Contacts of the helix formed by residues 242 - 258 (chain A) in PDB entry 1JNK
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 GLU 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A HIS* 3.0 62.9 + - - +
186A ILE* 3.5 21.1 - - - +
241A LYS* 1.3 80.5 - - + +
243A ASN* 1.3 53.6 + - - +
244A VAL* 2.8 14.9 + - - +
245A ASP* 3.4 6.6 + - - +
350A VAL* 5.2 3.6 - - + -
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Residues in contact with ASN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A HIS* 5.2 0.2 - - - -
233A GLU* 4.3 1.4 - - - +
241A LYS* 3.3 30.7 - - + +
242A GLU* 1.3 74.3 - - - +
244A VAL* 1.3 63.0 + - - +
245A ASP 3.1 2.0 - - - -
246A ILE* 3.2 24.4 + - + +
344A PRO* 2.9 33.5 + - - +
347A ARG* 3.0 44.7 + - - +
348A ILE 3.6 16.6 - - - +
349A SER* 4.3 10.1 - - - -
350A VAL* 5.2 2.0 - - - +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.4 25.8 - - + -
188A ARG* 3.6 18.6 - - + -
231A ALA* 3.4 24.5 + - + +
233A GLU* 3.8 15.0 - - + +
234A VAL* 3.9 16.2 - - + -
240A TYR* 4.0 11.0 - - + -
241A LYS 3.1 18.9 + - - +
242A GLU 2.8 6.4 + - - +
243A ASN* 1.3 76.2 + - - +
245A ASP* 1.3 66.1 + - - +
247A TRP* 3.4 18.2 + - - +
248A SER* 3.9 6.2 + - - -
347A ARG* 3.9 8.5 - - - +
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Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.9 21.4 - - + +
181A HIS* 2.8 24.7 + - + -
186A ILE* 3.9 3.1 - - - +
187A HIS* 3.4 24.2 + - - +
188A ARG* 2.9 28.7 + - - -
190A LEU* 3.6 14.4 - - + +
242A GLU 3.4 4.7 + - - +
243A ASN 3.1 0.4 - - - -
244A VAL* 1.3 78.9 - - - +
246A ILE* 1.3 64.0 + - + +
247A TRP 3.2 2.2 - - - -
248A SER* 3.3 9.1 + - - +
249A VAL* 3.1 27.1 + - - +
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Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.5 32.1 - - + -
177A ILE* 6.0 0.4 - - + -
243A ASN* 3.2 21.1 + - - +
245A ASP* 1.3 77.4 - - - +
247A TRP* 1.3 65.6 + - - +
249A VAL* 3.3 4.6 + - + +
250A GLY* 3.0 20.4 + - - -
339A MET* 3.5 38.6 - - + +
347A ARG* 4.0 5.6 - - - -
348A ILE* 3.3 29.4 - - + +
349A SER 4.1 9.0 - - - +
350A VAL* 4.0 21.3 - - + +
353A ALA* 4.3 0.2 - - + -
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Residues in contact with TRP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR 5.1 0.4 + - - -
229A TYR 3.7 1.1 - - - -
230A ARG 3.3 27.9 + - - -
231A ALA* 3.6 8.5 - - + -
232A PRO* 3.8 13.2 - - + -
235A ILE* 6.0 0.9 - - + -
243A ASN 3.8 1.8 + - - -
244A VAL 3.4 12.6 + - - +
245A ASP 3.2 0.4 - - - -
246A ILE* 1.3 80.5 - - - +
248A SER* 1.3 57.7 + - - +
250A GLY* 3.2 1.9 + - - -
251A CYS* 3.0 45.1 + - - -
263A PHE* 3.2 26.0 - + - -
275A VAL* 3.8 19.7 - - + -
279A LEU* 3.6 22.7 - - + -
339A MET 3.9 15.3 - - - -
340A LEU* 3.8 7.3 - - + +
341A VAL 3.2 43.5 - - - -
342A ILE* 3.7 7.4 - - + -
347A ARG* 3.4 22.9 - - - +
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 4.9 5.4 + - - -
189A ASP 5.1 0.2 - - - -
190A LEU* 3.8 38.4 + - - -
229A TYR* 2.6 27.8 + - - -
230A ARG* 4.6 2.3 - - - -
231A ALA 4.9 0.7 + - - -
244A VAL 4.2 7.1 + - - -
245A ASP* 3.3 12.9 + - - -
246A ILE 3.3 0.6 - - - -
247A TRP* 1.3 79.6 - - - +
249A VAL* 1.3 55.6 + - - +
251A CYS* 3.2 5.6 + - - +
252A ILE* 3.0 34.8 + - - +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 3.5 27.3 - - + +
173A MET* 4.9 10.1 - - + -
174A LEU* 4.4 15.0 - - + -
177A ILE* 3.7 26.5 - - + -
190A LEU* 4.9 2.2 - - + -
245A ASP 3.1 18.0 + - - +
246A ILE* 3.5 10.3 - - + +
247A TRP 3.3 0.2 - - - -
248A SER* 1.3 75.9 - - - +
250A GLY* 1.3 57.1 + - - +
252A ILE* 3.3 9.9 + - + +
253A MET* 2.9 26.7 + - - +
339A MET* 3.5 24.0 - - + -
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Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE 3.0 13.5 + - - -
