Contacts of the helix formed by residues 243 - 258 (chain E) in PDB entry 3IZ0
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 PHE 243 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228E TYR* 5.1 0.9 - - - +
232E CYS* 3.4 53.4 - - + -
235E SER* 4.4 8.3 - - - -
236E PHE* 4.0 20.6 - + + -
240E ALA 4.6 4.9 - - - -
241E ASP 3.8 18.4 - - - -
242E SER* 1.3 81.4 - - - +
244E ASP* 1.3 60.3 + - - +
245E GLU 3.5 2.2 - - - -
246E MET* 4.0 10.8 - - - -
247E ASN* 2.8 42.8 + - - +
130F PHE* 4.0 24.0 - + - -
134F CYS* 6.5 0.2 - - - -
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Residues in contact with ASP 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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242E SER* 3.3 24.5 + - - -
243E PHE* 1.3 69.6 + - - +
245E GLU* 1.3 58.7 + - - +
247E ASN* 4.3 8.1 + - - +
248E ALA* 2.7 38.7 + - + +
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Residues in contact with GLU 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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243E PHE 3.5 0.2 - - - -
244E ASP* 1.3 78.6 - - - +
246E MET* 1.3 78.4 + - + +
248E ALA* 3.7 4.8 - - - +
249E GLU* 3.0 29.1 + - - +
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Residues in contact with MET 246 (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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228E TYR* 3.8 10.6 - - + +
231E LYS* 4.1 18.4 - - + +
232E CYS* 3.7 39.3 - - - +
235E SER* 3.1 34.5 - - - +
242E SER 5.1 0.4 - - - +
243E PHE* 3.5 23.3 + - - +
245E GLU* 1.3 97.6 - - + +
247E ASN* 1.3 60.7 + - - +
249E GLU* 3.4 9.4 + - - +
250E LEU* 2.9 28.2 + - - +
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Residues in contact with ASN 247 (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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228E TYR* 2.7 30.7 + - - -
243E PHE* 2.8 35.4 + - - +
244E ASP* 3.8 7.7 + - - +
246E MET* 1.3 74.1 - - - +
248E ALA* 1.3 66.1 + - - +
250E LEU* 3.1 7.2 + - - +
251E GLN* 3.0 31.3 + - - +
137F THR* 3.8 5.7 - - - +
141F PHE* 3.7 27.5 - - + -
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Residues in contact with ALA 248 (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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244E ASP 2.7 22.6 + - - +
245E GLU* 3.7 5.6 - - - +
247E ASN* 1.3 73.9 - - - +
249E GLU* 1.3 61.9 + - - +
251E GLN* 3.2 13.1 + - - +
252E SER* 3.1 23.4 + - - -
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Residues in contact with GLU 249 (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 ASP* 4.5 0.2 - - - +
231E LYS* 2.9 41.6 + - - +
245E GLU 3.0 17.9 + - - +
246E MET* 3.8 7.8 - - - +
248E ALA* 1.3 75.7 - - - +
250E LEU* 1.3 62.6 + - - +
252E SER* 3.4 9.7 + - - -
253E LYS* 3.3 51.5 + - + +
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Residues in contact with LEU 250 (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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224E LEU* 4.0 23.1 - - + -
228E TYR* 3.9 33.0 - - + -
246E MET 2.9 18.3 + - - +
247E ASN 3.1 6.3 + - - +
249E GLU* 1.3 76.6 - - - +
251E GLN* 1.3 55.4 + - - +
253E LYS* 3.4 6.5 + - - +
254E LEU* 3.1 34.7 + - + +
138F TYR* 3.7 41.3 - - + -
141F PHE* 3.6 31.9 - - + -
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Residues in contact with GLN 251 (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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247E ASN* 3.0 23.7 + - - +
248E ALA* 3.2 10.4 + - - +
250E LEU* 1.3 75.7 - - - +
252E SER* 1.3 64.4 + - - +
254E LEU* 3.3 4.9 + - - +
255E LYS* 3.0 39.8 + - - +
141F PHE* 3.5 39.9 - - + -
144F GLN* 5.7 2.8 - - - +
145F TYR* 3.4 29.3 + - + +
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Residues in contact with SER 252 (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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248E ALA 3.1 12.3 + - - -
249E GLU* 3.5 15.4 - - - -
250E LEU 3.4 0.2 - - - -
251E GLN* 1.3 77.2 - - - +
253E LYS* 1.3 65.2 + - - +
255E LYS* 3.4 16.4 + - - +
256E ASP* 3.4 20.5 + - - +
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Residues in contact with LYS 253 (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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224E LEU* 3.5 32.7 - - + +
227E ASP* 2.9 29.3 + - - -
231E LYS* 4.0 1.4 - - - +
249E GLU* 3.3 46.1 + - + +
250E LEU* 3.8 7.0 - - - +
252E SER* 1.3 79.2 - - - +
254E LEU* 1.3 59.4 + - - +
256E ASP* 3.5 10.0 + - - +
257E LEU* 3.1 27.4 + - - +
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Residues in contact with LEU 254 (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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224E LEU* 4.0 20.6 - - + -
250E LEU* 3.1 34.1 + - + +
251E GLN* 3.3 4.9 + - - +
253E LYS* 1.3 74.4 - - - +
255E LYS* 1.3 64.2 + - - +
256E ASP 3.3 0.2 - - - -
257E LEU* 3.7 6.7 - - + -
258E PHE* 3.4 39.6 + - + +
138F TYR* 5.0 2.7 - - + +
141F PHE* 3.7 35.7 - - + +
142F LEU* 3.9 26.5 - - + +
145F TYR* 3.7 29.7 - - + -
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Residues in contact with LYS 255 (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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251E GLN* 3.0 25.7 + - - +
252E SER* 3.6 12.3 - - - +
254E LEU* 1.3 77.7 - - - +
256E ASP* 1.3 63.1 + - - +
258E PHE 3.1 21.1 - - - +
259E ASN* 3.5 8.5 + - - +
260E VAL 3.0 25.7 + - - +
261E ASP* 4.5 17.0 - - + +
145F TYR* 3.3 28.6 + - + -
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Residues in contact with ASP 256 (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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252E SER* 3.4 16.1 + - - +
253E LYS* 3.8 10.0 - - - +
254E LEU 3.3 0.4 - - - -
255E LYS* 1.3 78.1 - - - +
257E LEU* 1.3 62.7 + - - +
258E PHE* 3.4 0.7 - - - -
259E ASN* 4.2 12.2 - - - +
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Residues in contact with LEU 257 (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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221E HIS* 3.9 44.4 - - + +
224E LEU* 4.7 16.2 - - + -
253E LYS 3.1 15.0 + - - +
254E LEU* 3.5 10.7 + - + +
255E LYS 3.3 0.6 - - - -
256E ASP* 1.3 78.5 - - - +
258E PHE* 1.3 82.2 + - + +
259E ASN 4.1 0.4 - - - -
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Residues in contact with PHE 258 (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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221E HIS* 4.3 15.7 - + - -
254E LEU* 3.4 32.1 + - + +
255E LYS 3.1 7.6 - - - +
257E LEU* 1.3 110.4 - - + +
259E ASN* 1.3 53.1 + - - +
260E VAL* 2.5 31.2 + - + +
142F LEU* 4.4 8.7 - - + -
145F TYR* 3.6 31.4 - - + +
146F LYS* 4.2 20.0 - - + -
149F ALA* 3.8 26.9 - - + -
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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