Contacts of the helix formed by residues 252 - 263 (chain D) in PDB entry 4UQJ
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 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D ASP* 3.3 32.6 + - - +
250D TYR 4.3 0.2 - - - +
251D ASP* 1.3 78.3 - - - +
253D SER* 1.3 55.1 + - - +
254D LEU* 4.0 8.9 - - + +
255D VAL* 3.1 16.4 + - + +
256D SER* 2.7 35.7 + - - -
339D GLU* 5.5 2.3 - - - +
340D GLY 5.3 2.4 - - - +
341D LEU 5.2 1.6 - - - +
343D GLY* 5.1 11.1 + - - -
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Residues in contact with SER 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ASP 3.5 4.2 + - - -
252D ASP* 1.3 72.5 - - - +
254D LEU* 1.3 58.6 + - - +
256D SER* 3.9 8.8 - - - -
257D LYS* 3.0 30.0 + - - +
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Residues in contact with LEU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D ASP* 3.0 8.4 - - + +
253D SER* 1.3 85.1 + - - +
255D VAL* 1.3 63.2 + - + +
257D LYS* 3.5 5.0 + - - +
258D PHE* 3.2 17.9 + - + +
286D TYR* 5.8 4.5 - - + +
339D GLU* 3.7 45.3 - - + +
340D GLY* 4.1 15.7 - - - +
341D LEU* 3.9 20.4 - - + -
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D VAL* 3.9 18.6 - - + -
249D ASP 3.3 28.9 - - - +
250D TYR* 4.0 10.5 - - + -
252D ASP* 3.1 12.6 + - + +
254D LEU* 1.3 75.3 - - + +
256D SER* 1.3 67.1 + - - +
258D PHE* 3.0 2.4 + - - +
259D ILE* 3.0 47.2 + - + +
340D GLY 4.8 1.3 - - - +
341D LEU* 3.6 46.4 - - + +
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Residues in contact with SER 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D TYR* 4.3 14.1 + - - +
251D ASP 5.3 0.9 - - - -
252D ASP 2.7 22.1 + - - -
253D SER* 3.9 10.1 - - - -
255D VAL* 1.3 74.4 - - - +
257D LYS* 1.3 60.0 + - - +
259D ILE* 3.6 7.8 + - - +
260D GLU* 3.2 21.0 + - - +
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Residues in contact with LYS 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D SER 3.0 19.5 + - - +
254D LEU* 3.7 5.8 - - - +
256D SER* 1.3 75.3 - - - +
258D PHE* 1.3 65.7 + - - +
260D GLU* 3.3 20.8 + - - +
261D ARG* 3.5 7.4 + - - +
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Residues in contact with PHE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D VAL* 4.2 10.3 - - + -
254D LEU* 3.2 7.3 + - + +
255D VAL 3.0 9.5 + - - +
257D LYS* 1.3 80.0 - - - +
259D ILE* 1.3 73.7 + - + +
261D ARG* 3.2 7.3 + - - +
262D TRP* 2.8 71.9 + + + +
278D ILE* 4.1 14.6 - - + -
286D TYR* 3.4 51.8 - + + -
341D LEU* 3.8 33.7 - - + -
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Residues in contact with ILE 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D TYR* 4.0 15.3 - - + -
255D VAL* 3.0 38.9 + - + +
256D SER* 3.9 7.6 - - - +
258D PHE* 1.3 91.6 - - + +
260D GLU* 1.3 61.5 + - - +
262D TRP* 3.9 9.0 - - + -
263D SER* 2.8 41.2 + - - +
275D THR 5.3 0.7 - - - +
276D ALA* 3.3 42.4 - - + +
277D THR* 5.0 1.1 - - - -
278D ILE* 4.7 6.3 - - + -
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Residues in contact with GLU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D SER 3.2 12.5 + - - +
257D LYS* 3.3 15.5 - - - +
258D PHE 3.2 0.8 - - - -
259D ILE* 1.3 80.1 - - - +
261D ARG* 1.3 56.3 + - - +
263D SER* 3.8 3.0 + - - -
264D THR* 3.2 25.8 + - - +
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Residues in contact with ARG 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D LYS 3.5 6.0 + - - +
258D PHE* 3.2 7.8 + - - +
259D ILE 3.1 0.2 - - - -
260D GLU* 1.3 77.1 - - + +
262D TRP* 1.3 63.7 + - - +
263D SER 3.5 0.4 - - - -
264D THR* 2.9 20.1 + - - -
265D LEU* 3.1 21.1 - - + +
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Residues in contact with TRP 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN* 3.7 29.1 - - + +
27D SER* 4.1 2.9 - - - -
28D ALA* 3.7 39.7 - - + -
31D VAL* 3.8 21.1 - - + -
258D PHE* 2.8 49.2 + + + +
259D ILE* 3.8 8.5 - - + +
261D ARG* 1.3 73.1 - - - +
263D SER* 1.3 57.9 + - - +
264D THR 3.0 5.9 + - - -
265D LEU* 3.2 19.4 + - + +
273D ALA* 2.6 63.2 + - + +
275D THR* 3.3 21.8 + - - -
277D THR 3.8 18.5 + - - -
278D ILE* 4.6 7.9 - - + -
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Residues in contact with SER 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D ILE* 2.8 29.3 + - - +
260D GLU* 3.8 8.0 + - - -
262D TRP* 1.3 74.4 - - - +
264D THR* 1.3 62.3 + - - +
273D ALA 4.1 1.1 - - - -
274D HIS* 3.4 30.2 + - - -
275D THR 3.3 29.8 - - - +
276D ALA* 4.3 8.3 - - - -
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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
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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