Contacts of the helix formed by residues 252 - 263 (chain D) in PDB entry 3GXM
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 THR 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240D LEU* 4.0 23.7 - - + +
251D PHE* 1.3 75.7 - - - +
253D PRO* 1.3 77.0 - - + +
254D GLU* 3.5 13.9 + - - +
255D HIS* 3.0 27.2 + - + +
256D GLN* 2.9 18.7 + - - +
291D TRP* 3.8 0.7 - - - -
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Residues in contact with PRO 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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240D LEU* 5.7 1.8 - - + -
252D THR* 1.3 86.4 - - + +
254D GLU* 1.3 63.5 + - - +
256D GLN* 3.5 0.3 + - - +
257D ARG* 2.9 29.5 + - - +
290D HIS* 4.2 17.9 - - + +
291D TRP* 3.4 55.6 - - + +
294D VAL* 3.7 25.8 - - + +
295D VAL* 3.7 5.4 - - + +
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Residues in contact with GLU 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 THR* 3.5 12.3 - - - +
253D PRO* 1.3 88.2 - - - +
255D HIS* 1.3 59.1 + - - +
257D ARG* 3.5 26.0 - - - +
258D ASP* 3.0 35.8 + - - +
290D HIS* 4.5 6.2 + - - -
294D VAL* 3.8 27.9 - - + +
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Residues in contact with HIS 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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196D SER* 4.0 27.4 - - - -
197D LEU* 4.2 13.0 - - + -
199D GLY 5.3 1.8 - - - -
201D PRO* 3.9 16.0 - - + +
206D HIS* 2.7 36.5 + + - -
250D GLY 4.2 2.0 + - - -
251D PHE* 3.7 23.1 - + + -
252D THR* 3.0 27.7 + - + +
254D GLU* 1.3 72.1 - - - +
256D GLN* 1.3 60.1 + - - +
258D ASP* 3.4 2.4 + - - -
259D PHE* 2.8 27.9 + - + +
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Residues in contact with GLN 256 (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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232D ALA* 3.5 32.1 + - + +
233D GLU* 4.6 2.8 - - - +
236D PRO* 4.3 14.3 - - - +
251D PHE* 3.9 16.7 - - + +
252D THR 2.9 9.5 + - - +
253D PRO 3.8 1.8 - - - +
255D HIS* 1.3 74.3 - - - +
257D ARG* 1.3 65.8 + - - +
259D PHE* 3.4 4.1 + - + +
260D ILE* 3.0 38.9 + - + +
280D MET* 3.4 10.0 - - - +
281D LEU 3.0 29.2 + - - +
291D TRP* 3.4 34.3 - - + -
295D VAL* 4.4 4.5 - - + -
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Residues in contact with ARG 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 PRO 2.9 18.9 + - - +
254D GLU* 3.5 29.3 - - - +
256D GLN* 1.3 76.8 - - - +
258D ASP* 1.3 87.2 + - - +
260D ILE* 3.8 0.6 - - - +
261D ALA* 3.1 28.1 + - + +
294D VAL* 3.4 33.9 + - + +
295D VAL* 4.0 17.3 - - - -
298D ASP* 3.1 30.4 + - + +
301D ALA* 3.7 20.4 - - + +
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Residues in contact with ASP 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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201D PRO* 3.7 25.8 - - + -
254D GLU* 3.0 14.2 + - - +
255D HIS* 4.8 0.4 - - - -
257D ARG* 1.3 110.1 + - - +
259D PHE* 1.3 59.8 + - - +
261D ALA* 4.6 4.7 - - - +
262D ARG* 2.8 42.3 + - + +
298D ASP* 4.4 4.5 - - - +
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Residues in contact with PHE 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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197D LEU* 4.5 2.2 - - + -
201D PRO* 4.1 3.7 - - - +
206D HIS* 3.6 34.1 - + + -
209D TRP* 3.4 31.9 - + + -
210D ALA* 4.2 8.5 - - - -
213D PHE* 4.5 3.1 - + - -
232D ALA* 4.4 15.3 - - + -
251D PHE* 4.0 22.0 - + + -
255D HIS* 2.8 25.7 + - + +
256D GLN* 3.8 5.8 - - + +
258D ASP* 1.3 73.1 - - - +
260D ILE* 1.3 60.1 + - + +
263D ASP* 2.8 49.6 + - + +
264D LEU* 2.8 45.0 + - + -
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Residues in contact with ILE 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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232D ALA* 4.3 15.0 - - + -
256D GLN* 3.0 44.4 + - + +
257D ARG 3.8 3.1 - - - +
259D PHE* 1.3 75.9 - - + +
261D ALA* 1.3 66.8 + - - +
264D LEU* 4.2 11.0 - - + -
265D GLY* 2.8 28.8 + - - +
266D PRO* 3.5 0.5 - - - +
278D LEU* 3.8 27.8 - - + -
280D MET* 4.6 5.4 - - + -
295D VAL* 4.6 6.3 - - + -
301D ALA* 3.9 14.6 - - + +
304D TYR* 3.8 17.7 - - + -
305D VAL* 4.1 17.7 - - + -
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Residues in contact with ALA 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 ARG 3.1 17.1 + - - +
258D ASP* 4.2 5.2 - - - +
260D ILE* 1.3 77.8 - - - +
262D ARG* 1.3 63.9 + - + +
266D PRO* 3.3 19.9 - - - +
298D ASP* 5.0 2.9 - - - +
300D GLU* 3.4 52.2 - - + +
301D ALA* 3.7 3.1 - - + +
304D TYR* 4.0 4.4 - - - -
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Residues in contact with ARG 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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201D PRO* 3.8 23.0 + - + -
202D GLY* 3.5 25.8 + - - +
207D GLN* 3.6 8.3 + - - -
258D ASP* 2.8 29.0 + - + +
261D ALA* 1.3 79.2 - - + +
263D ASP* 1.3 67.0 + - - +
266D PRO* 3.8 10.7 - - - +
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Residues in contact with ASP 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PRO* 3.7 3.8 - - - +
202D GLY* 3.2 28.4 + - - -
206D HIS* 3.3 27.3 - - - +
207D GLN* 2.3 41.1 + - - +
210D ALA* 3.9 1.8 - - + -
259D PHE* 2.8 32.4 + - + +
261D ALA 3.5 0.8 - - - -
262D ARG* 1.3 78.3 - - - +
264D LEU* 1.3 64.9 + - - +
265D GLY 3.4 1.1 - - - -
266D PRO* 3.5 2.5 - - - +
267D THR* 2.7 32.7 + - - -
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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