Contacts of the helix formed by residues 230 - 245 (chain E) in PDB entry 4Q9U
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 ASP 230 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229E THR* 1.3 86.8 + - - +
231E ASP* 1.3 54.3 + - - -
232E GLU 3.4 2.7 - - - -
233E LYS* 2.9 29.0 + - + +
234E LYS* 2.7 72.2 + - + +
332E GLN* 3.9 9.9 + - - +
336E GLN* 4.9 2.9 + - - -
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Residues in contact with ASP 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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225E CYS* 4.1 5.8 - - - -
226E PRO* 3.3 5.7 - - - +
229E THR* 3.1 28.0 + - + -
230E ASP* 1.3 75.4 - - - +
232E GLU* 1.3 61.8 + - - +
234E LYS 3.2 0.3 + - - -
235E ASP* 2.7 34.5 + - - +
332E GLN* 3.3 20.8 - - - +
333E SER* 2.4 38.0 + - - +
336E GLN* 3.9 2.8 + - - +
340E ARG* 2.2 37.0 + - - -
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Residues in contact with GLU 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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225E CYS* 3.6 22.4 - - - -
229E THR 5.0 1.7 + - - +
230E ASP 3.4 0.2 - - - -
231E ASP* 1.3 76.9 - - - +
233E LYS* 1.3 74.3 + - + +
235E ASP* 3.0 26.7 + - - +
236E LEU* 3.0 32.8 + - + +
330E ARG* 5.4 1.9 - - - +
564H LEU* 4.9 5.4 - - + -
565H ARG* 3.9 13.4 + - + +
568H ASN* 2.9 45.6 - - + +
569H ASP* 3.9 2.4 + - - +
572H GLU* 2.7 29.5 - - - +
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Residues in contact with LYS 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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227E GLU 4.6 7.6 + - - -
228E THR 4.9 2.8 + - - -
229E THR* 2.9 32.3 + - - +
230E ASP* 2.9 24.2 + - + +
232E GLU* 1.3 86.8 - - + +
234E LYS* 1.3 56.7 + - + +
236E LEU* 3.0 11.8 + - - +
237E ALA* 3.0 21.7 + - - +
563G MET* 5.6 13.9 - - + -
561H GLN* 5.3 4.6 - - - +
564H LEU* 6.3 2.9 - - - -
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Residues in contact with LYS 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 ASP* 2.7 57.6 + - + +
233E LYS* 1.3 71.4 - - + +
235E ASP* 1.3 58.8 + - - +
237E ALA* 3.2 15.2 - - + +
238E ILE* 3.0 32.8 + - + +
332E GLN* 3.5 31.0 - - + +
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Residues in contact with ASP 235 (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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225E CYS* 4.7 0.7 - - - -
231E ASP 2.7 30.2 + - - +
232E GLU* 3.0 18.1 + - - +
234E LYS* 1.3 78.7 - - - +
236E LEU* 1.3 62.0 + - + +
238E ILE* 2.9 28.3 - - - +
239E GLN* 3.0 13.4 + - - +
330E ARG* 3.8 24.4 + - - +
331E LEU 3.1 5.6 - - - +
332E GLN* 2.3 38.0 + - - +
333E SER* 2.9 14.2 + - - -
572H GLU* 4.2 5.8 - - - +
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Residues in contact with LEU 236 (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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232E GLU* 3.0 35.4 + - + +
233E LYS* 3.0 10.2 + - - +
235E ASP* 1.3 80.9 - - - +
237E ALA* 1.3 64.1 + - - +
239E GLN* 3.9 9.6 - - + +
240E LYS* 2.9 38.5 + - - +
568H ASN* 4.8 4.5 - - - +
571H LEU* 3.6 31.4 - - + -
572H GLU* 3.3 28.9 - - + +
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Residues in contact with ALA 237 (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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233E LYS 3.0 7.7 + - - +
234E LYS* 3.2 26.9 - - + +
236E LEU* 1.3 76.6 - - - +
238E ILE* 1.3 59.9 + - + +
240E LYS* 3.2 12.9 - - - +
241E ARG* 3.0 33.6 + - - +
367E GLU* 6.3 2.5 - - + -
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Residues in contact with ILE 238 (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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234E LYS 3.0 14.4 + - - +
