Contacts of the helix formed by residues 243 - 264 (chain A) in PDB entry 3CKI
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 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A TYR* 3.6 3.3 - - - -
240A GLY 2.8 14.1 + - - +
241A ARG* 4.1 5.1 - - + +
242A GLY* 1.3 83.6 - - - +
244A GLU* 1.3 69.2 + - - +
245A SER* 3.8 16.2 + - - +
246A THR* 3.3 19.1 + - - +
247A THR* 3.1 23.4 + - - -
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Residues in contact with GLU 244 (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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236A TYR* 3.6 13.1 + - - -
243A GLU* 1.3 74.8 - - - +
245A SER* 1.3 64.8 + - - +
247A THR* 3.1 5.7 + - - -
248A THR* 2.9 30.8 + - - +
284A ILE* 4.0 19.7 - - + -
286A LYS* 2.8 43.0 + - - +
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLU* 3.8 16.4 + - - +
244A GLU* 1.3 80.3 - - - +
246A THR* 1.3 62.4 + - - +
248A THR* 3.8 5.8 - - - -
249A ASN* 2.8 46.9 + - - +
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Residues in contact with THR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET 4.3 7.0 - - - +
240A GLY* 3.5 29.3 + - - +
241A ARG* 5.4 5.6 - - + -
243A GLU* 3.3 19.3 + - - +
244A GLU 3.2 0.8 - - - -
245A SER* 1.3 79.4 + - - +
247A THR* 1.3 65.7 + - - +
249A ASN* 4.2 4.2 - - - +
250A TYR* 3.1 25.1 + - + +
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Residues in contact with THR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ALA* 4.0 16.8 - - + -
235A PHE* 3.9 26.0 - - + -
236A TYR* 3.5 16.7 - - - -
240A GLY* 3.3 18.7 - - - -
243A GLU 3.1 11.9 + - - -
244A GLU 3.1 7.5 + - - -
246A THR* 1.3 75.1 - - - +
248A THR* 1.3 68.1 + - - +
250A TYR* 3.2 5.9 + - - +
251A LEU* 3.1 31.2 + - + +
284A ILE* 4.0 19.5 - - + -
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Residues in contact with THR 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 2.9 24.3 + - - +
245A SER* 3.8 6.7 - - - -
247A THR* 1.3 76.7 - - - +
249A ASN* 1.3 67.2 + - - +
251A LEU* 3.3 5.7 + - - +
252A ILE* 3.0 43.2 + - + +
282A ILE* 4.1 15.8 - - + +
284A ILE* 3.2 21.4 - - - +
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Residues in contact with ASN 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 2.8 36.4 + - - +
246A THR* 4.3 4.5 - - - +
248A THR* 1.3 76.1 - - - +
250A TYR* 1.3 66.5 + - - +
252A ILE* 4.6 8.8 - - - +
253A GLU* 3.0 45.3 + - + +
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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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235A PHE* 3.7 28.9 - + + -
239A MET* 3.6 30.8 - - + +
246A THR* 3.1 21.2 + - + +
247A THR* 3.2 6.7 + - - +
249A ASN* 1.3 78.5 - - - +
251A LEU* 1.3 61.2 + - + +
253A GLU* 3.9 4.4 - - - +
254A LEU* 3.0 46.9 + - + +
257A ARG* 4.8 4.3 + - - -
338A PHE* 5.8 0.4 - + - -
387A THR* 3.7 8.9 - - + +
394A ILE 5.1 2.3 + - - -
396A THR* 4.1 28.9 + - + -
399A ALA* 3.2 27.5 - - - +
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Residues in contact with LEU 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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229A VAL* 3.9 25.8 - - + -
231A ALA* 3.9 25.1 - - + -
235A PHE* 3.7 20.4 - - + -
247A THR* 3.1 22.9 + - + +
248A THR* 3.8 5.4 - - - +
250A TYR* 1.3 77.3 - - + +
252A ILE* 1.3 60.1 + - - +
254A LEU* 3.1 3.7 + - + +
255A ILE* 2.8 37.4 + - + +
279A ILE* 4.6 1.1 - - + -
282A ILE* 4.2 17.3 - - + -
338A PHE* 3.7 39.0 - - + -
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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
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248A THR* 3.0 37.7 + - + +
249A ASN* 4.1 8.5 - - - +
251A LEU* 1.3 75.1 - - - +
253A GLU* 1.3 64.4 + - + +
255A ILE* 3.3 1.7 + - - +
256A ASP* 2.8 32.1 + - + +
279A ILE* 4.0 14.6 - - + -
282A ILE* 3.7 18.2 - - + -
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Residues in contact with GLU 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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249A ASN* 3.0 34.7 + - + +
250A TYR* 4.0 4.1 - - - +
252A ILE* 1.3 81.3 - - + +
254A LEU* 1.3 62.9 + - - +
256A ASP* 3.4 7.5 + - - +
257A ARG* 3.1 47.7 + - - +
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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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250A TYR* 3.0 42.0 + - + +
251A LEU* 3.5 6.5 - - - +
253A GLU* 1.3 77.7 - - - +
255A ILE* 1.3 68.9 + - + +
257A ARG* 3.2 16.2 + - - +
258A VAL* 3.0 36.3 + - + +
338A PHE* 4.3 14.4 - - + -
385A THR* 5.7 0.2 - - + -
387A THR* 5.6 1.1 - - + -
399A ALA* 4.0 23.8 - - + +
400A ASP* 3.2 20.5 - - - +
403A THR* 3.8 24.7 - - + +
