Contacts of the helix formed by residues 232 - 248 (chain B) in PDB entry 4MZ7
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 THR 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ASP* 3.9 7.2 - - - -
230B LYS 5.5 0.2 - - - -
231B TRP* 1.3 92.3 - - - +
233B HIS* 1.3 65.0 + - - +
234B GLU* 3.4 16.4 + - - +
235B GLN* 3.1 40.7 + - - +
236B GLY 3.1 15.8 + - - -
273B VAL* 5.3 0.5 - - - +
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Residues in contact with HIS 233 (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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206B HIS 4.7 4.5 - - - -
207B ASP* 3.8 11.1 + - - -
209B GLY* 3.4 20.8 - - - +
210B HIS* 3.3 51.1 + + - +
211B GLY 5.4 0.2 - - - +
218B ASP* 2.8 36.8 + - + +
231B TRP* 4.6 2.9 - - - +
232B THR* 1.3 74.2 - - - +
234B GLU* 1.3 82.2 + - + +
236B GLY* 3.1 2.8 + - - -
237B SER* 2.8 36.9 + - - -
804B DGT 5.7 4.7 - - - -
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B HIS 5.3 2.2 - - - +
218B ASP* 4.8 0.2 - - - +
232B THR* 3.4 19.3 - - - +
233B HIS* 1.3 108.5 + - + +
235B GLN* 1.3 61.2 + - - +
237B SER* 3.1 19.4 + - - -
238B VAL* 3.2 16.8 + - - +
272B ILE* 4.0 21.7 - - + +
273B VAL* 3.9 18.8 - - + +
804B DGT 5.7 1.2 + - - -
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Residues in contact with GLN 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LYS* 2.8 30.3 + - - +
231B TRP* 3.9 10.9 - - + +
232B THR* 3.1 41.0 + - - +
234B GLU* 1.3 75.3 - - - +
236B GLY* 1.3 62.1 - - - +
238B VAL* 3.3 7.8 + - - +
239B MET* 3.1 32.4 + - - +
273B VAL* 4.1 14.5 - - + +
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Residues in contact with GLY 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLY* 3.3 11.8 - - - -
231B TRP* 3.3 30.6 - - - -
232B THR 3.1 4.8 + - - -
233B HIS 3.1 8.2 + - - -
235B GLN* 1.3 77.0 - - - +
237B SER* 1.3 58.2 + - - +
239B MET* 3.4 4.1 + - - +
240B MET* 2.8 32.6 + - - +
416B MET* 4.4 2.4 - - - +
419B TYR* 5.3 0.7 - - - -
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B CYS 3.7 11.4 - - - +
206B HIS 2.7 28.3 + - - -
207B ASP* 3.5 1.6 - - - -
208B LEU* 3.3 5.9 + - - +
209B GLY* 2.8 23.2 + - - +
233B HIS 2.8 18.3 + - - -
234B GLU 3.1 8.9 + - - -
236B GLY* 1.3 72.5 - - - +
238B VAL* 1.3 59.1 + - - +
240B MET* 4.0 0.5 - - - +
241B PHE* 2.8 32.8 + - - +
272B ILE* 3.8 11.4 - - - -
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLU 3.2 6.0 + - - +
235B GLN* 3.3 9.4 + - - +
237B SER* 1.3 78.1 - - - +
239B MET* 1.3 60.8 + - + +
241B PHE* 3.6 5.3 - - - +
242B GLU* 3.0 28.9 + - + +
269B LYS* 3.8 44.9 - - + +
272B ILE* 4.5 7.0 - - + -
273B VAL* 3.8 36.8 - - + -
276B LEU* 5.4 5.2 - - + -
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Residues in contact with MET 239 (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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231B TRP* 4.1 17.9 - - - -
235B GLN* 3.1 20.3 + - - +
236B GLY 3.8 3.4 - - - +
238B VAL* 1.3 78.0 - - + +
240B MET* 1.3 58.5 + - - +
242B GLU* 3.5 6.8 + - - +
243B HIS* 3.0 28.2 + - - +
413B ILE 3.6 20.9 - - - +
414B ASP* 4.7 11.2 - - - +
416B MET* 3.7 24.8 - - + +
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Residues in contact with MET 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 3.7 39.7 - - + +
143B ARG* 4.4 9.4 - - - +
208B LEU* 3.9 32.1 - - + +
209B GLY* 5.0 0.4 - - - -
236B GLY 2.8 21.9 + - - +
239B MET* 1.3 70.4 - - - +
241B PHE* 1.3 55.2 + - - +
243B HIS* 3.4 9.0 + - - +
244B LEU* 2.7 32.7 + - - +
416B MET* 3.6 24.4 - - - +
419B TYR* 3.7 20.6 - - + -
420B THR* 3.7 28.0 - - - +
