Contacts of the helix formed by residues 207 - 219 (chain B) 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 GLU 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B SER* 3.1 12.2 + - - +
202B PHE* 2.9 45.1 - - + +
204B THR* 2.7 29.4 + - - +
205B THR 3.1 1.0 - - - +
206B ALA* 1.4 81.3 - - + +
208B ARG* 1.3 61.6 + - - +
209B GLU 3.0 1.1 - - - -
210B ILE* 3.0 19.9 + - + +
211B VAL* 3.2 10.6 + - - +
245B PRO* 6.6 0.2 - - + -
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TYR* 5.3 6.3 + - - -
185B ARG* 4.3 21.1 + - - +
188B THR* 3.8 16.4 - - - +
189B ASP* 2.7 29.1 + - - -
192B MET* 3.0 42.3 - - + +
202B PHE* 3.9 6.1 - - - +
203B VAL* 4.7 5.2 - - + -
204B THR 4.2 13.5 - - - +
205B THR* 3.5 13.0 + - - +
207B GLU* 1.3 78.3 - - - +
209B GLU* 1.3 59.4 + - - +
211B VAL* 3.4 4.3 + - - +
212B ARG* 3.3 21.0 + - - +
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN* 3.8 19.7 + - - -
205B THR* 3.0 24.1 + - - +
206B ALA* 3.4 14.3 - - - +
208B ARG* 1.3 75.7 - - - +
210B ILE* 1.3 62.9 + - + +
212B ARG* 3.7 31.0 + - - +
213B ASP* 3.2 22.5 + - - +
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B PHE* 4.5 8.5 - - + -
206B ALA 2.7 24.9 - - - +
207B GLU* 3.0 17.4 + - + +
209B GLU* 1.3 79.1 - - + +
211B VAL* 1.3 58.7 + - - +
213B ASP* 3.7 4.4 - - + +
214B ILE* 3.0 34.5 + - + +
242B TYR* 3.9 18.8 + - + +
244B LEU* 3.7 27.1 - - + -
245B PRO* 3.3 35.0 - - + -
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B THR* 3.8 15.9 - - + +
191B LEU* 3.8 17.4 - - + +
192B MET* 3.7 35.7 - - + +
195B LEU* 4.5 3.8 - - + -
202B PHE* 3.7 38.1 - - + -
207B GLU 3.2 14.5 + - - +
208B ARG* 3.4 7.6 + - - +
209B GLU 3.4 0.2 - - - -
210B ILE* 1.3 75.8 - - - +
212B ARG* 1.3 66.1 + - - +
214B ILE* 3.0 9.2 + - - +
215B LYS* 2.9 21.5 + - - +
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Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ASP* 5.7 2.0 - - - -
188B THR* 4.1 23.9 - - + +
208B ARG* 3.3 12.3 + - - +
209B GLU* 3.9 37.6 + - - +
211B VAL* 1.3 79.6 - - - +
213B ASP* 1.3 60.1 + - - +
215B LYS* 3.2 5.5 + - - +
216B GLU* 2.9 73.3 + - - +
400B ATP 3.6 19.0 - - - +
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Residues in contact with ASP 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B GLU 3.2 16.6 + - - +
210B ILE* 3.7 6.5 - - + +
211B VAL 3.1 0.6 - - - -
212B ARG* 1.3 80.9 + - - +
214B ILE* 1.3 64.5 + - - +
216B GLU* 3.9 9.3 - - - +
217B LYS* 3.0 58.5 + - - +
242B TYR* 2.6 29.7 + - - +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 4.2 9.6 - - + -
195B LEU* 4.2 16.6 - - + -
202B PHE* 5.3 1.6 - - + -
210B ILE* 3.0 32.2 + - + +
211B VAL* 3.0 11.5 + - + +
213B ASP* 1.3 76.3 - - - +
215B LYS* 1.3 57.6 + - - +
217B LYS* 4.8 0.2 - - - -
218B LEU* 2.8 41.2 + - + +
219B CYS* 3.9 0.6 + - - -
242B TYR* 3.8 29.4 - - + -
250B ILE* 3.7 28.7 - - + -
252B ILE* 3.6 31.0 - - + -
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B GLY* 3.3 21.4 + - - -
187B LEU* 4.0 14.4 - - + -
188B THR* 2.9 30.4 + - - +
191B LEU* 3.8 9.4 - - + +
211B VAL 2.9 12.2 + - - +
212B ARG* 3.3 8.3 - - - +
214B ILE* 1.3 78.4 - - - +
216B GLU* 1.3 73.2 + - - +
219B CYS* 3.1 43.8 + - - +
259B CYS* 4.2 5.8 - - - -
308B TYR* 3.1 34.7 + - + +
400B ATP 2.8 32.8 + - - -
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ARG* 2.9 47.8 + - - +
213B ASP* 4.2 9.5 - - - +
215B LYS* 1.3 80.4 - - - +
217B LYS* 1.3 62.1 + - + +
219B CYS 5.1 1.5 - - - +
309B PRO* 6.1 0.9 - - - +
338B LYS* 5.2 2.4 + - - -
400B ATP 2.8 89.7 + - + +
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Residues in contact with LYS 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ASP* 3.0 50.0 + - - +
214B ILE* 4.2 1.6 - - - +
216B GLU* 1.3 82.0 - - + +
218B LEU* 1.3 77.3 + - + +
219B CYS 3.8 1.5 - - - +
242B TYR* 5.1 7.0 - - + -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ILE* 2.8 28.5 + - + +
217B LYS* 1.3 91.8 - - + +
219B CYS* 1.3 64.4 + - - +
220B TYR* 4.8 0.2 - - - +
240B LYS* 4.0 24.0 - - + -
241B SER 4.2 13.2 - - - +
242B TYR* 4.0 26.9 - - + -
252B ILE* 3.8 32.5 - - + -
256B ARG* 2.8 38.0 + - - +
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Residues in contact with CYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 4.3 9.9 - - - -
214B ILE 4.5 1.1 - - - -
215B LYS* 3.1 38.3 + - - +
216B GLU 5.5 1.0 - - - +
217B LYS 5.1 1.7 - - - +
218B LEU* 1.3 78.9 + - - +
220B TYR* 1.3 63.7 + - - +
252B ILE* 5.6 2.7 - - - -
255B GLU 4.4 0.9 - - - -
256B ARG* 3.2 24.5 - - - +
259B CYS* 4.0 20.0 - - - -
260B PRO* 3.8 3.1 - - + -
308B TYR* 3.7 20.0 - - + -
309B PRO* 3.4 17.0 - - - +
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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