Contacts of the helix formed by residues 238 - 255 (chain B) in PDB entry 6JKG
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 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B HIS* 5.9 1.0 - - - -
236B ASP 4.4 5.6 - - - +
237B PHE* 1.3 77.6 - - - +
239B PHE* 1.3 53.9 + - - +
240B VAL* 3.7 8.3 + - - +
241B GLU* 2.8 38.0 + - - +
242B ASN* 2.8 37.8 + - - -
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Residues in contact with PHE 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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269A GLU* 4.0 21.1 - - + +
270A HIS* 3.7 31.2 - - - +
271A HIS* 3.1 33.2 - - - +
201B HIS 3.4 28.9 - - - -
202B GLY* 5.8 0.2 - - - -
203B ILE 4.9 14.8 - - - -
238B THR* 1.3 72.3 - - - +
240B VAL* 1.3 76.0 + - + +
242B ASN* 3.0 18.2 + - - +
243B VAL* 3.0 32.6 + - + +
267B ILE* 6.3 0.4 - - + -
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.5 34.5 - - + -
49B LEU* 4.2 16.2 - - + -
52B HIS* 3.7 40.8 - - + +
203B ILE 5.7 4.7 - - - +
238B THR* 3.4 6.7 + - - +
239B PHE* 1.3 89.4 - - + +
241B GLU* 1.3 62.3 + - - +
243B VAL* 3.1 10.7 + - - +
244B VAL* 3.1 26.5 + - - +
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS* 4.7 17.1 + - + +
56B GLN* 4.1 23.6 + - - +
236B ASP 4.5 1.4 - - - +
237B PHE* 3.4 50.2 - - + -
238B THR* 2.8 34.5 + - - +
240B VAL* 1.3 77.5 - - + +
242B ASN* 1.3 57.1 + - - +
244B VAL* 3.6 9.0 + - - +
245B HIS* 3.1 19.4 + - - +
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Residues in contact with ASN 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ILE* 5.1 2.3 - - - +
239A PHE* 6.3 1.6 - - - -
269A GLU* 3.2 32.2 + - - +
234B LEU* 4.4 0.7 - - - +
237B PHE* 3.1 29.6 + - - +
238B THR 2.8 23.5 + - - -
239B PHE* 3.0 6.9 + - - +
241B GLU* 1.3 77.6 - - - +
243B VAL* 1.3 60.1 + - - +
244B VAL 3.2 0.2 - - - -
245B HIS* 3.8 5.7 - - - +
246B GLY* 3.0 24.9 + - - -
267B ILE* 4.4 7.1 - - - +
270B HIS* 3.0 38.8 + - + +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 6.1 0.9 - - - +
49B LEU* 4.0 16.8 - - + -
200B PRO* 3.5 31.9 - - + -
203B ILE 4.9 6.5 - - - +
239B PHE* 3.0 43.4 + - + +
240B VAL* 3.4 10.3 - - - +
242B ASN* 1.3 76.3 - - - +
244B VAL* 1.3 55.9 + - - +
246B GLY* 3.5 1.9 + - - -
247B HIS* 2.5 50.9 + - + -
267B ILE* 3.8 12.8 - - + +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.9 19.7 - - + -
52B HIS* 4.0 21.8 - - + -
53B MET* 3.6 34.3 - - - +
56B GLN* 3.7 14.8 - - + +
240B VAL 3.1 15.6 + - - +
241B GLU* 3.9 7.2 - - - +
243B VAL* 1.3 73.2 - - - +
245B HIS* 1.3 66.5 + - - +
246B GLY 3.0 1.3 - - - -
247B HIS* 2.9 16.9 + - - +
248B ILE* 3.0 31.8 + - + +
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Residues in contact with HIS 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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214A ILE* 4.6 9.9 - - + -
56B GLN* 5.3 1.7 - - + +
60B ARG* 3.6 28.8 + - - -
229B GLY* 5.2 1.8 - - - -
230B ASN 5.3 1.2 + - - -
233B ASN* 4.6 16.6 + - - -
234B LEU* 3.5 32.7 - - + +
237B PHE* 4.2 19.0 - + + -
241B GLU 3.1 19.1 + - - +
242B ASN* 3.4 8.7 + - - +
244B VAL* 1.3 76.4 - - - +
246B GLY* 1.3 59.6 + - - +
248B ILE* 4.1 9.6 - - - +
249B LEU* 3.0 59.4 + - + +
270B HIS* 5.8 1.1 - + + -
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Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ILE* 4.5 8.0 - - - +
215A LEU* 3.5 33.1 - - - +
198B ILE* 5.1 2.2 - - - -
242B ASN 3.0 16.0 + - - -
243B VAL 3.8 2.5 - - - -
244B VAL 3.0 1.2 - - - -
245B HIS* 1.3 74.2 - - - +
247B HIS* 1.3 65.2 + - - +
248B ILE 3.1 0.7 + - - -
249B LEU* 3.3 1.8 + - - -
250B ALA* 3.2 19.4 + - - +
267B ILE* 5.1 3.1 - - - -
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Residues in contact with HIS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.6 1.3 - - + -
53B MET* 3.6 27.6 - - + -
102B PHE* 3.7 11.7 - + + -
141B ILE* 4.0 19.2 - - + +
143B THR* 2.5 44.7 - - + +
198B ILE* 4.0 29.4 - - + +
200B PRO* 4.6 4.9 - - + -
243B VAL* 2.5 49.7 + - + -
244B VAL* 2.9 10.3 + - - +
