Contacts of the helix formed by residues 219 - 234 (chain E) in PDB entry 6IWQ
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 219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173E PHE* 3.6 27.6 - - - +
177E MET* 3.8 17.2 - - - -
217E ASN 3.5 3.0 + - - -
218E GLU* 1.3 81.1 + - - +
220E TRP* 1.3 66.6 + - - -
221E SER 3.4 2.2 - - - -
222E THR* 2.9 17.1 + - - -
223E LEU* 3.0 9.4 + - - +
253E HIS* 3.9 1.1 - - - -
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Residues in contact with TRP 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E MET* 4.2 3.0 - - + +
181E ASP* 6.0 0.2 - - - +
185E LEU* 4.8 8.7 - - + +
218E GLU 4.4 0.2 - - - -
219E GLY* 1.3 70.8 - - - -
221E SER* 1.3 68.3 + - - +
223E LEU* 3.1 6.8 + - + +
224E MET* 2.8 52.1 + - + +
253E HIS* 3.2 45.6 - - + +
254E LEU* 5.2 4.5 - - + -
257E LYS* 3.3 53.4 - - + +
258E LEU* 3.9 17.7 - - + -
261E TYR* 3.6 49.9 - + + -
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Residues in contact with SER 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E MET* 3.4 6.8 - - - +
180E SER* 2.7 33.7 + - - -
181E ASP* 2.8 29.1 + - - -
185E LEU* 3.6 17.1 - - - +
219E GLY 3.4 0.4 - - - -
220E TRP* 1.3 89.9 - - - +
222E THR* 1.3 63.2 + - - +
225E ARG* 3.1 27.4 + - - +
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Residues in contact with THR 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E PHE* 4.7 4.8 - - + -
177E MET* 4.2 12.2 - - - -
180E SER* 3.6 23.8 - - - +
218E GLU* 2.9 27.3 + - - +
219E GLY* 2.9 17.4 + - - -
221E SER* 1.3 78.0 + - - +
223E LEU* 1.3 61.1 + - - +
225E ARG* 4.1 9.0 - - - +
226E THR* 2.9 27.0 + - - -
302E ALA 3.4 2.1 - - - +
303E HIS* 4.3 2.6 - - - -
338E TYR* 4.5 3.6 - - - +
441E ILE* 3.7 29.4 - - + -
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Residues in contact with LEU 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ILE* 4.1 25.4 - - + -
215E PHE* 4.2 28.9 - - + -
218E GLU* 3.8 9.4 - - + +
219E GLY 3.0 16.1 + - - +
220E TRP* 3.7 4.0 - - + +
222E THR* 1.3 78.5 + - - +
224E MET* 1.3 84.7 + - + +
226E THR* 3.3 16.6 - - - -
227E VAL* 3.3 9.0 + - + +
244E LEU* 4.7 11.4 - - + -
254E LEU* 4.0 23.8 - - + -
258E LEU* 4.5 4.9 - - + -
302E ALA* 3.4 16.8 + - + +
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Residues in contact with MET 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 3.9 20.9 - - + -
220E TRP* 2.8 48.4 + - + +
223E LEU* 1.3 94.2 - - + +
225E ARG* 1.3 60.4 + - - +
226E THR 3.0 1.6 - - - -
227E VAL* 3.2 9.3 + - - +
228E HIS* 2.8 37.3 + - + -
244E LEU* 5.1 2.2 - - + -
258E LEU* 2.7 40.2 - - + -
261E TYR* 4.0 20.0 - - + -
262E ILE* 4.3 9.4 - - + -
265E TRP* 4.6 9.6 - - - -
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Residues in contact with ARG 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E SER* 2.5 45.2 + - - +
183E ILE* 3.0 35.4 + - - +
184E SER 3.1 18.8 + - - -
185E LEU* 3.6 32.3 - - + +
187E ARG* 4.3 6.6 - - + +
221E SER* 3.1 22.1 + - - +
222E THR* 4.1 11.5 - - - +
224E MET* 1.3 75.8 - - - +
226E THR* 1.3 55.1 + - - +
228E HIS 3.6 0.2 - - - -
229E SER* 2.6 37.1 + - - -
304E CYS 4.4 0.9 - - - +
305E GLU* 3.9 36.6 + - + +
338E TYR* 4.2 12.5 - - - -
441E ILE* 5.7 0.6 - - - +
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Residues in contact with THR 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ILE* 3.9 24.5 - - + -
222E THR 2.9 9.8 + - - -
223E LEU* 3.3 10.8 - - - -
224E MET 3.0 0.4 - - - -
225E ARG* 1.3 79.8 - - - +
227E VAL* 1.3 62.2 + - - +
229E SER* 3.1 5.6 + - - +
230E VAL* 3.0 31.2 + - + +
300E LEU* 5.1 2.9 - - + -
301E ASP 3.9 15.0 - - - +