247A TRP 3.7 4.0 - - - -
248A SER 3.2 0.2 - - - -
249A VAL* 1.3 74.1 - - - +
251A CYS* 1.3 60.0 - - - +
252A ILE 3.1 0.2 - - - -
253A MET* 4.4 3.1 - - - -
254A GLY* 3.0 24.8 + - - -
336A LEU* 3.5 10.6 - - - +
339A MET* 3.9 22.7 - - - -
340A LEU* 3.7 15.1 - - - +
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Residues in contact with CYS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR 4.0 14.6 - - - +
229A TYR* 3.8 20.9 - - + -
247A TRP* 3.0 49.3 + - - -
248A SER* 3.2 8.3 + - - +
250A GLY* 1.3 77.2 - - - +
252A ILE* 1.3 61.4 + - - +
255A GLU* 3.4 24.3 + - - +
262A LEU* 4.0 18.6 + - + +
263A PHE* 3.9 19.5 - - - -
340A LEU* 4.1 1.8 - - - -
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.8 22.2 - - + -
157A ILE* 4.8 2.0 - - + +
170A LEU* 5.6 0.2 - - + -
173A MET* 4.1 12.3 - - + -
190A LEU* 4.6 5.8 - - + -
191A LYS* 4.3 8.5 - - - +
192A PRO* 4.0 21.8 - - + -
195A ILE* 3.7 28.0 - - + -
229A TYR* 4.0 15.3 - - + -
248A SER 3.0 23.4 + - - +
249A VAL* 3.6 7.0 - - + +
251A CYS* 1.3 76.9 - - - +
253A MET* 1.3 55.0 + - - +
255A GLU* 2.9 8.5 + - - +
256A MET* 2.8 47.7 + - + +
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Residues in contact with MET 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MET* 5.2 7.4 - - - -
170A LEU* 4.2 23.6 - - + -
249A VAL 2.9 18.0 + - - +
250A GLY* 3.9 1.1 - - - +
252A ILE* 1.3 73.7 - - - +
254A GLY* 1.3 59.8 + - - +
256A MET* 2.8 32.3 + - - +
257A VAL* 2.9 20.7 + - + +
332A ALA* 3.7 26.0 - - + +
335A LEU* 3.8 28.9 - - + -
336A LEU* 3.7 28.9 - - + -
339A MET* 4.7 4.3 - - - +
358A TYR* 3.6 30.7 - - + +
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Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLY 3.0 17.9 + - - -
252A ILE 3.2 0.2 - - - -
253A MET* 1.3 77.0 - - - +
255A GLU* 1.3 55.9 + - - +
257A VAL* 4.5 0.4 - - - -
258A ARG* 2.9 32.1 + - - +
262A LEU* 3.4 13.4 - - - +
313A PHE* 3.5 16.1 - - - -
336A LEU* 3.6 15.2 - - - +
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ILE* 3.8 36.9 - - + +
229A TYR* 2.9 36.4 + - - -
251A CYS 3.4 11.1 + - - +
252A ILE 2.9 9.2 + - - +
254A GLY* 1.3 73.4 - - - +
256A MET* 1.3 60.4 + - - +
257A VAL 3.0 1.8 - - - -
258A ARG 4.3 0.2 - - - +
259A HIS* 2.8 31.4 + - - -
260A LYS* 3.5 23.5 - - - +
261A ILE* 3.3 31.5 + - - +
262A LEU* 3.9 2.5 + - + +
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Residues in contact with MET 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 4.0 13.2 - - + -
157A ILE* 4.0 22.7 - - + +
159A MET 4.6 3.3 - - - +
161A LEU* 3.7 26.0 + - + +
166A MET* 4.2 21.5 - - + +
169A LEU* 3.4 35.7 - - + -
170A LEU* 3.4 33.2 - - + -
173A MET* 4.4 2.2 - - + -
252A ILE* 2.8 29.8 + - + +
253A MET* 2.8 12.8 + - - +
255A GLU* 1.3 77.9 - - - +
257A VAL* 1.3 58.7 + - - +
259A HIS* 3.6 18.5 + - - -
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MET* 4.0 21.5 - - + -
253A MET* 2.9 26.5 + - + +
254A GLY* 3.9 5.2 - - - +
256A MET* 1.3 79.3 - - - +
258A ARG* 1.3 63.5 + - - +
259A HIS* 3.3 18.3 + - - -
313A PHE* 4.4 6.1 - - + -
317A LEU* 3.7 41.6 - - + +
318A PHE* 3.6 43.1 - - + -
336A LEU* 4.6 3.4 - - + -
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLY 2.9 22.1 + - - +
257A VAL* 1.3 73.0 - - - +
259A HIS* 1.3 72.0 + - - +
260A LYS* 3.4 20.2 + - + +
261A ILE 5.2 1.9 + - - -
262A LEU* 4.1 20.4 + - - +
278A GLN* 3.2 34.9 + - - +
312A LEU* 3.1 45.4 + - - +
313A PHE* 3.6 20.8 - - + -
317A LEU* 4.0 23.4 - - + +
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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
------------------------------------------------------------
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