8 6.3 - - + -
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Residues in contact with PRO 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D GLY 3.2 27.4 - - - +
226D GLY* 4.9 0.7 - - - -
227D GLY 3.9 0.4 - - - +
228D ALA 3.2 6.1 - - - +
229D PHE* 1.3 93.9 - - + +
231D PHE* 1.3 58.0 + - - +
233D VAL* 3.9 8.6 - - + +
276D LEU* 3.7 11.8 - - + +
277D LEU* 3.9 17.7 - - + -
280D VAL* 3.8 36.8 - - + +
281D ILE* 4.7 8.3 - - + -
231E PHE* 3.7 28.0 - - + -
273E SER* 4.1 3.6 + - - -
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Residues in contact with PHE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D ALA* 2.8 8.9 + - - +
230D PRO* 1.3 81.4 - - - +
232D THR* 1.3 66.0 + - + +
233D VAL* 3.4 1.3 + - - -
234D GLY 4.5 2.9 + - - -
276D LEU* 4.1 1.8 - - + -
224E HIS 5.2 0.4 - - - -
225E GLY 4.1 8.1 - - - -
227E GLY 3.2 26.9 - - - -
228E ALA* 4.4 7.0 - - - -
230E PRO* 3.8 26.2 - - + -
231E PHE* 3.7 24.7 - - + -
268E VAL* 4.2 24.7 - - + +
273E SER* 2.8 60.4 + - - -
276E LEU* 3.7 26.2 - - + -
277E LEU* 4.5 4.9 - - + -
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Residues in contact with THR 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D THR* 4.4 2.4 - - - +
228D ALA* 3.0 30.4 + - + +
229D PHE* 3.7 4.3 - - - -
231D PHE* 1.3 82.8 - - + +
233D VAL* 1.3 64.2 + - - +
234D GLY 3.1 3.1 - - - -
235D ARG* 3.0 14.2 + - + +
236D ILE* 2.9 34.5 + - - +
192E LEU 5.0 4.0 - - - -
196E PRO* 4.3 23.1 - - + -
227E GLY 3.9 21.3 - - - +
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D PHE* 2.8 47.4 + - + +
230D PRO 3.9 14.1 - - - +
231D PHE 4.9 0.7 - - - -
232D THR* 1.3 77.3 - - - +
234D GLY* 1.3 59.1 + - - +
236D ILE* 4.4 8.1 - - + -
237D SER* 2.8 31.7 + - - +
255D PRO* 5.2 4.5 - - + -
256D LYS* 4.6 21.3 - - + -
259D LEU* 4.6 9.9 - - + -
280D VAL* 4.1 17.7 - - + -
270E ASP* 4.2 11.4 - - - +
273E SER* 5.7 1.8 - - - +
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Residues in contact with GLY 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D PHE 4.5 3.0 + - - -
232D THR* 3.1 1.6 - - - +
233D VAL* 1.3 84.8 - - - +
235D ARG* 1.3 51.3 + - - +
237D SER* 3.7 1.6 - - - -
238D HIS* 2.7 36.0 + - - +
256D LYS* 4.5 3.6 - - - -
268E VAL 4.1 5.4 - - - -
269E HIS* 3.9 8.1 - - - +
270E ASP* 3.4 33.4 + - - +
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Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D THR* 3.0 16.0 + - + +
234D GLY* 1.3 73.0 - - - +
236D ILE* 1.3 60.4 + - - +
238D HIS* 3.8 0.7 - - - +
239D GLY* 2.7 28.6 + - - -
191E TRP* 3.0 25.5 + - - +
192E LEU* 3.6 22.1 + - - +
195E MET* 2.9 34.9 - - - +
196E PRO* 4.0 13.6 - - - +
224E HIS* 3.6 33.7 + - - +
267E LEU* 5.2 3.4 + - - +
268E VAL* 4.1 4.8 + - - +
269E HIS* 3.4 33.7 + - + +
296E LEU* 3.1 31.8 + - + +
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D THR* 4.1 8.3 - - + -
204D CYS* 3.7 26.2 - - - -
208D MET* 3.9 27.6 - - + -
229D PHE* 3.8 23.1 - - + -
232D THR* 2.9 35.2 + - - +
233D VAL* 3.8 4.3 - - - +
235D ARG* 1.3 74.4 - - - +
237D SER* 1.3 58.4 + - - +
239D GLY* 3.3 1.0 + - - -
240D PHE* 2.9 27.5 + - - +
255D PRO* 4.2 16.4 - - + -
