Contacts of the helix formed by residues 239 - 253 (chain B) in PDB entry 1K86
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 SER 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B ASP* 2.9 15.7 + - - +
184B GLN* 2.8 34.8 + - - -
231B SER* 4.6 2.7 - - - -
233B ARG* 3.5 25.3 - - - +
238B GLY* 1.3 73.8 - - - -
240B TRP* 1.3 60.7 + - - +
241B PHE 4.3 0.2 - - - -
242B VAL* 3.0 23.7 + - - +
243B GLN* 2.9 30.0 + - - +
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Residues in contact with TRP 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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231B SER* 5.4 0.8 + - - -
232B TRP* 3.8 28.6 + + + +
233B ARG 5.3 0.4 - - - -
234B SER* 4.5 15.0 + - - -
237B ARG* 6.1 1.2 - - - +
238B GLY 5.1 1.1 - - - -
239B SER* 1.3 71.3 - - - +
241B PHE* 1.3 57.3 + - - +
243B GLN* 3.5 21.3 + - - +
244B ALA* 2.7 37.6 + - - +
269B VAL* 3.9 26.7 - - + -
272B HIS* 4.7 28.5 - - + -
274B GLU 4.7 4.5 - - - -
275B SER* 3.7 37.5 - - - -
287B GLN* 3.9 18.6 - - + +
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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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182B PHE* 5.0 3.4 - - + -
183B ILE 4.5 8.3 - - - -
184B GLN* 3.5 24.0 - - + +
222B ALA* 3.9 36.1 - - + -
223B TYR 4.2 1.6 - - - -
224B SER* 3.8 22.9 - - - +
231B SER* 4.5 2.9 - - - +
239B SER 3.4 0.2 - - - -
240B TRP* 1.3 78.9 - - - +
242B VAL* 1.3 61.2 + - + +
244B ALA* 3.6 1.7 - - - +
245B LEU* 2.7 56.7 + - + +
262B LEU* 4.9 5.2 - - + -
265B VAL* 3.6 28.4 - - + +
266B ASN* 5.3 0.4 - - - -
269B VAL* 3.7 11.9 - - + +
287B GLN* 4.7 2.7 - - - +
289B PRO* 3.8 29.6 - - + -
291B VAL* 6.5 0.2 - - + -
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Residues in contact with VAL 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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93B ASP* 3.5 36.1 - - + +
96B ALA* 4.8 2.5 - - + -
97B LEU* 3.4 39.7 - - + -
142B LEU* 4.6 1.1 - - + -
184B GLN* 3.9 20.0 - - + +
239B SER* 3.0 21.0 + - - +
240B TRP 3.3 0.4 - - - -
241B PHE* 1.3 79.0 - - + +
243B GLN* 1.3 65.5 + - - +
245B LEU* 3.8 6.2 - - + +
246B CYS* 3.1 29.4 + - - -
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Residues in contact with GLN 243 (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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93B ASP* 4.9 0.6 + - - +
96B ALA* 6.3 1.3 - - - -
237B ARG* 3.1 41.1 + - - +
238B GLY 5.6 0.4 - - - -
239B SER 2.9 18.5 + - - +
240B TRP* 3.5 24.1 + - - +
242B VAL* 1.3 77.3 - - - +
244B ALA* 1.3 60.9 + - - +
246B CYS* 3.9 3.3 + - - +
247B SER* 3.2 22.9 + - - -
268B ARG* 4.9 0.2 + - - -
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Residues in contact with ALA 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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240B TRP 2.7 21.0 + - - +
241B PHE 3.6 3.1 - - - +
243B GLN* 1.3 71.6 - - - +
245B LEU* 1.3 66.4 + - - +
247B SER* 3.0 5.8 + - - -
248B ILE* 2.9 29.9 + - - +
265B VAL* 4.3 15.9 - - + -
268B ARG* 4.0 33.0 - - + +
269B VAL* 4.3 5.2 - - + -
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Residues in contact with LEU 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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97B LEU* 4.0 21.3 - - + -
101B PHE* 4.6 5.8 - - + -
182B PHE* 4.0 31.9 - - + -
241B PHE* 2.7 37.1 + - + +
242B VAL* 3.8 5.6 - - + +
244B ALA* 1.3 72.8 - - - +
246B CYS* 1.3 57.9 + - - +
248B ILE* 3.9 1.0 - - - +
249B LEU* 2.9 49.7 + - + +
261B ILE* 4.5 8.7 - - + -
262B LEU* 4.0 24.5 - - + -
265B VAL* 3.8 16.9 - - + +
