Contacts of the strand formed by residues 245 - 254 (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 LEU 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A LYS 4.2 1.0 - - - +
240A VAL* 3.8 0.3 - - - -
241A ASN* 2.5 60.4 + - + +
243A SER* 3.1 20.2 - - - +
244A SER* 1.3 94.1 - - - +
246A ILE* 1.3 60.9 + - - +
247A GLY 3.9 1.5 + - - -
265A LEU* 4.8 17.5 - - + -
267A ASP* 4.3 2.2 - - - -
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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
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239A LYS 4.4 0.9 - - - -
240A VAL* 3.9 24.9 - - + -
241A ASN 3.4 14.4 - - - +
244A SER* 4.0 4.4 + - - +
245A LEU* 1.3 94.1 - - - +
247A GLY* 1.3 57.8 + - - +
248A LEU* 4.6 6.0 - - + +
265A LEU* 3.6 5.0 - - - +
266A LEU* 2.3 48.6 + - + +
267A ASP* 4.4 10.3 + - - +
268A GLY 5.6 1.1 - - - +
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Residues in contact with GLY 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 3.9 0.9 - - - -
239A LYS* 2.3 42.8 + - - +
240A VAL* 4.3 0.2 - - - +
246A ILE* 1.3 74.5 - - - +
248A LEU* 1.3 73.6 + - - +
264A ALA 3.6 5.6 - - - -
265A LEU* 3.1 27.7 - - - +
266A LEU* 3.9 1.3 - - - -
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 3.7 3.5 - - - +
237A SER 3.7 18.6 - - - +
238A ALA* 4.8 3.6 - - - -
239A LYS* 4.1 6.5 - - - +
240A VAL* 4.6 12.3 - - + -
246A ILE* 4.6 7.9 - - + +
247A GLY* 1.3 100.2 - - - +
249A GLY* 1.3 57.9 + - - +
250A TYR* 2.8 36.3 + - + +
263A SER* 3.1 7.0 + - - -
264A ALA 2.9 20.2 + - - +
266A LEU* 4.8 8.5 - - + +
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Residues in contact with GLY 249 (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* 3.4 24.7 - - - +
236A PHE* 3.2 0.3 - - - -
237A SER* 2.5 57.7 + - - +
239A LYS* 4.2 0.4 - - - +
248A LEU* 1.3 70.1 - - - +
250A TYR* 1.3 66.2 + - - -
251A THR 4.0 0.2 - - - -
263A SER* 3.5 3.6 - - - -
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Residues in contact with TYR 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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24A GLY 4.6 0.6 - - - +
235A CYS 3.7 0.2 - - - -
236A PHE* 3.0 32.3 - + + -
237A SER 5.4 0.4 - - - -
248A LEU* 2.8 44.1 + - + +
249A GLY* 1.3 78.8 - - - -
251A THR* 1.3 54.1 + - - +
252A GLN* 2.4 38.8 + - - +
261A THR* 3.6 2.0 - - - +
262A LEU* 2.4 41.9 + - + +
263A SER* 3.5 15.7 - - - -
264A ALA* 3.6 23.2 + - + +
266A LEU* 4.6 7.4 - - - +
278A LEU* 5.2 4.9 - - + -
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Residues in contact with THR 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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22A THR* 2.9 39.6 + - - +
227A LYS* 5.3 5.2 - - - +
234A ALA* 3.3 3.1 - - - +
235A CYS* 2.4 56.4 + - + +
236A PHE* 3.9 2.0 - - - +
237A SER* 5.0 0.5 + - - -
249A GLY 4.0 0.2 - - - -
250A TYR* 1.3 68.9 - - - +
252A GLN* 1.3 73.5 + - - +
253A THR* 4.9 5.2 - - - +
259A LYS* 6.0 2.0 - - + -
261A THR* 3.6 19.3 - - + +
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Residues in contact with GLN 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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234A ALA* 4.0 11.0 - - + +
236A PHE* 3.6 15.1 - - + -
250A TYR* 2.4 50.4 + - - +
251A THR* 1.3 79.4 - - - +
253A THR* 1.3 64.0 + - - +
254A LEU* 4.5 9.9 - - + -
259A LYS* 3.5 9.7 - - - +
260A LEU* 2.7 44.0 + - + +
261A THR* 2.9 2.8 + - - +
262A LEU* 2.7 27.4 - - - +
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Residues in contact with THR 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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233A ASP* 2.6 65.3 + - + +
234A ALA* 4.1 1.2 + - - -
235A CYS* 5.8 1.6 - - - -
251A THR* 4.9 6.4 - - - +
252A GLN* 1.3 74.9 + - - +
254A LEU* 1.3 73.2 + - - +
255A LYS* 3.7 6.7 - - - +
258A ILE 4.9 0.7 - - - +
259A LYS* 4.1 18.2 - - + +
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Residues in contact with LEU 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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252A GLN* 4.4 11.2 - - + -
253A THR* 1.3 101.2 - - - +
255A LYS* 1.3 72.6 + - - +
256A PRO* 2.8 6.8 - - - +
258A ILE* 3.0 23.5 + - + +
259A LYS* 4.0 1.3 - - - +
260A LEU* 3.7 38.6 - - + +
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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