192E LEU* 4.1 30.3 - - + +
193E VAL* 4.4 3.6 - - + -
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Residues in contact with SER 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D VAL* 2.8 20.4 + - - -
234D GLY 3.9 2.7 - - - -
236D ILE* 1.3 70.8 - - - +
238D HIS* 1.3 65.0 + - - +
240D PHE* 3.5 3.5 + - - -
241D SER* 3.1 21.1 + - - -
254D ASN* 2.4 40.4 + - - +
255D PRO* 4.5 5.1 - - - +
256D LYS* 3.5 29.8 + - - +
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Residues in contact with HIS 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D GLY 2.7 22.4 + - - +
235D ARG 3.8 3.1 - - - +
237D SER* 1.3 74.5 - - - +
239D GLY* 1.3 61.5 + - - +
241D SER* 3.1 9.7 + - - -
242D MET* 3.1 44.9 + - + +
269E HIS* 3.2 32.6 + + + +
295E PRO 3.4 17.5 + - - -
296E LEU* 3.7 10.4 + - - +
297E GLY 3.0 28.4 + - - -
299E LEU* 3.8 20.5 - - + +
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Residues in contact with GLY 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ARG 2.7 21.5 + - - -
236D ILE 3.7 0.9 - - - -
238D HIS* 1.3 69.8 - - - +
240D PHE* 1.3 66.0 + - - +
242D MET* 2.9 12.3 + - - +
243D ARG* 3.0 14.0 + - - +
247D CYS* 4.4 1.5 - - - -
188E TRP* 3.9 13.9 - - - -
192E LEU* 3.7 17.9 - - - -
296E LEU* 4.0 12.5 - - - +
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Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D MET* 4.2 10.3 - - + -
236D ILE 2.9 17.1 + - - +
237D SER 3.7 5.6 - - - +
238D HIS 3.3 0.2 - - - -
239D GLY* 1.3 76.0 - - - +
241D SER* 1.3 64.8 + - - +
243D ARG 3.9 1.2 - - - -
244D PRO* 3.8 20.4 - - + +
247D CYS* 3.5 42.4 - - + -
248D ALA* 3.6 15.7 - - + -
251D ASN 3.6 7.2 - - - -
252D PRO 3.4 26.7 - - - -
253D MET 3.3 20.0 - - - -
254D ASN* 3.5 26.7 - - + -
255D PRO* 3.5 22.9 - - + -
192E LEU* 4.8 0.4 - - - +
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Residues in contact with SER 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D SER* 3.1 12.4 + - - -
238D HIS* 3.1 13.2 + - - -
239D GLY 3.0 0.4 - - - -
240D PHE* 1.3 83.3 - - - +
242D MET* 1.3 80.3 + - - +
244D PRO* 3.8 8.7 - - - +
254D ASN* 3.4 12.1 + - - -
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Residues in contact with MET 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D HIS* 3.1 36.7 + - + +
239D GLY* 2.9 8.3 + - - +
241D SER* 1.3 106.8 - - - +
243D ARG* 1.3 69.8 + - + +
244D PRO* 3.3 7.8 - - - +
188E TRP* 4.9 2.2 - - + -
295E PRO* 3.6 41.6 - - + +
296E LEU* 5.0 0.4 - - - +
299E LEU* 5.6 4.5 - - + -
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Residues in contact with ARG 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D GLY 3.0 6.4 + - - +
240D PHE 3.9 3.4 - - - -
242D MET* 1.3 85.2 - - + +
244D PRO* 1.4 60.1 - - - +
245D ASP* 2.8 35.3 + - - +
246D LEU* 3.0 28.2 + - + +
247D CYS* 2.9 27.9 + - - +
47E ARG* 4.6 12.1 - - - +
188E TRP* 3.3 53.9 - - + +
295E PRO* 5.0 12.2 - - - +
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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
------------------------------------------------------------
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