Contacts of the helix formed by residues 249 - 265 (chain A) in PDB entry 3I58
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 ASP 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A GLN* 5.9 0.9 + - - -
248A TRP* 1.3 76.5 - - - +
250A ASP* 1.3 61.1 + - - +
251A LEU* 3.3 12.3 + - + +
252A SER* 3.0 29.6 + - - -
253A ALA* 2.9 25.3 + - - +
294A PHE 5.2 3.5 + - - +
295A GLY* 3.7 20.4 + - - +
296A GLY* 4.7 0.4 - - - -
297A LYS* 5.7 1.1 - - - -
299A ARG* 3.4 3.6 - - - +
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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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249A ASP* 1.3 75.9 - - - +
251A LEU* 1.3 69.1 + - + +
253A ALA* 3.7 0.9 - - - +
254A VAL* 3.1 30.8 + - - +
297A LYS* 3.8 17.2 + - - +
299A ARG* 3.2 21.7 + - - +
307A LEU* 3.8 18.7 - - + +
310A GLN* 5.6 3.5 + - - +
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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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249A ASP* 3.3 10.6 + - + +
250A ASP* 1.3 81.4 - - + +
252A SER* 1.3 65.4 + - - +
254A VAL* 3.0 28.2 - - + +
255A ALA* 3.1 6.8 + - - +
310A GLN* 6.0 2.2 - - - +
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Residues in contact with SER 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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229A PHE* 4.0 10.6 - - - -
248A TRP* 3.6 37.5 - - - -
249A ASP* 3.0 18.6 + - - -
251A LEU* 1.3 76.2 - - - +
253A ALA* 1.3 61.4 + - - +
255A ALA* 3.0 10.4 + - - +
256A ILE* 2.8 34.6 + - - +
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Residues in contact with ALA 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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245A LEU* 3.9 17.6 - - + +
248A TRP* 4.0 8.7 - - + +
249A ASP 2.9 19.2 + - - +
250A ASP 3.7 3.4 - - - +
251A LEU 3.2 0.2 - - - -
252A SER* 1.3 77.3 - - - +
254A VAL* 1.3 57.5 + - - +
256A ILE* 3.3 4.3 + - - +
257A LEU* 2.8 32.9 + - - +
299A ARG* 4.0 9.0 - - - +
307A LEU* 3.7 27.6 - - + -
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Residues in contact with VAL 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* 3.1 15.0 + - + +
251A LEU* 3.0 20.2 - - + +
253A ALA* 1.3 72.4 - - - +
255A ALA* 1.3 62.5 + - + +
257A LEU* 4.2 8.5 - - - -
258A ARG* 2.6 62.7 + - - +
307A LEU* 3.6 34.1 - - + +
310A GLN* 4.2 26.7 - - + +
311A ALA* 4.1 2.0 - - + +
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Residues in contact with ALA 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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229A PHE* 3.9 19.7 - - + -
251A LEU 3.1 8.9 + - - +
252A SER* 3.0 14.3 + - - +
254A VAL* 1.3 86.9 - - + +
256A ILE* 1.3 63.8 + - - +
258A ARG* 3.4 12.9 - - - +
259A ARG* 3.1 26.1 + - - +
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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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228A PHE* 3.5 45.3 - - + +
229A PHE* 3.6 15.2 - - + -
241A LEU* 3.9 31.6 - - + -
244A VAL* 4.2 4.5 - - + -
245A LEU* 4.5 5.2 - - + -
248A TRP* 3.4 36.8 - - + +
252A SER 2.8 18.7 + - - +
253A ALA* 3.6 7.6 - - - +
255A ALA* 1.3 76.6 - - - +
257A LEU* 1.3 63.0 + - - +
259A ARG* 3.3 5.7 + - - +
260A CYS* 3.2 21.1 + - - -
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Residues in contact with LEU 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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241A LEU* 3.8 20.4 - - + -
245A LEU* 4.1 19.7 - - + -
253A ALA 2.8 22.4 + - - +
254A VAL* 3.8 3.4 - - - +
256A ILE* 1.3 73.6 - - - +
258A ARG* 1.3 64.5 + - - +
260A CYS* 3.1 8.2 + - - +
261A ALA* 2.9 21.0 + - - +
