Contacts of the helix formed by residues 294 - 306 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H TYR* 3.6 1.2 + - - -
211H PHE 5.5 0.4 - - - -
237H THR* 5.3 0.7 - - - -
239H ARG* 3.4 31.2 - - - +
241H GLU* 4.2 6.7 - - - -
292H PHE 4.6 1.6 - - - +
293H LYS* 1.3 76.0 - - - +
295H VAL* 1.3 60.1 + - - +
296H ALA* 3.5 9.8 + - - +
297H GLU* 2.7 39.1 + - - +
298H GLY* 2.8 27.4 + - - -
157T GLU* 5.0 6.1 - - - +
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Residues in contact with VAL 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H TYR* 3.8 8.1 - - - +
211H PHE* 3.6 44.9 + - + +
241H GLU* 3.1 34.2 + - + +
245H ALA* 4.0 11.0 - - + +
246H VAL* 3.8 34.8 - - + +
249H ALA* 4.5 1.6 - - + -
294H THR* 1.3 72.8 - - - +
296H ALA* 1.3 67.4 + - - +
299H VAL* 2.9 37.0 + - + +
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Residues in contact with ALA 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H GLU* 4.8 1.6 + - - -
249H ALA* 4.3 12.8 - - + +
294H THR* 3.3 9.0 + - - +
295H VAL* 1.3 82.1 - - - +
297H GLU* 1.3 54.2 + - + +
300H THR* 2.5 35.8 + - - +
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Residues in contact with GLU 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H PHE 4.2 1.4 - - - +
293H LYS* 3.3 20.7 - - + -
294H THR* 2.7 45.9 + - - +
296H ALA* 1.3 80.2 - - + +
298H GLY* 1.3 64.2 + - - +
300H THR* 3.3 6.4 + - - -
301H GLU* 3.0 24.6 + - - +
157T GLU* 5.6 0.9 - - - +
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Residues in contact with GLY 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H TYR* 3.2 21.3 - - - -
213H TYR* 3.7 19.0 - - - -
293H LYS* 4.2 8.0 - - - +
294H THR 2.8 14.8 + - - -
297H GLU* 1.3 74.1 - - - +
299H VAL* 1.3 56.8 + - - +
301H GLU* 3.3 5.6 + - - +
302H TYR* 2.9 30.0 + - - +
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Residues in contact with VAL 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H TYR* 3.7 24.0 - - + -
185H ALA* 4.7 3.8 - - + -
246H VAL* 4.2 16.6 - - + +
249H ALA* 3.7 17.0 - - + -
250H THR* 3.4 29.4 - - - +
295H VAL* 2.9 38.4 + - + +
298H GLY* 1.3 71.1 - - - -
300H THR* 1.3 59.4 + - - +
302H TYR* 3.3 5.2 + - - +
303H MET* 2.8 45.3 + - + +
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Residues in contact with THR 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H ALA* 3.8 24.5 - - + +
252H ALA* 5.6 2.5 - - + -
253H TYR* 4.3 21.4 - - + +
296H ALA 2.5 26.8 + - - +
297H GLU* 3.3 7.8 + - - -
299H VAL* 1.3 78.4 - - - +
301H GLU* 1.3 61.5 + - - +
303H MET* 3.1 6.7 + - - +
304H ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H TYR* 3.3 23.9 + - - +
293H LYS* 2.9 38.7 + - - +
297H GLU 3.0 17.5 + - - +
298H GLY 3.6 4.5 - - - +
300H THR* 1.3 76.8 - - - +
302H TYR* 1.3 63.1 + - - +
304H ALA* 3.4 7.3 + - - +
305H TRP* 3.1 21.3 + - + +
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Residues in contact with TYR 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H TYR* 4.0 11.2 - + - -
172H GLY* 3.1 35.8 + - - -
173H PRO* 3.3 21.3 - - + -
174H ARG 5.2 0.2 + - - -
175H GLU* 2.6 34.5 + - - +
183H SER* 3.9 9.4 - - - -
185H ALA* 4.0 13.9 - - + -
186H PHE* 3.3 19.9 - - - -
213H TYR* 4.1 11.6 - - + -
298H GLY 2.9 15.8 + - - +
299H VAL* 3.4 6.3 - - - +
301H GLU* 1.3 74.4 - - - +
303H MET* 1.3 62.0 + - + +
305H TRP* 3.1 6.3 + + - -
306H LEU* 2.9 57.0 + - + +
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Residues in contact with MET 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H ALA* 3.6 34.3 - - + +
189H ASN* 3.6 28.0 - - + +
250H THR* 3.6 28.0 - - + +
253H TYR* 3.5 37.4 + - + -
254H HIS* 3.9 9.2 - - - -
299H VAL* 2.8 36.8 + - + +
300H THR* 3.1 3.8 + - - +
302H TYR* 1.3 76.1 - - + +
304H ALA* 1.3 62.2 + - - +
306H LEU* 3.3 11.8 + - + -
307H ASN* 2.6 29.2 + - - +
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Residues in contact with ALA 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H TYR* 3.4 20.9 + - + +
300H THR 3.0 12.1 + - - +
301H GLU* 3.5 11.7 - - + +
302H TYR 3.2 0.2 - - - -
303H MET* 1.3 77.5 - - - +
305H TRP* 1.3 63.0 + - - +
307H ASN 3.1 21.1 + - - -
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Residues in contact with TRP 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H PRO* 3.6 49.9 - - + +
174H ARG* 4.0 29.2 - - + +
213H TYR* 5.7 0.7 - - - +
301H GLU* 3.1 9.8 + - + +
302H TYR* 3.1 9.2 + + - +
304H ALA* 1.3 79.2 - - - +
306H LEU* 1.3 88.1 + - + +
307H ASN 3.1 3.7 + - - +
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Residues in contact with LEU 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H PHE* 4.1 24.7 - - + -
189H ASN* 3.6 38.6 + - + +
193H ASN* 5.2 1.2 + - - -
302H TYR* 2.9 54.2 + - + +
303H MET* 4.1 13.0 - - + -
304H ALA 3.2 0.4 - - - -
305H TRP* 1.3 91.4 - - + +
307H ASN* 1.3 74.7 + - - +
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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