Contacts of the helix formed by residues 294 - 306 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G TYR* 3.6 1.9 + - - -
237G THR* 5.3 0.4 - - - -
239G ARG* 3.4 31.6 - - - +
241G GLU* 4.2 7.0 - - - +
292G PHE 3.4 2.0 + - - +
293G LYS* 1.3 75.7 - - - +
295G VAL* 1.3 60.2 + - - +
296G ALA* 3.5 9.4 + - - +
297G GLU* 2.7 39.7 + - - +
298G GLY* 2.8 27.5 + - - -
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Residues in contact with VAL 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G TYR* 3.8 8.1 - - - +
211G PHE* 3.6 44.5 + - + +
241G GLU* 3.1 33.9 + - + +
245G ALA* 4.0 10.5 - - + +
246G VAL* 3.7 35.0 - - + +
249G ALA* 4.4 1.8 - - + -
294G THR* 1.3 72.5 - - - +
296G ALA* 1.3 66.6 + - - +
299G VAL* 2.9 37.7 + - + +
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Residues in contact with ALA 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G GLU* 5.1 1.2 + - - -
249G ALA* 4.3 13.0 - - + +
294G THR* 3.3 9.4 + - - +
295G VAL* 1.3 82.3 - - - +
297G GLU* 1.3 54.8 + - + +
300G THR* 2.5 36.3 + - - +
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Residues in contact with GLU 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G PHE 4.2 1.7 - - - +
293G LYS* 3.3 22.2 - - + +
294G THR* 2.7 46.4 + - - +
296G ALA* 1.3 80.9 - - + +
298G GLY* 1.3 63.9 + - - +
300G THR* 3.3 6.2 + - - -
301G GLU* 3.0 24.9 + - - +
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Residues in contact with GLY 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G TYR* 3.2 21.8 - - - -
213G TYR* 3.7 18.5 - - - -
293G LYS* 4.2 8.2 - - - +
294G THR 2.8 15.0 + - - -
297G GLU* 1.3 75.1 - - - +
299G VAL* 1.3 55.1 + - - +
301G GLU* 3.3 6.4 + - - +
302G TYR* 2.9 30.0 + - - +
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Residues in contact with VAL 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G TYR* 3.6 24.7 + - + -
185G ALA* 4.7 3.6 - - + -
246G VAL* 4.2 16.4 - - + +
249G ALA* 3.7 17.7 - - + -
250G THR* 3.4 28.9 - - - +
295G VAL* 2.9 38.4 + - + +
298G GLY* 1.3 71.8 - - - -
300G THR* 1.3 59.4 + - - +
302G TYR* 3.3 5.1 + - - +
303G MET* 2.8 45.8 + - + +
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Residues in contact with THR 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G ALA* 3.8 24.9 - - + +
252G ALA* 5.6 2.5 - - + -
253G TYR* 4.3 21.8 - - + +
296G ALA 2.5 25.2 + - - +
297G GLU* 3.3 8.1 + - - -
299G VAL* 1.3 78.0 - - - +
301G GLU* 1.3 62.2 + - - +
303G MET* 3.1 6.6 + - - +
304G ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G TYR* 3.3 23.4 + - - +
293G LYS* 2.9 38.8 + - - +
297G GLU 3.0 18.2 + - - +
298G GLY 3.6 4.3 - - - +
300G THR* 1.3 77.4 + - - +
302G TYR* 1.3 61.7 + - - +
304G ALA* 3.4 7.7 + - + +
305G TRP* 3.1 21.2 + - + +
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Residues in contact with TYR 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G TYR* 3.9 11.2 - + + -
172G GLY* 3.0 35.4 + - - -
173G PRO* 3.3 21.8 - - + -
175G GLU* 2.6 34.2 + - - +
183G SER* 3.9 9.6 - - - -
185G ALA* 4.0 15.0 - - + -
186G PHE* 3.3 20.2 - + - -
213G TYR* 4.1 12.0 - - + -
298G GLY 2.9 17.1 + - - +
299G VAL* 3.4 5.4 - - - +
301G GLU* 1.3 74.0 - - - +
303G MET* 1.3 61.8 + - + +
305G TRP* 3.1 6.2 + + - -
306G LEU* 2.9 57.0 + - + +
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Residues in contact with MET 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G ALA* 3.6 31.9 - - + +
189G ASN* 3.6 29.2 - - + +
250G THR* 3.6 28.7 - - + +
253G TYR* 3.5 37.7 + - + -
254G HIS* 3.9 9.9 - - - -
299G VAL* 2.8 36.2 + - + +
300G THR* 3.1 4.0 + - - +
302G TYR* 1.3 74.8 - - + +
304G ALA* 1.3 61.6 + - - +
306G LEU* 3.3 12.0 + - + -
307G ASN* 2.6 29.1 + - - +
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Residues in contact with ALA 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253G TYR* 3.4 21.2 + - + +
300G THR 3.0 11.7 + - - +
301G GLU* 3.5 11.4 - - - +
303G MET* 1.3 76.7 - - - +
305G TRP* 1.3 62.2 + - - +
307G ASN 3.1 21.1 + - - -
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Residues in contact with TRP 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G PRO* 3.6 48.6 - - + +
174G ARG* 4.0 29.4 - - + +
213G TYR* 5.7 0.7 - - - +
301G GLU* 3.1 9.4 + - + +
302G TYR* 3.1 8.8 + + - +
304G ALA* 1.3 80.0 - - - +
306G LEU* 1.3 86.7 + - + +
307G ASN 3.1 3.7 + - - +
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Residues in contact with LEU 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G PHE* 4.1 25.4 - - + -
189G ASN* 3.6 38.1 + - + +
193G ASN* 5.2 0.9 + - - -
302G TYR* 2.9 53.1 + - + +
303G MET* 4.1 13.2 - - + -
304G ALA 3.2 0.4 - - - -
305G TRP* 1.3 90.7 - - + +
307G ASN* 1.3 74.9 + - - +
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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