246B GLY* 1.3 70.7 - - - +
248B ILE* 1.3 57.9 + - - +
250B ALA* 4.0 1.9 - - - +
251B ALA* 3.0 27.7 + - - +
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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
----------------------------------------------------------
53B MET* 5.2 0.7 - - - -
56B GLN* 3.9 19.7 - - + +
57B LEU* 3.8 32.3 - - + -
60B ARG* 4.5 22.0 - - + +
62B TYR* 4.9 10.3 - - + -
102B PHE* 4.5 6.1 - - + -
244B VAL* 3.0 38.8 + - + +
245B HIS* 4.1 8.7 - - - +
247B HIS* 1.3 75.8 - - + +
249B LEU* 1.3 62.3 + - + +
251B ALA* 3.0 8.7 + - + +
252B GLU* 2.8 47.0 + - + +
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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
----------------------------------------------------------
214A ILE* 4.0 12.1 - - + -
215A LEU* 5.1 0.2 - - + -
60B ARG* 3.3 30.3 - - - +
227B VAL* 4.0 12.3 - - + -
228B ILE 4.1 6.3 - - - +
229B GLY* 3.7 27.4 - - - -
245B HIS* 3.0 51.2 + - + +
246B GLY* 3.3 4.2 + - - +
248B ILE* 1.3 78.2 - - + +
250B ALA* 1.3 52.2 + - - +
252B GLU* 3.3 15.9 - - - +
253B GLN* 2.7 38.5 + - - +
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Residues in contact with ALA 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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215A LEU* 3.7 24.2 - - + +
141B ILE* 5.4 0.2 - - - -
196B THR* 4.7 11.0 - - + +
198B ILE* 4.1 16.4 - - + -
227B VAL* 4.7 4.9 - - + -
246B GLY 3.2 8.2 + - - +
247B HIS 4.0 3.4 - - - +
249B LEU* 1.3 78.3 - - - +
251B ALA* 1.3 53.1 + - - +
253B GLN* 3.0 5.0 + - - -
254B LEU* 2.5 40.0 + - - +
260B LEU* 4.4 11.9 - - + +
265B PHE* 5.5 1.8 - - + -
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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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100B THR* 4.8 4.7 - - + +
102B PHE* 3.7 17.0 - - + -
139B LYS* 3.8 12.5 + - - +
141B ILE* 3.7 29.5 - - + +
247B HIS 3.0 16.4 + - - +
248B ILE* 3.0 10.4 + - + +
250B ALA* 1.3 77.7 - - - +
252B GLU* 1.3 62.5 + - - +
254B LEU* 3.2 16.8 + - - +
255B SER 3.5 4.3 + - - -
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Residues in contact with GLU 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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60B ARG* 2.8 34.1 + - - -
62B TYR* 4.7 15.2 + - + +
139B LYS* 4.9 3.6 - - - +
248B ILE* 2.8 29.9 + - + +
249B LEU* 3.3 22.7 - - - +
251B ALA* 1.3 74.1 - - - +
253B GLN* 1.3 57.8 + - - +
255B SER* 2.2 31.0 + - - +
256B ARG* 3.2 33.6 + - - +
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Residues in contact with GLN 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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227B VAL* 5.1 11.8 - - + +
228B ILE 5.0 9.6 - - - +
249B LEU 2.7 24.9 + - - +
250B ALA* 3.7 3.4 - - - +
252B GLU* 1.3 73.6 - - - +
254B LEU* 1.3 64.6 + - - +
255B SER 3.1 1.3 - - - -
256B ARG* 3.3 43.0 + - - +
257B ASP* 3.2 25.2 + - + +
260B LEU* 4.2 19.7 - - + +
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Residues in contact with LEU 254 (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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139B LYS* 4.1 15.3 - - + -
140B LEU 5.3 0.2 - - - +
141B ILE* 5.0 6.3 - - + -
194B LEU* 3.8 54.9 - - + +
195B THR 4.4 2.5 - - - -
196B THR* 3.9 29.4 - - + -
250B ALA* 2.5 16.4 + - + +
251B ALA 3.2 11.9 + - - +
253B GLN* 1.3 72.0 - - - +
255B SER* 1.3 61.1 + - - +
256B ARG 3.0 2.1 + - - -
257B ASP 3.3 20.1 + - - +
258B SER* 4.1 0.5 + - - -
260B LEU* 3.5 29.3 - - + +
261B GLY* 3.5 16.8 - - - +
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS* 3.6 28.9 - - - +
194B LEU* 5.8 0.2 - - - -
251B ALA 3.5 1.4 + - - -
252B GLU* 2.2 32.3 + - - -
254B LEU* 1.3 77.0 - - - +
256B ARG* 1.3 62.0 + - - +
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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
------------------------------------------------------------
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