Contacts of the helix formed by residues 294 - 306 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171T TYR* 3.6 1.9 + - - -
211T PHE 5.5 0.2 - - - -
237T THR* 5.3 0.4 - - - -
239T ARG* 3.4 31.6 - - - +
241T GLU* 4.2 6.3 - - - -
292T PHE 4.6 1.3 - - - +
293T LYS* 1.3 75.1 - - - +
295T VAL* 1.3 60.8 + - - +
296T ALA* 3.5 9.5 + - - +
297T GLU* 2.7 39.3 + - - +
298T GLY* 2.8 27.4 + - - -
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Residues in contact with VAL 295 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171T TYR* 3.9 8.1 - - - +
211T PHE* 3.6 45.2 + - + +
241T GLU* 3.1 33.9 + - + +
245T ALA* 4.0 10.3 - - + +
246T VAL* 3.7 34.5 - - + +
249T ALA* 4.4 3.1 - - + -
294T THR* 1.3 73.5 - - - +
296T ALA* 1.3 65.3 + - - +
299T VAL* 2.9 37.9 + - + +
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Residues in contact with ALA 296 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241T GLU* 4.8 1.6 + - - -
249T ALA* 4.3 12.9 - - + +
294T THR* 3.3 8.6 + - - +
295T VAL* 1.3 81.0 - - - +
297T GLU* 1.3 55.1 + - + +
300T THR* 2.5 35.6 + - - +
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Residues in contact with GLU 297 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292T PHE 4.2 1.6 - - - +
293T LYS* 3.3 21.9 - - + -
294T THR* 2.7 45.9 + - - +
296T ALA* 1.3 79.8 - - + +
298T GLY* 1.3 64.0 + - - +
300T THR* 3.3 6.5 + - - -
301T GLU* 3.0 24.6 + - - +
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Residues in contact with GLY 298 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171T TYR* 3.2 21.1 - - - -
213T TYR* 3.7 19.2 - - - -
293T LYS* 4.2 7.8 - - - +
294T THR 2.8 13.9 + - - -
297T GLU* 1.3 74.9 - - - +
299T VAL* 1.3 56.6 + - - +
301T GLU* 3.3 6.0 + - - +
302T TYR* 2.9 30.3 + - - +
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Residues in contact with VAL 299 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171T TYR* 3.6 23.3 + - + -
185T ALA* 4.7 4.0 - - + -
246T VAL* 4.2 16.4 - - + +
249T ALA* 3.7 17.9 - - + -
250T THR* 3.4 28.3 - - - +
295T VAL* 2.9 38.9 + - + +
298T GLY* 1.3 71.2 - - - -
300T THR* 1.3 57.8 + - - +
302T TYR* 3.3 5.3 + - - +
303T MET* 2.8 46.2 + - + +
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Residues in contact with THR 300 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249T ALA* 3.8 24.7 - - + +
252T ALA* 5.6 2.0 - - + -
253T TYR* 4.3 22.3 - - + +
296T ALA 2.5 26.1 + - - +
297T GLU* 3.3 8.1 + - - -
299T VAL* 1.3 76.5 - - - +
301T GLU* 1.3 62.1 + - - +
303T MET* 3.1 6.5 + - - +
304T ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 301 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213T TYR* 3.3 24.4 + - - +
293T LYS* 2.9 38.0 + - - +
297T GLU 3.0 16.8 + - - +
298T GLY 3.3 4.9 + - - +
300T THR* 1.3 76.8 - - - +
302T TYR* 1.3 62.7 + - - +
304T ALA* 3.4 7.1 + - - +
305T TRP* 3.1 21.1 + - + +
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Residues in contact with TYR 302 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171T TYR* 3.9 11.4 - + + -
172T GLY* 3.0 35.4 + - - -
173T PRO* 3.3 21.9 - - + +
174T ARG 5.2 0.2 + - - -
175T GLU* 2.6 34.8 + - - +
183T SER* 3.9 9.2 - - - -
185T ALA* 4.0 14.4 - - + -
186T PHE* 3.3 18.9 - - - -
213T TYR* 4.1 11.4 - - + -
298T GLY 2.9 17.5 + - - +
299T VAL* 3.4 5.4 - - - +
301T GLU* 1.3 75.6 - - - +
303T MET* 1.3 62.5 + - + +
305T TRP* 3.1 6.2 + + - -
306T LEU* 2.8 56.8 + - + +
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Residues in contact with MET 303 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185T ALA* 3.6 33.9 - - + +
189T ASN* 3.6 28.7 - - + +
250T THR* 3.6 26.9 - - + +
253T TYR* 3.5 37.8 + - + -
254T HIS* 3.9 9.4 - - - -
299T VAL* 2.8 37.8 + - + +
300T THR* 3.1 3.8 + - - +
302T TYR* 1.3 75.1 - - + +
304T ALA* 1.3 62.3 + - - +
306T LEU* 3.3 10.7 + - + -
307T ASN* 2.6 28.9 + - - +
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Residues in contact with ALA 304 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253T TYR* 3.4 20.7 + - + +
300T THR 3.0 12.9 + - - +
301T GLU* 3.5 11.0 - - - +
303T MET* 1.3 76.9 - - - +
305T TRP* 1.3 63.0 + - - +
307T ASN 3.1 21.5 + - - -
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Residues in contact with TRP 305 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T PRO* 3.6 48.4 - - + +
174T ARG* 4.0 27.9 - - + +
213T TYR* 5.6 0.7 - - - +
301T GLU* 3.1 10.5 + - + +
302T TYR* 3.1 9.7 + + - +
304T ALA* 1.3 79.2 - - - +
306T LEU* 1.3 88.4 + - + +
307T ASN 3.1 3.3 + - - +
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Residues in contact with LEU 306 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186T PHE* 4.1 25.8 - - + -
189T ASN* 3.6 37.1 + - + +
193T ASN* 5.2 0.7 + - - -
302T TYR* 2.8 54.9 + - + +
303T MET* 4.1 11.9 - - + -
304T ALA 3.2 0.6 - - - -
305T TRP* 1.3 91.0 - - + +
307T ASN* 1.3 74.4 + - - +
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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