Contacts of the strand formed by residues 243 - 251 (chain B) in PDB entry 3ME9
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 CYS 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLN* 3.6 28.7 - - - +
175B TRP 3.5 2.5 - - - -
176B ILE* 4.1 2.2 - - - -
237B LEU* 3.4 4.9 - - - -
238B TYR 2.9 26.0 + - - -
241B THR* 3.1 3.7 + - - +
242B THR* 1.3 82.6 - - - +
244B PHE* 1.3 59.5 + - - +
245B TYR* 3.5 26.5 - - + +
1D ALA* 4.0 15.3 - - - -
2D ARG 3.5 17.7 - - - +
3D THR* 3.8 18.4 - - - -
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA* 3.6 25.8 - - + -
174B GLN* 2.9 21.8 + - - -
175B TRP* 2.9 25.7 + - + +
176B ILE 3.8 11.2 - - - -
177B LEU* 3.7 26.5 - - + -
213B LEU* 3.9 26.9 - - + -
235B LEU* 4.1 20.9 - - + +
236B ALA* 3.3 10.8 - - - +
237B LEU* 3.5 34.3 - - + -
243B CYS* 1.3 73.0 - - - +
245B TYR* 1.3 61.5 + - - +
283B TYR* 3.5 27.4 - + - -
285B VAL* 4.6 4.3 - - + -
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Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLN* 3.6 20.9 + - - -
235B LEU* 3.5 8.2 - - - -
236B ALA 2.9 29.5 + - - +
238B TYR* 3.7 24.9 - - + -
241B THR* 4.3 1.1 - - - -
243B CYS* 3.5 37.4 - - + +
244B PHE* 1.3 76.2 - - - +
246B ARG* 1.3 65.6 + - - +
247B ALA 3.5 0.3 + - - -
264B PHE* 3.9 9.7 - - + -
3D THR* 3.8 7.1 - - - -
4D M3L 3.0 72.4 + - + +
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Residues in contact with ARG 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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224A PRO* 6.4 0.6 - - - +
225A GLU* 4.4 5.3 + - - +
233B LEU* 3.9 30.1 - - + +
234B VAL 3.5 5.8 - - - +
235B LEU* 3.8 7.1 - - + +
245B TYR* 1.3 75.6 - - - +
247B ALA* 1.3 61.4 + - - +
264B PHE* 3.7 4.7 - - - -
265B GLU* 2.8 72.4 + - + +
287B CYS* 3.8 16.8 - - - -
289B GLU* 2.8 40.3 + - + +
290B PRO* 3.8 11.9 - - - +
291B LYS* 3.5 34.9 - - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 3.5 8.7 - - - +
234B VAL* 2.9 40.7 + - + +
236B ALA* 4.3 1.8 - - + -
245B TYR 4.1 4.3 - - - +
246B ARG* 1.3 77.9 - - - +
248B LEU* 1.3 63.6 + - - +
262B VAL* 4.0 18.2 - - + -
263B LEU 3.2 16.6 - - - +
264B PHE* 3.9 18.4 - - + -
265B GLU* 4.3 2.9 - - - +
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Residues in contact with LEU 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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229A GLN* 4.0 19.5 - - + +
231B GLU* 3.4 40.2 - - - +
232B GLN 3.3 4.9 - - - +
233B LEU* 4.0 19.5 - - + -
247B ALA* 1.3 73.1 - - - +
249B ILE* 1.3 67.2 + - - +
262B VAL* 3.3 5.9 - - - +
263B LEU* 2.8 50.6 + - + +
265B GLU* 6.0 0.4 - - + +
273B TYR* 3.8 37.7 - - + +
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Residues in contact with ILE 249 (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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228B PHE* 3.8 19.1 - - + +
229B GLN 3.2 33.4 - - - +
230B LYS* 3.7 3.6 - - - +
231B GLU* 2.9 27.9 + - - +
232B GLN* 2.9 20.2 + - + +
234B VAL* 3.9 25.4 - - + -
248B LEU* 1.3 72.5 - - - +
250B HIS* 1.3 61.5 + - - +
251B ALA 3.7 26.0 - - - +
252B PRO 4.0 2.9 - - - -
260B TYR* 3.7 23.8 - - + -
261B SER 3.9 2.2 - - - +
262B VAL* 3.9 11.4 - - + +
263B LEU* 5.5 0.9 - - - +
284B VAL* 4.2 4.7 - - + -
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Residues in contact with HIS 250 (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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230B LYS* 3.5 23.7 - - + +
248B LEU 3.3 2.0 + - - -
249B ILE* 1.3 75.2 - - - +
251B ALA* 1.3 63.8 + - + +
261B SER* 2.8 40.3 + - - +
263B LEU* 4.0 28.5 - - + +
276B PRO* 3.8 22.8 - - + +
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Residues in contact with ALA 251 (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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249B ILE* 3.8 4.5 - - - -
250B HIS* 1.3 86.1 - - + +
252B PRO* 1.3 77.8 - - + +
259B ASP 4.5 0.3 - - - +
260B TYR* 3.6 3.1 - - - -
261B SER* 2.9 40.6 + - - +
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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