Contacts of the strand formed by residues 258 - 266 (chain A) in PDB entry 2JK4
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 ILE 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A THR* 4.9 0.5 - - - +
254A LEU* 3.0 27.5 + - + +
255A LYS 2.8 21.5 + - - +
256A PRO* 5.2 6.5 - - + -
257A GLY* 1.3 84.0 - - - +
259A LYS* 1.3 65.7 + - - +
283A GLU 3.0 17.5 - - - +
284A PHE* 4.5 15.3 - - + -
285A GLN 4.4 9.9 - - - +
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Residues in contact with LYS 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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25A TYR* 2.7 35.9 + - - -
251A THR* 6.0 2.0 - - + -
252A GLN 3.5 15.5 - - - +
253A THR* 4.1 18.8 - - + +
254A LEU* 4.0 5.8 - - - +
258A ILE* 1.3 78.6 - - - +
260A LEU* 1.3 60.9 + - - +
261A THR* 3.9 17.0 - - - +
281A GLY 6.2 0.4 - - - -
282A LEU* 3.6 2.0 - - - -
283A GLU* 2.8 67.0 + - + +
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Residues in contact with LEU 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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252A GLN* 2.7 43.2 + - + +
254A LEU* 3.7 28.1 - - + +
259A LYS* 1.3 72.9 - - - +
261A THR* 1.3 57.8 + - - +
262A LEU* 3.7 34.8 - - + -
280A LEU* 5.8 0.2 - - + -
281A GLY 2.9 26.7 - - - +
282A LEU* 4.8 9.6 - - + -
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Residues in contact with THR 261 (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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22A THR 4.5 0.4 - - - +
24A GLY* 3.3 32.1 - - - -
25A TYR* 4.7 11.1 + - + -
250A TYR 3.6 10.1 - - - +
251A THR* 3.6 22.2 - - + +
252A GLN* 2.9 14.1 + - - +
259A LYS* 3.9 17.5 + - - +
260A LEU* 1.3 73.7 - - - +
262A LEU* 1.3 65.8 + - - +
280A LEU 3.7 0.3 - - - -
281A GLY* 2.7 46.4 + - - -
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Residues in contact with LEU 262 (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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24A GLY* 4.7 0.4 - - - -
250A TYR* 2.4 44.4 + - + +
252A GLN* 2.7 15.6 - - - +
260A LEU* 3.7 30.3 - - + -
261A THR* 1.3 92.8 - - - +
263A SER* 1.3 61.2 + - - +
278A LEU* 5.1 7.2 - - + -
279A GLY 3.7 1.8 - - - +
280A LEU* 3.0 45.5 - - + -
281A GLY 3.5 2.7 - - - +
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Residues in contact with SER 263 (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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23A LYS* 2.9 58.5 + - - +
24A GLY* 3.6 4.9 - - - -
26A GLY 4.7 3.6 - - - -
27A PHE 4.6 0.7 - - - -
248A LEU 3.1 1.4 + - - -
249A GLY* 3.6 7.9 - - - -
250A TYR* 3.5 10.1 - - - -
262A LEU* 1.3 76.7 - - - +
264A ALA* 1.3 71.1 + - - +
278A LEU* 2.9 7.9 - - - +
279A GLY 2.8 30.4 + - - -
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Residues in contact with ALA 264 (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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23A LYS* 3.1 11.2 + - - +
27A PHE 4.2 1.1 - - - -
248A LEU 2.9 32.6 + - - +
250A TYR* 3.6 16.3 + - + +
263A SER* 1.3 81.7 + - - +
265A LEU* 1.3 60.5 + - - +
266A LEU* 4.2 6.6 - - + +
277A LYS 3.9 6.3 - - - +
278A LEU* 3.8 26.2 - - + +
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Residues in contact with LEU 265 (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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23A LYS* 3.9 13.9 - - - +
27A PHE* 4.7 18.6 - - + -
239A LYS* 5.2 0.9 - - + +
245A LEU* 4.7 17.3 - - + -
246A ILE 3.6 11.4 - - - +
247A GLY* 3.1 37.5 - - - +
264A ALA* 1.3 76.8 - - - +
266A LEU* 1.3 66.8 + - - +
267A ASP* 4.2 7.4 - - + +
275A GLY 3.9 3.2 - - - +
276A HIS* 3.4 23.0 + - - +
277A LYS 3.3 15.5 + - - +
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Residues in contact with LEU 266 (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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246A ILE* 2.3 50.1 + - + +
247A GLY* 4.4 3.6 - - - -
248A LEU* 4.8 7.9 - - + +
250A TYR* 4.6 9.4 - - - +
264A ALA* 4.2 11.7 - - + +
265A LEU* 1.3 82.7 - - - +
267A ASP* 1.3 60.8 + - - +
268A GLY 3.4 3.2 + - - +
276A HIS* 2.8 34.8 - - + +
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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