Contacts of the helix formed by residues 294 - 306 (chain O) in PDB entry 2X86
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 294 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255H LYS* 6.2 1.8 - - - +
171O TYR* 3.6 2.3 + - - -
211O PHE 5.5 0.7 - - - -
237O THR* 5.3 0.9 - - - -
239O ARG* 3.4 30.7 - - - +
241O GLU* 4.2 6.7 - - - +
292O PHE 3.4 1.3 + - - +
293O LYS* 1.3 75.4 - - - +
295O VAL* 1.3 59.2 + - - +
296O ALA* 3.5 9.1 + - - +
297O GLU* 2.7 38.6 + - - +
298O GLY* 2.8 27.0 + - - -
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Residues in contact with VAL 295 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171O TYR* 3.8 8.1 - - - +
211O PHE* 3.6 44.9 + - + +
241O GLU* 3.1 33.7 + - + +
245O ALA* 4.0 10.5 - - + +
246O VAL* 3.7 34.3 - - + +
249O ALA* 4.5 1.6 - - + -
294O THR* 1.3 72.4 - - - +
296O ALA* 1.3 66.4 + - - +
299O VAL* 2.9 33.5 + - + +
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Residues in contact with ALA 296 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241O GLU* 4.8 1.6 + - - -
249O ALA* 4.3 13.0 - - + +
294O THR* 3.3 8.1 + - - +
295O VAL* 1.3 81.7 - - - +
297O GLU* 1.3 55.2 + - + +
300O THR* 2.5 36.0 + - - +
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Residues in contact with GLU 297 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292O PHE 4.2 1.4 - - - +
293O LYS* 3.3 21.2 - - + -
294O THR* 2.7 46.0 + - - +
296O ALA* 1.3 81.3 - - + +
298O GLY* 1.3 64.3 + - - +
300O THR* 3.3 5.4 + - - -
301O GLU* 3.0 24.7 + - - +
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Residues in contact with GLY 298 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171O TYR* 3.2 22.0 - - - -
213O TYR* 3.7 18.4 - - - -
293O LYS* 4.2 8.2 - - - +
294O THR 2.8 14.5 + - - -
297O GLU* 1.3 73.4 - - - +
299O VAL* 1.3 55.7 + - - +
301O GLU* 3.3 5.9 + - - +
302O TYR* 2.9 29.6 + - - +
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Residues in contact with VAL 299 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171O TYR* 3.6 23.3 + - + -
185O ALA* 4.7 3.6 - - + -
246O VAL* 4.2 16.4 - - + +
249O ALA* 3.7 17.9 - - + -
250O THR* 3.4 29.4 - - - +
295O VAL* 2.9 38.8 + - + +
298O GLY* 1.3 71.4 - - - -
300O THR* 1.3 59.3 + - - +
302O TYR* 3.3 4.8 + - - +
303O MET* 2.8 46.1 + - + +
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Residues in contact with THR 300 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249O ALA* 3.8 25.6 - - + +
252O ALA* 5.6 2.2 - - + -
253O TYR* 4.3 21.3 - - + +
296O ALA 2.5 26.2 + - - +
297O GLU* 3.3 8.0 + - - -
299O VAL* 1.3 77.6 - - - +
301O GLU* 1.3 62.4 + - - +
303O MET* 3.1 6.5 + - - +
304O ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 301 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213O TYR* 3.4 23.5 + - - +
293O LYS* 2.9 38.6 + - - +
297O GLU 3.0 17.2 + - - +
298O GLY 3.6 4.5 - - - +
300O THR* 1.3 77.3 - - - +
302O TYR* 1.3 63.0 + - - +
304O ALA* 3.4 7.9 + - + +
305O TRP* 3.1 20.8 + - + +
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Residues in contact with TYR 302 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O TYR* 4.0 11.4 - + + -
172O GLY* 3.0 35.2 + - - -
173O PRO* 3.3 21.7 - - + +
174O ARG 5.2 0.2 + - - -
175O GLU* 2.6 34.7 + - - +
183O SER* 3.9 9.2 - - - -
185O ALA* 4.0 14.8 - - + -
186O PHE* 3.3 19.8 - + - -
213O TYR* 4.1 11.8 - - + -
298O GLY 2.9 16.7 + - - +
299O VAL* 3.4 5.2 - - - +
301O GLU* 1.3 74.3 - - - +
303O MET* 1.3 62.5 + - + +
305O TRP* 3.1 6.8 + + - -
306O LEU* 2.9 56.1 + - + +
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Residues in contact with MET 303 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185O ALA* 3.6 33.7 - - + +
189O ASN* 3.6 29.2 - - + +
250O THR* 3.6 27.8 - - + +
253O TYR* 3.5 36.1 + - + -
254O HIS* 3.9 9.2 - - - -
299O VAL* 2.8 36.7 + - + +
300O THR* 3.1 4.0 + - - +
302O TYR* 1.3 74.9 - - + +
304O ALA* 1.3 62.5 + - - +
306O LEU* 3.3 11.6 + - + -
307O ASN* 2.6 28.5 + - - +
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Residues in contact with ALA 304 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253O TYR* 3.4 21.2 + - + +
300O THR 3.0 12.0 + - - +
301O GLU* 3.5 11.7 - - + +
302O TYR 3.2 0.2 - - - -
303O MET* 1.3 76.3 - - - +
305O TRP* 1.3 62.2 + - - +
307O ASN 3.1 21.1 + - - -
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Residues in contact with TRP 305 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O PRO* 3.6 49.0 - - + +
174O ARG* 4.0 29.0 - - + +
213O TYR* 5.6 0.9 - - - +
301O GLU* 3.1 10.0 + - + +
302O TYR* 3.1 9.3 + + - +
304O ALA* 1.3 80.2 - - - +
306O LEU* 1.3 87.4 + - + +
307O ASN 3.2 3.1 + - - +
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Residues in contact with LEU 306 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186O PHE* 4.1 24.7 - - + -
189O ASN* 3.6 37.4 + - + +
193O ASN* 5.2 1.0 + - - -
302O TYR* 2.9 53.3 + - + +
303O MET* 4.1 13.2 - - + -
304O ALA 3.2 0.6 - - - -
305O TRP* 1.3 91.5 - - + +
307O ASN* 1.3 75.1 + - - +
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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