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Residues in contact with PHE 241 (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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135B ILE* 5.1 3.1 - - + -
201B ILE* 3.7 19.1 - - + -
205B CYS* 3.7 25.6 - - + -
208B LEU* 3.8 11.4 - - + +
237B SER 2.8 20.1 + - - +
238B VAL* 3.6 4.3 - - - +
240B MET* 1.3 74.9 - - - +
242B GLU* 1.3 61.9 + - - +
244B LEU* 3.2 6.2 + - + +
245B ILE* 2.9 62.3 + - + +
254B MET* 4.3 3.8 - - + -
265B ILE* 4.1 20.4 - - + -
268B ILE* 3.5 45.5 - - + -
269B LYS* 4.2 18.6 - - + -
272B ILE* 5.2 4.0 - - + -
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Residues in contact with GLU 242 (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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238B VAL* 3.0 18.3 + - + +
239B MET* 3.7 7.2 - - - +
240B MET 3.4 0.2 - - - -
241B PHE* 1.3 77.2 - - - +
243B HIS* 1.3 60.6 + - - +
245B ILE* 3.4 7.5 + - - +
246B ASN* 2.8 56.4 + - - +
251B LYS* 5.6 4.5 + - - -
265B ILE* 4.3 8.7 - - - +
269B LYS* 2.6 35.7 + - - +
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Residues in contact with HIS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 3.7 33.8 - - - +
239B MET 3.0 18.3 + - - +
240B MET* 3.6 4.8 - - - +
242B GLU* 1.3 75.4 - - - +
244B LEU* 1.3 64.4 + - - +
246B ASN* 4.8 4.3 - - + +
247B SER* 2.7 52.7 + - - -
416B MET* 3.6 27.7 + - + +
417B GLU* 3.9 36.6 + - + +
420B THR* 4.1 2.0 - - - -
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Residues in contact with LEU 244 (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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135B ILE* 3.9 36.1 - - + +
138B THR* 3.6 27.8 - - + +
140B GLN* 3.9 21.1 - - + +
141B PHE* 4.2 8.5 - - + +
205B CYS* 4.8 1.6 - - - -
208B LEU* 4.0 21.8 - - + -
240B MET 2.7 19.9 + - - +
241B PHE* 3.2 7.2 + - + +
243B HIS* 1.3 72.5 + - - +
245B ILE* 1.3 70.0 + - + +
248B ASN* 2.9 33.1 + - - +
250B ILE* 4.1 16.8 - - + -
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Residues in contact with ILE 245 (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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135B ILE* 5.0 2.2 - - + -
241B PHE* 2.9 56.7 + - + +
242B GLU* 3.7 8.1 - - - +
244B LEU* 1.3 82.2 - - + +
246B ASN* 1.3 65.0 + - - +
249B GLY* 3.3 5.0 + - - -
250B ILE* 3.3 52.1 + - + -
251B LYS* 3.7 35.6 - - + +
254B MET* 3.9 9.2 - - + -
265B ILE* 3.9 15.0 - - + -
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Residues in contact with ASN 246 (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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242B GLU* 2.8 52.2 + - - +
243B HIS* 4.2 5.1 - - + +
245B ILE* 1.3 78.8 - - - +
247B SER* 1.3 61.1 + - - +
248B ASN 3.5 0.3 + - - -
249B GLY* 4.1 5.0 + - - -
251B LYS* 4.1 22.2 + - - -
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Residues in contact with SER 247 (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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450A TYR* 5.3 2.3 + - - -
140B GLN* 4.5 8.7 - - - -
243B HIS* 2.7 48.0 + - - -
246B ASN* 1.3 76.7 - - - +
248B ASN* 1.3 73.1 + - - +
249B GLY 3.7 0.2 - - - -
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Residues in contact with ASN 248 (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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450A TYR* 3.4 31.2 + - - -
134B ARG* 5.1 8.0 + - - -
138B THR* 3.5 19.0 - - + +
139B PRO* 4.1 0.9 - - - +
140B GLN* 2.9 27.9 + - - +
244B LEU 2.9 26.8 + - - +
247B SER* 1.3 87.7 - - - +
249B GLY* 1.3 66.0 + - - +
250B ILE* 3.4 20.8 + - + +
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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