Contacts of the helix formed by residues 249 - 260 (chain A) in PDB entry 2JC6
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLU* 2.6 35.1 + - - -
247A ASP 3.9 0.6 + - - -
248A ILE* 1.3 78.1 - - - +
250A ASP* 1.3 63.4 + - - +
251A SER* 3.7 10.2 + - - -
252A ALA 3.2 16.1 + - - -
253A LYS* 3.3 22.4 + - - +
278A TRP* 4.1 0.3 + - - -
283A THR 3.9 8.0 + - - -
285A LEU* 3.9 21.0 - - - +
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Residues in contact with ASP 250 (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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248A ILE 3.7 1.6 + - - +
249A SER* 1.3 73.6 - - - +
251A SER* 1.3 56.4 + - - +
253A LYS* 3.2 17.2 + - - +
254A ASP* 2.9 30.6 + - - +
257A ARG* 4.9 1.2 + - - -
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Residues in contact with SER 251 (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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249A SER* 3.1 10.8 + - - -
250A ASP* 1.3 78.7 - - - +
252A ALA* 1.3 57.3 + - - +
254A ASP* 3.3 6.1 + - - +
255A PHE* 2.9 23.6 + - - +
276A HIS* 3.4 24.4 - - - -
277A PRO* 4.3 2.4 - - - +
278A TRP* 3.9 3.7 + - - +
283A THR* 2.6 43.0 + - - +
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Residues in contact with ALA 252 (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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118A GLU* 4.0 1.8 - - - +
215A LEU* 3.9 12.1 - - + -
248A ILE* 3.8 22.2 - - + -
249A SER* 3.2 11.9 + - - +
250A ASP 3.3 0.2 - - - -
251A SER* 1.3 77.2 - - - +
253A LYS* 1.3 58.3 + - - +
255A PHE* 3.2 5.2 + - - +
256A ILE* 3.0 33.7 + - - +
278A TRP* 3.5 36.5 - - + +
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Residues in contact with LYS 253 (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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240A PHE* 3.7 47.4 + - + +
245A TRP* 2.9 52.1 + - + +
246A ASP* 4.7 4.0 + - - +
248A ILE* 3.6 16.6 + - + +
249A SER 3.3 11.2 + - - +
250A ASP* 3.2 19.0 + - - +
252A ALA* 1.3 75.5 - - - +
254A ASP* 1.3 58.9 + - - +
256A ILE* 3.4 1.1 + - - -
257A ARG* 3.0 47.0 + - - +
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Residues in contact with ASP 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 ASP 2.9 13.2 + - - +
251A SER* 3.4 11.2 - - - +
253A LYS* 1.3 74.3 - - - +
255A PHE* 1.3 62.2 + - - +
257A ARG* 3.4 17.1 + - - +
258A ASN* 2.7 44.8 + - - -
268A TYR* 5.1 0.3 + - - -
276A HIS* 2.8 25.1 + - + +
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Residues in contact with PHE 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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125A ILE* 3.9 20.2 - - + -
129A LEU* 4.0 6.1 - - + -
211A ALA* 4.2 6.5 - - + -
251A SER 2.9 14.0 + - - +
252A ALA* 3.2 11.9 - - - +
254A ASP* 1.3 79.1 - - - +
256A ILE* 1.3 72.2 + - + +
258A ASN* 3.3 12.5 + - - +
259A LEU* 3.5 38.3 + - + +
268A TYR* 5.0 2.0 - + - -
273A ALA* 3.5 21.3 - - + -
276A HIS* 3.6 33.6 + + + +
278A TRP* 3.8 22.0 - + + -
279A ILE* 3.4 34.3 - - + -
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Residues in contact with ILE 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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208A GLY* 3.8 6.5 - - - +
211A ALA* 4.0 22.9 - - + +
212A TYR* 3.8 18.2 - - + +
215A LEU* 4.2 7.4 - - + -
238A TYR* 4.3 1.3 - - - +
240A PHE* 4.0 18.6 - - + -
245A TRP* 3.7 31.6 - - + -
252A ALA 3.0 16.8 + - - +
253A LYS 3.9 4.0 - - - +
254A ASP 3.3 0.2 - - - -
255A PHE* 1.3 77.6 - - + +
257A ARG* 1.3 56.3 + - - +
259A LEU* 3.2 3.9 + - - +
260A MET* 2.7 60.8 + - + +
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Residues in contact with ARG 257 (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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238A TYR* 3.5 18.6 - - + +
240A PHE* 3.4 33.9 - - + -
250A ASP* 4.9 1.2 + - - +
253A LYS* 3.0 40.0 + - - +
254A ASP* 3.8 17.2 + - - +
255A PHE 3.4 0.2 - - - -
256A ILE* 1.3 76.3 - - - +
258A ASN* 1.3 63.8 + - - +
259A LEU 3.6 0.2 + - - -
260A MET 3.7 14.2 - - - +
261A GLU* 3.7 11.6 + - - +
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Residues in contact with ASN 258 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASP* 2.7 42.6 + - - -
255A PHE* 3.3 6.2 + - - +
256A ILE 3.2 0.8 - - - -
257A ARG* 1.3 78.6 - - - +
259A LEU* 1.3 59.2 + - - +
261A GLU* 3.9 3.5 - - - +
266A LYS 4.8 2.0 - - - +
267A ARG* 3.5 8.7 - - - +
268A TYR* 2.9 76.0 + - + -
276A HIS* 4.4 0.4 - - - -
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Residues in contact with LEU 259 (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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129A LEU* 5.4 2.0 - - + -
204A CYS* 3.4 38.1 - - + +
205A TRP* 3.6 8.6 - - - -
207A ILE* 4.1 11.9 - - + -
208A GLY* 3.6 25.4 - - - +
255A PHE* 3.5 43.7 + - + +
256A ILE 3.2 4.1 + - - +
258A ASN* 1.3 76.8 - - - +
260A MET* 1.3 59.3 + - - +
261A GLU 2.9 10.8 + - - -
267A ARG* 3.2 21.9 + - - -
268A TYR* 3.8 21.3 - - + +
269A THR 4.7 0.7 - - - +
273A ALA* 4.1 14.8 - - + -
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Residues in contact with MET 260 (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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205A TRP* 3.5 22.0 - - + +
208A GLY* 3.6 35.2 - - - +
209A VAL* 3.9 12.8 - - + +
212A TYR* 4.3 3.8 - - - -
220A PRO* 3.7 18.6 - - + -
221A PHE* 3.3 39.0 - - + -
236A ALA* 5.1 1.6 - - - +
238A TYR* 3.4 38.3 + - + +
256A ILE* 2.7 30.9 + - - +
257A ARG 3.7 5.9 - - - +
259A LEU* 1.3 67.4 - - - +
261A GLU* 1.3 58.9 + - - +
262A LYS 4.1 0.7 + - - -
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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