Contacts of the strand formed by residues 232 - 242 (chain B) in PDB entry 6MZL
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 LYS 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B THR* 3.8 0.9 - - - +
208B VAL* 2.9 42.5 + - + +
209B ASP 4.8 0.4 - - - +
210B ALA* 3.7 33.7 - - + +
223B THR* 3.6 6.6 - - - +
224B VAL 2.4 38.6 + - - -
225B TYR* 3.3 20.4 - - + +
226B THR* 4.0 6.5 - - - +
227B HIS* 4.0 2.6 + - - -
231B LYS* 1.3 80.9 - - - +
233B THR* 1.3 69.3 + - - +
234B PHE* 3.5 23.6 - - + -
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Residues in contact with THR 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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205B GLU* 3.6 35.2 - - + +
206B PHE 2.9 16.6 + - - +
207B THR* 4.1 10.8 + - - +
222B GLU 4.1 2.6 - - - +
223B THR* 3.6 5.9 + - - -
226B THR* 3.1 40.0 + - + +
227B HIS* 3.2 17.4 + - - -
232B LYS* 1.3 85.5 + - - +
234B PHE* 1.3 64.5 + - - +
235B HIS* 4.9 5.2 - - - +
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Residues in contact with PHE 234 (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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204B LEU 3.1 6.2 - - - +
205B GLU* 3.3 3.3 - - - -
206B PHE* 2.9 44.5 + + + +
208B VAL* 3.6 28.9 - - + -
209B ASP 5.0 0.4 - - - -
210B ALA 5.8 0.9 - - - -
212B MET 4.5 0.7 - - - -
213B VAL* 3.9 20.6 - - + -
214B ALA* 3.4 42.8 - - + -
220B LEU* 6.5 0.2 - - + -
223B THR* 3.3 20.6 - - + +
232B LYS* 3.5 32.3 - - + -
233B THR* 1.3 79.3 - - - +
235B HIS* 1.3 63.4 + - - +
236B TYR* 3.9 11.9 - + + -
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Residues in contact with HIS 235 (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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203B LYS* 3.4 32.8 - - + +
204B LEU 3.2 8.9 + - - +
205B GLU* 4.2 31.1 + - + +
219B ASP 3.1 0.5 - - - +
220B LEU* 3.7 1.2 - - - -
221B VAL* 2.9 32.6 + - + -
222B GLU* 3.2 56.2 + - + +
223B THR* 3.5 1.5 + - - -
226B THR* 5.6 5.0 - - + +
233B THR* 4.9 7.3 - - + +
234B PHE* 1.3 74.2 + - - +
236B TYR* 1.3 67.4 - - - +
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Residues in contact with TYR 236 (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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203B LYS* 4.7 0.4 - - - -
204B LEU* 2.9 38.3 + - + +
206B PHE* 3.5 15.4 - + + -
213B VAL* 5.1 4.2 - - - +
214B ALA 3.2 28.0 + - - -
215B VAL* 3.6 11.1 - - + +
216B SER* 3.1 41.5 - - - +
217B ASN 3.4 19.1 - - - +
218B GLY 5.2 0.7 - - - -
219B ASP* 2.9 15.5 - - - +
220B LEU* 3.5 39.9 - - + +
221B VAL* 4.3 0.2 - - - -
223B THR* 5.8 1.3 - - - -
234B PHE* 3.9 13.4 - + + -
235B HIS* 1.3 80.7 - - - +
237B MET* 1.3 61.7 + - - +
238B LEU 4.0 0.4 - - - -
268B PHE* 5.4 2.3 - - - -
305B LYS* 5.3 4.3 - - + +
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Residues in contact with MET 237 (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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30B HIS* 5.3 5.6 - - + -
201B THR* 5.2 1.1 - - - +
202B TRP 3.3 15.9 - - - +
203B LYS* 3.7 37.2 - - + +
218B GLY* 3.4 1.1 - - - -
219B ASP* 2.9 35.5 + - - +
221B VAL* 3.6 27.1 - - + +
236B TYR* 1.3 74.1 - - - +
238B LEU* 1.3 61.1 + - - +
239B THR* 3.7 23.5 + - - +
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Residues in contact with LEU 238 (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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201B THR* 2.3 28.6 + - - -
202B TRP* 2.9 33.5 + - + +
204B LEU* 5.5 2.4 - - + +
217B ASN* 4.0 24.9 - - + +
218B GLY* 3.7 23.5 - - - +
219B ASP* 5.6 0.2 - - - +
236B TYR 4.0 1.4 - - - -
237B MET* 1.3 71.2 - - - +
239B THR* 1.3 53.6 - - - +
240B ILE* 3.3 43.3 - - + +
242B THR* 3.3 33.2 - - + +
301B TYR* 4.5 9.2 - - + +
320B ALA* 5.0 3.1 - - + -
321B SER* 5.9 0.4 - - - +
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Residues in contact with THR 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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201B THR* 3.4 14.8 + - - +
219B ASP* 5.2 4.8 + - - -
221B VAL* 6.0 0.5 - - - +
237B MET* 3.7 24.6 + - - +
238B LEU* 1.3 74.3 - - - +
240B ILE* 1.3 72.4 + - - +
241B PRO* 3.3 7.1 - - - +
485B SER* 5.4 7.6 - - - -
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Residues in contact with ILE 240 (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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200B CYS 4.0 2.1 - - - +
219B ASP* 4.8 12.3 - - - +
238B LEU* 3.3 35.5 - - + +
239B THR* 1.3 82.4 - - - +
241B PRO* 1.3 75.2 - - + +
242B THR* 3.1 9.9 + - + +
300B PRO 5.4 0.4 - - - +
301B TYR* 3.8 28.3 - - + -
302B SER* 5.1 9.0 - - - +
358B PHE* 3.6 33.2 - - + -
484B SER* 5.1 4.5 - - - +
485B SER* 5.5 8.1 - - - +
496B MET* 5.6 0.2 - - + -
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Residues in contact with PRO 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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199B LEU* 3.9 10.6 - - + +
200B CYS 3.2 14.1 - - - +
201B THR* 4.9 1.6 - - - -
239B THR 3.3 8.3 - - - +
240B ILE* 1.3 88.3 - - + +
242B THR* 1.3 60.4 + - - +
484B SER* 3.7 16.4 - - - -
485B SER* 3.6 17.5 - - - +
493B TRP* 3.6 42.2 - - + +
496B MET* 3.5 23.9 - - - +
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Residues in contact with THR 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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198B GLU 3.3 1.1 - - - +
199B LEU* 3.4 8.0 - - - -
200B CYS 2.6 39.9 + - - +
202B TRP* 3.1 19.1 - - - -
217B ASN* 5.1 0.9 + - - -
238B LEU* 3.3 21.3 - - + +
240B ILE* 3.1 20.7 + - + +
241B PRO* 1.3 75.9 - - - +
243B ALA* 1.3 64.5 + - - +
246B ASN* 4.4 12.9 + - - +
301B TYR* 4.1 16.8 - - - +
320B ALA* 4.9 3.8 - - + -
357B CYS 4.6 15.3 - - - +
358B PHE* 4.9 1.6 - - + -
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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