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Residues in contact with CYS 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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96B ALA* 3.8 17.9 - - + +
97B LEU* 3.5 46.4 - - - -
100B CYS* 3.9 18.8 - - + -
242B VAL* 3.1 19.8 + - - +
243B GLN* 4.2 3.6 - - - +
245B LEU* 1.3 78.0 - - - +
247B SER* 1.3 58.2 + - - +
249B LEU* 3.7 0.2 - - - +
250B GLU* 2.9 38.7 + - + +
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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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243B GLN 3.2 16.0 + - - -
244B ALA 3.0 3.4 + - - -
246B CYS* 1.3 80.1 - - - +
248B ILE* 1.3 62.1 + - - +
250B GLU* 3.3 4.5 + - - +
251B GLU* 3.0 35.6 + - - +
268B ARG* 2.5 39.9 + - - -
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Residues in contact with ILE 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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244B ALA 2.9 19.0 + - - +
245B LEU 4.0 2.2 - - - +
247B SER* 1.3 74.3 + - - +
249B LEU* 1.3 58.4 + - - +
251B GLU* 4.1 7.0 - - - +
252B HIS* 2.8 40.6 + - + +
253B GLY 3.4 2.4 + - - -
261B ILE* 4.2 19.8 - - + +
264B ARG* 4.1 40.2 - - + -
265B VAL* 3.9 12.6 - - + -
268B ARG* 3.2 45.8 - - + +
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Residues in contact with LEU 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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100B CYS* 3.5 27.1 - - - -
101B PHE* 3.5 29.2 - - + -
104B LEU* 4.0 15.0 - - + +
182B PHE* 6.2 0.4 - - + -
245B LEU* 2.9 31.3 + - + +
248B ILE* 1.3 75.6 - - - +
250B GLU* 1.3 63.0 + - - +
253B GLY* 2.7 32.2 + - - +
254B LYS* 4.1 7.3 + - - -
258B ILE* 6.3 0.4 - - + -
261B ILE* 3.8 38.8 - - + -
301B PHE* 4.4 13.0 - - + -
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Residues in contact with GLU 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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99B LYS* 4.5 4.9 - - - +
100B CYS* 3.7 30.9 + - + +
103B SER* 3.0 26.9 + - - -
104B LEU* 5.7 0.2 - - - +
246B CYS* 2.9 29.2 + - + +
247B SER* 3.8 4.9 - - - +
249B LEU* 1.3 79.4 - - - +
251B GLU* 1.3 65.7 + - + +
253B GLY 4.5 0.2 + - - -
254B LYS* 4.2 13.5 + - - +
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Residues in contact with GLU 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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247B SER* 3.0 34.9 + - - +
248B ILE* 3.9 3.8 - - - +
250B GLU* 1.3 81.1 - - + +
252B HIS* 1.3 85.0 + - + +
254B LYS* 5.3 1.6 + - - +
255B ASP* 4.1 6.1 - - - +
268B ARG* 3.3 17.8 + - - -
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Residues in contact with HIS 252 (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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58A TYR* 5.4 2.2 + - - -
248B ILE* 2.8 22.8 + - + +
251B GLU* 1.3 98.3 + - + +
253B GLY* 1.3 64.3 + - - +
254B LYS 2.8 5.9 + - - -
255B ASP* 2.9 33.5 + - - +
256B LEU* 3.1 35.6 + - + +
261B ILE* 4.9 1.8 - - + -
264B ARG* 3.4 25.5 + - - -
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Residues in contact with GLY 253 (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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104B LEU* 4.1 9.9 - - - -
248B ILE 3.4 2.6 + - - -
249B LEU* 2.7 44.4 + - - -
250B GLU 4.5 0.4 + - - -
251B GLU 3.7 1.0 - - - -
252B HIS* 1.3 71.9 - - - +
254B LYS* 1.3 61.3 + - - +
255B ASP 3.8 0.2 + - - -
256B LEU 4.3 6.4 - - - +
261B ILE* 4.3 3.8 - - - +
301B PHE* 3.5 27.7 + - - +
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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