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Residues in contact with ILE 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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227A LEU* 3.8 22.2 - - + -
229A VAL* 4.3 6.5 - - + -
251A LEU 2.8 22.7 + - - +
252A ILE 3.8 2.9 - - - +
254A LEU* 1.3 77.0 - - + +
256A ASP* 1.3 61.5 + - - +
258A VAL* 3.2 5.0 + - + +
259A ASP* 2.8 26.9 + - - +
277A ILE* 4.1 26.2 - - + +
278A GLN* 4.9 0.7 - - - -
279A ILE* 3.9 33.9 - - + +
338A PHE* 4.2 22.2 - - + -
403A THR* 4.5 9.0 - - + -
407A LEU* 4.9 4.9 - - + -
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Residues in contact with ASP 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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252A ILE* 2.8 22.0 + - + +
253A GLU* 3.7 9.1 - - - +
254A LEU 3.2 0.2 - - - -
255A ILE* 1.3 75.9 - - - +
257A ARG* 1.3 66.8 + - - +
259A ASP* 3.3 7.1 + - - +
260A ASP* 3.0 25.8 + - - +
263A ARG* 3.7 19.3 + - - -
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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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250A TYR* 4.8 4.9 + - - -
253A GLU* 3.1 42.9 + - - +
254A LEU* 3.2 18.1 + - - +
256A ASP* 1.3 80.0 - - - +
258A VAL* 1.3 65.4 + - - +
260A ASP* 3.5 9.3 + - - +
261A ILE* 3.5 24.8 + - - +
396A THR* 4.0 21.4 - - - +
400A ASP* 2.6 47.7 + - + +
448A LYS* 5.6 7.9 + - - +
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Residues in contact with VAL 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 LEU* 3.0 29.7 + - + +
255A ILE* 3.2 10.1 + - + +
257A ARG* 1.3 74.8 - - - +
259A ASP* 1.3 65.6 + - - +
261A ILE* 3.2 5.0 + - - +
262A TYR* 3.1 51.4 + - + -
277A ILE* 4.7 3.8 - - + -
400A ASP* 3.7 14.1 - - + +
403A THR* 4.3 3.6 - - + -
404A THR* 3.6 30.1 - - - +
407A LEU* 3.8 22.7 - - + -
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Residues in contact with ASP 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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255A ILE 2.8 16.6 + - - +
256A ASP* 3.5 8.6 - - - +
258A VAL* 1.3 79.4 - - - +
260A ASP* 1.3 56.0 - - - +
262A TYR* 3.2 4.6 + - - -
263A ARG* 2.8 43.5 + - - +
276A GLY* 3.5 4.9 - - - -
277A ILE* 2.9 47.1 + - - +
278A GLN* 6.2 0.2 - - - -
473A ARG* 2.7 39.9 + - - -
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Residues in contact with ASP 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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256A ASP* 3.0 14.0 + - - +
257A ARG* 3.6 14.4 - - - +
258A VAL 3.2 0.4 - - - -
259A ASP* 1.3 77.7 - - - +
261A ILE* 1.3 63.8 + - + +
263A ARG* 3.4 28.9 + - - +
264A ASN* 2.7 38.6 + - - +
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Residues in contact with ILE 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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257A ARG 3.5 14.5 + - - +
258A VAL* 3.2 7.8 + - - +
260A ASP* 1.3 81.2 - - + +
262A TYR* 1.3 62.9 + - + +
264A ASN* 3.5 2.7 + - - +
265A THR* 2.8 26.5 + - - +
400A ASP* 6.0 2.2 - - + -
401A LEU* 4.1 19.5 - - + -
404A THR* 3.8 27.6 - - + +
434A VAL* 6.1 0.2 - - + -
448A LYS* 3.5 48.9 - - + +
449A MET* 4.9 0.7 - - - -
450A PHE* 3.8 26.9 - - + -
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Residues in contact with TYR 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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258A VAL* 3.1 36.3 + - + +
259A ASP* 3.6 5.8 - - - +
261A ILE* 1.3 80.7 - - - +
263A ARG* 1.3 59.0 + - - +
265A THR* 2.9 32.0 + - - +
267A TRP* 4.2 17.5 + + - -
275A TYR 3.2 15.8 + - - +
276A GLY* 4.1 6.7 - - - -
277A ILE* 3.5 25.1 - - + -
404A THR* 2.8 36.9 + - + -
407A LEU* 3.3 3.9 - - + -
408A GLY* 2.9 21.0 + - - -
411A PHE* 4.0 32.1 - + + -
450A PHE* 3.4 25.4 - + - -
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Residues in contact with ARG 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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256A ASP* 3.7 20.6 + - - -
259A ASP* 2.8 49.5 + - - +
260A ASP* 3.4 36.5 + - - +
262A TYR* 1.3 73.4 - - - +
264A ASN* 1.3 73.2 + - - +
265A THR 3.2 0.7 + - - -
273A LYS* 3.8 4.9 - - - +
274A GLY* 2.9 36.3 + - - +
275A TYR 3.2 13.8 + - - +
276A GLY* 4.9 0.4 - - - -
473A ARG* 3.4 22.0 - - - +
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Residues in contact with ASN 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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260A ASP* 2.7 41.0 + - - +
261A ILE* 3.9 3.1 - - - +
262A TYR 3.2 1.0 - - - -
263A ARG* 1.3 91.5 - - - +
265A THR* 1.3 62.2 + - - +
266A ALA* 3.7 2.1 + - - +
273A LYS* 3.9 25.3 + - - +
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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