Contacts of the strand formed by residues 243 - 251 (chain B) in PDB entry 3M2K
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 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B PHE* 5.2 1.1 - - + -
67B ALA* 3.8 29.5 + - + +
69B ALA* 4.7 1.8 - - + -
237B ALA* 3.0 6.8 - - - +
238B ALA* 2.8 45.5 + - + +
240B SER 3.5 16.5 + - - -
241B TYR* 3.8 4.0 + - - +
242B GLY* 1.3 72.0 - - - +
244B ARG* 1.4 58.0 + - - +
245B ASN* 3.8 15.9 - - - +
265B SER 3.1 15.4 + - - +
266B SER* 3.6 14.2 - - - -
274B TYR* 4.2 2.8 - - - -
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Residues in contact with ARG 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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1B CEF 4.1 18.2 + - - +
216B THR 4.4 9.7 + - - -
220B LEU* 3.6 28.4 - - + +
235B THR* 4.6 1.2 - - - -
236B GLY 3.1 29.6 + - - +
237B ALA* 3.6 9.9 - - - +
242B GLY 3.6 1.0 + - - -
243B THR* 1.4 69.1 - - - +
245B ASN* 1.3 63.0 + - - +
265B SER* 2.8 36.6 + - - +
274B TYR* 3.1 49.8 + - + -
275B ASP 5.5 0.7 - - - +
276B ASP* 3.0 28.6 + - - +
278B LEU* 6.2 0.2 - - + -
279B ILE* 3.6 26.9 - - + +
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Residues in contact with ASN 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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66B PHE* 4.8 2.6 - - - +
67B ALA 3.3 16.4 + - - +
68B PHE* 3.2 28.3 + - - +
69B ALA* 3.8 9.5 - - - +
71B THR* 4.0 8.5 - - + -
220B LEU* 4.1 8.2 - - - +
235B THR* 3.5 4.2 - - - -
236B GLY 2.9 28.0 + - - +
243B THR* 3.8 6.4 - - - +
244B ARG* 1.3 84.0 - - - +
246B ASP* 1.3 64.9 + - - +
263B VAL 3.3 5.6 - - - -
264B LEU* 3.5 27.0 - - + +
265B SER 3.3 21.3 + - - +
279B ILE* 4.9 2.2 - - - -
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Residues in contact with ASP 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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71B THR* 4.6 0.7 - - - -
220B LEU* 3.6 8.6 - - + +
221B ILE* 3.1 45.0 + - + +
233B ASP* 2.8 30.5 - - - +
234B LYS 3.0 12.1 - - - +
235B THR* 3.0 20.8 - - - +
245B ASN* 1.3 76.7 - - - +
247B ILE* 1.4 62.8 + - - +
263B VAL 2.9 29.4 + - - +
279B ILE* 4.2 12.6 - - + -
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Residues in contact with ILE 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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71B THR* 4.0 33.2 - - + +
74B ALA* 4.5 6.3 - - + -
75B LEU* 5.5 3.8 - - + -
186B LEU* 4.3 24.7 - - + +
187B VAL* 6.2 0.7 - - - -
190B LEU* 3.8 33.7 - - + -
211B MET* 4.3 1.3 - - + +
233B ASP* 3.4 0.9 - - - +
234B LYS* 2.8 48.7 + - + +
246B ASP* 1.4 75.0 - - - +
248B ALA* 1.3 64.1 + - - +
261B LEU 3.6 4.3 - - - +
262B ALA* 4.1 19.7 - - + -
264B LEU* 4.5 6.7 - - + -
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Residues in contact with ALA 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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190B LEU* 4.3 5.7 - - - +
221B ILE* 3.9 22.0 - - + -
231B VAL* 4.3 8.5 - - + -
232B ALA 3.1 15.3 - - - +
233B ASP* 3.8 11.4 - - + +
247B ILE* 1.3 77.2 - - - +
249B ILE* 1.4 69.9 - - - +
250B ILE* 4.8 4.7 - - + -
260B VAL* 3.5 4.9 - - - +
261B LEU 3.0 31.2 + - - +
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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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190B LEU* 3.4 27.4 - - + +
194B ALA* 4.0 23.8 - - + -
195B LEU* 3.8 21.1 - - + -
208B ILE* 5.6 1.8 - - + -
211B MET* 5.4 2.5 - - + -
231B VAL* 3.3 3.6 - - - +
232B ALA* 2.9 33.4 + - + +
248B ALA* 1.4 77.8 - - - +
250B ILE* 1.3 62.0 + - - +
251B TRP* 3.2 30.3 - - + -
258B PRO* 3.5 28.5 - - + -
259B VAL 3.1 9.4 - - - +
260B VAL* 4.0 8.5 - - + -
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Residues in contact with ILE 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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221B ILE* 4.1 11.4 - - + -
225B VAL* 3.8 37.0 - - + -
229B TRP* 4.1 22.0 - - + -
230B GLU 3.4 6.7 - - - +
231B VAL* 4.5 5.4 - - + +
248B ALA* 4.8 1.6 - - + -
249B ILE* 1.3 80.9 - - - +
251B TRP* 1.3 62.7 + - - +
252B PRO* 3.4 6.2 - - - +
258B PRO* 3.5 0.5 - - - +
259B VAL* 2.9 40.9 + - + +
261B LEU* 3.5 38.1 - - + -
287B MET* 4.2 16.2 - - + -
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Residues in contact with TRP 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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111A LYS* 5.6 9.6 - - - +
195B LEU* 4.9 5.3 - - + +
208B ILE* 4.3 31.2 - - + -
212B LYS* 4.2 15.3 - - - -
229B TRP* 3.8 8.7 - - - +
230B GLU* 2.7 55.6 + - + +
231B VAL 4.0 1.1 - - - -
232B ALA* 3.5 24.9 - - + -
249B ILE* 3.2 44.4 - - + -
250B ILE* 1.3 73.0 - - - +
252B PRO* 1.4 72.6 - - + +
256B GLY 4.7 7.0 - - - -
258B PRO* 3.6 25.2 - - + +
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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