Contacts of the helix formed by residues 224 - 235 (chain E) in PDB entry 1MDU
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 224 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A THR* 4.2 16.1 + - - -
222E ALA* 4.1 2.0 - - - +
223E LEU* 1.3 80.0 - - + +
225E PHE* 1.3 64.3 + - - +
226E GLU* 3.3 12.3 + - - +
227E ASN* 3.1 40.1 + - + +
228E GLU* 3.0 23.9 + - - +
317E LYS* 4.1 15.9 + - - +
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Residues in contact with PHE 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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222E ALA* 4.1 8.7 + - + +
223E LEU 4.1 1.2 + - - -
224E ASP* 1.3 72.4 + - - +
226E GLU* 1.3 72.7 + - + +
228E GLU* 3.2 4.2 + - - +
229E MET* 2.9 47.6 + - + +
257E PHE* 3.7 30.1 - + - -
258E ARG* 4.0 11.0 - - + -
261E GLU* 3.5 44.9 - - + +
265E GLN* 3.8 13.7 - - - +
268E PHE* 3.7 28.9 - + - -
314E ARG* 4.7 7.0 - - - +
317E LYS* 5.4 0.2 - - - +
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Residues in contact with GLU 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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224E ASP* 3.3 8.2 + - - +
225E PHE* 1.3 85.5 - - + +
227E ASN* 1.3 64.8 + - - +
229E MET* 3.2 8.8 + - - +
230E ALA* 3.0 22.3 + - - +
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Residues in contact with ASN 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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32A THR* 3.1 25.8 + - - +
33A ASN* 3.7 24.3 + - - +
35A TYR* 4.9 1.6 - - - +
472A TRS 3.1 34.9 + - - +
224E ASP* 3.1 34.8 + - + +
226E GLU* 1.3 79.7 - - - +
228E GLU* 1.3 58.5 + - + +
230E ALA* 3.2 7.7 + - - +
231E THR* 2.9 32.5 + - - -
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Residues in contact with GLU 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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111A LYS* 3.9 28.1 + - - +
472A TRS 4.9 4.7 + - - -
220E TYR* 2.5 36.8 + - - -
222E ALA* 3.1 27.8 - - + -
223E LEU 4.8 2.7 - - - +
224E ASP 3.0 11.3 + - - +
225E PHE 3.6 4.7 - - - +
227E ASN* 1.3 75.1 - - + +
229E MET* 1.3 65.3 + - - +
231E THR* 3.3 7.8 + - - -
232E ALA* 2.9 19.4 + - - +
238E LEU* 3.6 14.6 - - - +
257E PHE* 3.3 27.2 - - + -
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Residues in contact with MET 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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225E PHE* 2.9 46.1 + - + +
226E GLU* 3.5 10.8 - - - +
227E ASN 3.2 0.2 - - - -
228E GLU* 1.3 77.7 - - - +
230E ALA* 1.3 62.6 + - - +
232E ALA* 3.3 3.2 + - - +
233E ALA* 3.0 23.7 + - - +
254E ASN* 4.0 26.0 + - - +
257E PHE* 3.6 20.9 - - + -
258E ARG* 4.2 11.9 - - - -
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Residues in contact with ALA 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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226E GLU 3.0 13.0 + - - +
227E ASN* 3.2 11.2 + - - +
229E MET* 1.3 78.3 - - - +
231E THR* 1.3 63.2 + - - +
233E ALA* 3.2 6.7 + - - +
234E SER* 3.0 28.6 + - - +
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Residues in contact with THR 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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111A LYS* 3.8 15.0 - - + -
112A SER* 3.7 21.1 - - - -
472A TRS 3.9 24.8 + - - -
227E ASN 2.9 18.1 + - - -
228E GLU* 3.6 8.4 + - - -
230E ALA* 1.3 77.2 - - - +
232E ALA* 1.3 61.9 + - - +
234E SER* 3.1 13.0 + - - -
235E SER* 3.1 14.7 + - - -
237E SER* 3.7 22.0 - - - +
238E LEU* 3.9 13.0 - - + -
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Residues in contact with ALA 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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228E GLU 2.9 17.4 + - - +
229E MET 3.7 4.3 - - - +
231E THR* 1.3 76.9 - - - +
233E ALA* 1.3 57.7 + - - +
235E SER 3.2 18.1 - - - +
238E LEU* 4.0 18.6 - - + +
239E GLU* 4.7 9.0 - - - +
253E GLY 5.2 0.2 - - - -
254E ASN* 3.9 36.8 - - + +
257E PHE* 4.2 0.7 - - + -
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Residues in contact with ALA 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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229E MET 3.0 16.9 + - - +
230E ALA* 3.7 8.1 - - - +
231E THR 3.2 0.2 - - - -
232E ALA* 1.3 77.4 - - - +
234E SER* 1.3 61.1 + - - +
235E SER 3.7 0.2 - - - -
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Residues in contact with SER 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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112A SER* 5.3 6.1 - - - -
230E ALA* 3.0 16.8 + - - +
231E THR* 3.1 6.1 + - - -
233E ALA* 1.3 81.2 - - - +
235E SER* 1.3 61.2 + - - +
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Residues in contact with SER 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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112A SER* 3.7 18.1 - - - -
231E THR 3.1 11.6 + - - +
232E ALA* 3.2 19.6 - - - +
233E ALA 3.7 0.8 - - - -
234E SER* 1.3 79.2 - - - +
236E SER* 1.3 59.6 + - - +
237E SER* 3.0 27.7 + - - -
238E LEU 4.9 1.0 + - - -
239E GLU* 4.6 3.3 - - - +
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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
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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