235E ASP* 2.9 22.0 - - - +
236E LEU 3.2 0.4 - - - -
237E ALA* 1.3 74.9 - - + +
239E GLN* 1.3 85.9 + - + +
241E ARG* 3.3 4.0 + - - +
242E ILE* 3.0 47.3 + - + +
327E ASN* 4.2 1.8 - - - +
328E PRO 3.3 26.5 - - - +
329E PRO* 5.6 0.2 - - + -
330E ARG 5.6 0.7 - - - +
331E LEU* 3.7 31.0 - - + +
332E GLN* 5.2 6.3 - - + +
335E ILE* 5.6 2.5 - - + -
363E VAL* 5.3 13.0 - - + -
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Residues in contact with GLN 239 (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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235E ASP* 3.0 16.5 + - - +
236E LEU* 3.4 12.5 + - - +
238E ILE* 1.3 85.3 - - + +
240E LYS* 1.3 60.2 + - - +
243E ARG* 2.7 60.1 + - - +
327E ASN* 3.7 13.2 - - - +
329E PRO* 5.8 3.0 - - - +
330E ARG 5.4 5.3 - - - +
571H LEU* 4.2 3.9 - - - +
572H GLU* 3.1 57.5 + - - +
575H MET* 3.2 21.7 - - - +
576H LYS* 4.9 2.7 - - + -
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Residues in contact with LYS 240 (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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236E LEU* 2.9 33.2 + - - +
237E ALA* 3.2 13.0 - - - +
239E GLN* 1.3 75.3 - - - +
241E ARG* 1.3 75.1 + - - +
243E ARG* 3.2 15.3 + - - +
244E ALA* 2.9 23.5 + - - +
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Residues in contact with ARG 241 (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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237E ALA 3.0 20.7 + - - +
238E ILE* 3.8 5.4 - - - +
240E LYS* 1.3 76.8 - - - +
242E ILE* 1.3 58.0 + - + +
244E ALA* 2.9 23.6 + - - +
245E LEU* 3.0 39.2 + - + +
366E ILE* 3.4 10.9 + - + +
367E GLU* 2.5 42.1 + - - +
368E LYS* 4.0 7.5 - - - +
369E LEU* 3.6 27.5 + - - +
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Residues in contact with ILE 242 (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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238E ILE* 3.0 31.4 + - + +
241E ARG* 1.3 73.9 - - + +
243E ARG* 1.3 68.5 + - - +
245E LEU* 2.9 18.1 + - - +
246E ARG* 3.4 9.0 + - - +
323E VAL* 4.9 8.1 - - + +
324E LEU* 3.8 41.2 - - + +
327E ASN* 3.1 57.0 - - + +
328E PRO* 3.9 11.9 - - + -
331E LEU* 5.4 1.1 - - + -
366E ILE* 5.7 4.0 - - + -
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Residues in contact with ARG 243 (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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239E GLN* 2.7 62.0 + - - +
240E LYS* 3.4 11.5 - - - +
242E ILE* 1.3 82.1 - - - +
244E ALA* 1.3 58.5 + - - +
246E ARG* 2.9 67.3 + - - +
327E ASN* 3.5 9.3 - - - +
575H MET* 3.3 35.2 - - - +
576H LYS* 4.2 1.2 - - - +
579H GLN* 3.2 39.9 + - + +
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Residues in contact with ALA 244 (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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240E LYS 2.9 12.1 + - - +
241E ARG* 2.9 16.8 + - - +
243E ARG* 1.3 77.8 - - - +
245E LEU* 1.3 69.2 + - + +
246E ARG* 3.3 6.5 + - - +
247E TRP* 3.7 10.2 + - - -
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Residues in contact with LEU 245 (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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241E ARG* 3.1 43.3 - - + +
242E ILE* 2.9 11.5 + - - +
244E ALA* 1.3 89.4 - - + +
246E ARG* 1.3 51.1 + - - +
247E TRP* 2.8 32.6 + - - +
248E VAL* 3.0 24.6 + - + +
324E LEU* 3.8 23.3 - - + +
366E ILE* 4.6 18.8 - - + +
369E LEU* 5.0 11.2 - - + +
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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
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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