270A VAL* 4.0 12.3 - - + -
272A VAL* 4.2 5.2 - - + -
304A LEU* 4.9 0.4 - - + +
307A LEU* 3.9 29.4 - - + +
308A ALA* 4.0 14.8 - - - +
311A ALA* 4.0 12.6 - - + -
313A LEU* 3.9 8.4 - - + +
329A MET* 4.0 24.9 - - + -
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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 VAL* 2.6 49.0 + - - +
255A ALA* 3.4 12.9 - - - +
257A LEU* 1.3 72.5 - - - +
259A ARG* 1.3 63.8 + - - +
261A ALA* 2.8 17.7 + - + +
262A GLU* 2.9 33.0 + - + +
310A GLN* 3.0 29.2 + - - +
311A ALA* 3.7 15.7 - - + +
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Residues in contact with ARG 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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228A PHE 3.5 22.4 - - - +
229A PHE 2.7 24.6 + - - +
230A ASP* 3.5 14.0 + - - +
231A PRO* 3.5 34.2 - - - +
232A LEU* 4.0 16.4 + - + +
255A ALA 3.1 13.6 + - - +
256A ILE 3.3 7.6 + - - +
258A ARG* 1.3 79.8 - - - +
260A CYS* 1.3 64.1 + - - +
262A GLU* 3.0 35.0 + - - +
263A ALA* 3.0 23.7 + - - +
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Residues in contact with CYS 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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176A VAL* 3.9 17.7 - - - -
232A LEU* 3.9 22.4 - - - -
239A TYR* 4.4 10.4 - - + -
241A LEU* 3.8 27.4 - - - -
256A ILE 3.2 14.5 + - - -
257A LEU 3.1 9.3 + - - +
259A ARG* 1.3 75.7 - - - +
261A ALA* 1.3 61.4 + - - +
263A ALA* 3.8 2.0 - - - +
264A ALA* 2.8 33.5 + - - +
270A VAL* 4.0 21.7 - - + +
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Residues in contact with ALA 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 LEU 2.9 10.3 + - - +
258A ARG* 2.8 12.8 + - + +
260A CYS* 1.3 76.5 - - - +
262A GLU* 1.3 63.2 + - + +
264A ALA* 3.1 6.4 + - - +
265A GLY* 2.9 23.0 + - - +
270A VAL* 4.5 0.2 - - - +
311A ALA 3.5 24.2 - - - +
312A GLY 5.4 1.1 - - - +
313A LEU* 4.0 20.0 - - + -
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Residues in contact with GLU 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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231A PRO* 5.2 3.1 - - - +
234A ALA* 5.4 1.6 - - - +
258A ARG* 2.9 37.2 + - + +
259A ARG* 3.0 41.9 + - - +
261A ALA* 1.3 79.5 - - + +
263A ALA* 1.3 62.4 + - - +
265A GLY* 3.4 9.9 + - - -
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Residues in contact with ALA 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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232A LEU* 4.0 14.8 - - + +
233A PRO 3.6 8.7 - - - +
234A ALA* 4.1 11.7 - - - +
235A GLY* 2.9 27.9 + - - -
239A TYR* 3.1 34.3 + - + +
259A ARG 3.0 16.0 + - - +
260A CYS 4.0 1.6 - - - +
262A GLU* 1.3 78.7 - - - +
264A ALA* 1.3 62.1 + - - +
265A GLY* 4.6 0.2 - - - -
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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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235A GLY* 5.1 3.2 - - - -
236A ALA 4.4 3.9 - - - +
239A TYR* 3.6 17.2 - - + -
260A CYS 2.8 19.8 + - - +
261A ALA* 3.5 4.7 - - - +
263A ALA* 1.3 79.6 - - - +
265A GLY* 1.3 63.5 + - - +
267A GLY* 3.8 1.7 + - - -
268A GLY* 3.0 36.5 + - - +
270A VAL* 4.0 18.8 - - + -
313A LEU* 5.8 1.3 - - + -
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Residues in contact with GLY 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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261A ALA 2.9 13.7 + - - +
262A GLU 3.4 9.7 + - - -
263A ALA 4.6 0.4 - - - -
264A ALA* 1.3 80.6 - - - +
266A SER* 1.3 59.1 + - - -
267A GLY 2.9 11.8 + - - -
268A GLY 3.5 6.2 + - - +
331A ALA* 4.1 12.2 + - - +
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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