302E ALA 2.8 22.1 + - - +
304E CYS* 2.8 36.5 + - + +
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Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ILE* 4.0 21.8 - - + -
223E LEU* 3.3 11.2 + - + +
224E MET* 3.2 14.0 + - - +
226E THR* 1.3 76.8 - - - +
228E HIS* 1.3 67.2 + - - +
230E VAL* 3.0 9.0 + - - +
231E ILE* 2.9 23.8 + - + +
242E ILE* 4.3 12.1 - - + -
244E LEU* 4.0 22.9 - - + -
262E ILE* 6.1 0.2 - - + -
265E TRP* 3.6 32.1 - - + -
269E VAL* 4.2 17.0 - - + -
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Residues in contact with HIS 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 3.1 42.3 - - + +
186E ASP* 2.7 31.8 + - - +
224E MET* 2.8 30.9 + - + +
225E ARG 3.7 0.4 - - - +
227E VAL* 1.3 73.0 - - - +
229E SER* 1.3 61.7 + - - +
231E ILE* 3.3 5.4 + - - +
232E LYS* 2.9 27.9 + - - +
261E TYR* 2.8 28.1 + - - -
264E LEU* 4.8 6.3 - - + -
265E TRP* 3.7 29.0 + + - -
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Residues in contact with SER 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU 4.5 1.7 + - - -
225E ARG* 2.6 23.7 + - - -
226E THR 3.1 7.3 + - - -
228E HIS* 1.3 76.5 - - - +
230E VAL* 1.3 64.5 + - - +
232E LYS* 3.4 2.6 + - - +
233E ARG* 3.2 42.0 + - - +
305E GLU* 3.8 12.5 - - - -
306E VAL* 3.0 35.7 + - - +
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Residues in contact with VAL 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E VAL* 4.3 19.5 - - + -
213E ILE* 5.2 1.6 - - + -
226E THR* 3.0 21.6 + - + +
227E VAL* 3.0 7.8 + - - +
229E SER* 1.3 79.9 - - - +
231E ILE* 1.3 55.2 + - - +
234E THR* 2.6 55.0 + - + +
239E LEU* 4.6 3.8 - - + -
242E ILE* 3.8 21.5 - - + -
300E LEU* 4.1 23.8 - - + -
306E VAL* 4.4 10.3 - - + -
310E TRP* 4.2 7.9 - - + -
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Residues in contact with ILE 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E VAL* 2.9 17.2 + - + +
228E HIS* 3.9 5.2 - - - +
230E VAL* 1.3 76.6 - - - +
232E LYS* 1.3 63.1 + - - +
233E ARG 3.3 0.7 + - - -
234E THR* 3.8 16.0 + - - +
236E ARG* 6.2 0.2 - - - +
239E LEU* 4.7 4.7 - - + -
242E ILE* 3.7 23.3 - - + -
265E TRP* 3.1 49.4 - - + +
268E LEU* 4.4 12.1 - - + -
269E VAL* 4.2 5.8 - - + -
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Residues in contact with LYS 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E GLU* 2.5 37.2 + - + +
142E PRO* 2.9 30.9 + - - -
144E GLY 4.6 0.6 - - - +
186E ASP* 3.0 44.1 + - + +
188E SER 4.5 0.8 - - - +
228E HIS 2.9 18.4 + - - +
229E SER* 3.8 5.6 - - - +
231E ILE* 1.3 80.1 - - - +
233E ARG* 1.3 71.8 + - + +
234E THR 5.0 0.5 - - - +
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Residues in contact with ARG 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E GLU* 3.0 32.7 + - - +
187E ARG 3.0 27.3 + - - -
189E VAL* 3.6 26.8 - - - +
229E SER* 3.2 32.4 + - - +
231E ILE 3.3 0.2 - - - -
232E LYS* 1.3 91.1 - - + +
234E THR* 1.3 65.0 + - - +
235E PRO* 4.1 4.9 - - - +
305E GLU* 5.0 3.6 + - - +
306E VAL* 2.8 39.4 + - + +
307E ALA* 3.7 22.2 - - - +
308E VAL* 3.8 13.6 - - + +
309E ASN* 4.5 8.5 + - - +
310E TRP* 3.5 12.4 + - - -
311E TYR* 5.2 0.5 - - - +
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Residues in contact with THR 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E VAL* 2.6 34.2 + - + +
231E ILE 3.8 10.9 + - - +
232E LYS 3.6 0.9 - - - +
233E ARG* 1.3 79.6 - - - +
235E PRO* 1.4 74.9 - - - +
236E ARG* 3.3 6.1 + - - +
238E TYR* 6.2 0.9 - - - -
239E LEU* 3.6 24.8 - - + +
310E TRP* 3.0 44.4 - - + +
311E TYR* 4.9 6.7 - - + -
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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