Contacts of the helix formed by residues 294 - 306 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B TYR* 3.6 1.6 + - - -
237B THR* 5.3 0.4 - - - -
239B ARG* 3.4 31.6 - - - +
241B GLU* 4.2 7.0 - - - +
292B PHE 3.4 2.4 + - - +
293B LYS* 1.3 75.4 - - - +
295B VAL* 1.3 60.8 + - - +
296B ALA* 3.5 9.3 + - - +
297B GLU* 2.7 39.1 + - - +
298B GLY* 2.8 27.0 + - - -
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 3.8 7.9 - - - +
211B PHE* 3.6 44.7 + - + +
241B GLU* 3.1 34.8 + - + +
245B ALA* 4.0 10.3 - - + +
246B VAL* 3.7 35.0 - - + +
249B ALA* 4.5 2.0 - - + -
294B THR* 1.3 72.2 - - - +
296B ALA* 1.3 66.4 + - - +
299B VAL* 2.9 37.5 + - + +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B GLU* 4.8 1.2 + - - -
249B ALA* 4.3 12.4 - - + +
294B THR* 3.3 9.4 + - - +
295B VAL* 1.3 82.2 - - - +
297B GLU* 1.3 54.9 + - + +
300B THR* 2.5 36.4 + - - +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE 4.2 1.4 - - - +
293B LYS* 3.3 22.0 - - + -
294B THR* 2.7 45.6 + - - +
296B ALA* 1.3 79.6 - - + +
298B GLY* 1.3 64.2 + - - +
300B THR* 3.3 6.2 + - - -
301B GLU* 3.0 25.0 + - - +
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 3.2 21.5 - - - -
213B TYR* 3.7 18.9 - - - -
293B LYS* 4.2 8.2 - - - +
294B THR 2.8 14.8 + - - -
297B GLU* 1.3 75.3 - - - +
299B VAL* 1.3 55.0 + - - +
301B GLU* 3.3 6.2 + - - +
302B TYR* 2.9 29.3 + - - +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 3.6 24.0 + - + -
185B ALA* 4.7 4.3 - - + -
246B VAL* 4.2 16.4 - - + +
249B ALA* 3.7 17.7 - - + -
250B THR* 3.4 28.5 - - - +
295B VAL* 2.9 38.0 + - + +
298B GLY* 1.3 72.0 - - - +
300B THR* 1.3 58.4 + - - +
302B TYR* 3.3 5.2 + - - +
303B MET* 2.8 45.9 + - + +
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 3.8 25.4 - - + +
252B ALA* 5.6 2.5 - - + -
253B TYR* 4.3 21.4 - - + +
296B ALA 2.5 25.6 + - - +
297B GLU* 3.3 8.1 + - - -
299B VAL* 1.3 77.8 - - - +
301B GLU* 1.3 62.9 + - - +
303B MET* 3.1 6.6 + - - +
304B ALA* 3.0 22.7 + - - +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 3.3 23.7 + - - +
293B LYS* 2.9 38.8 + - - +
297B GLU 3.0 18.0 + - - +
298B GLY 3.6 4.5 - - - +
300B THR* 1.3 76.6 - - - +
302B TYR* 1.3 62.3 + - - +
304B ALA* 3.4 7.6 + - - +
305B TRP* 3.1 21.0 + - + +
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B TYR* 3.9 11.0 - + + -
172B GLY* 3.0 35.4 + - - -
173B PRO* 3.3 22.4 - - + +
175B GLU* 2.6 34.5 + - - +
183B SER* 3.9 9.4 - - - -
185B ALA* 4.0 15.3 - - + -
186B PHE* 3.3 20.2 - + - -
213B TYR* 4.1 12.5 - - + -
298B GLY 2.9 16.6 + - - +
299B VAL* 3.4 6.1 - - - +
301B GLU* 1.3 74.0 - - - +
303B MET* 1.3 61.5 + - + +
305B TRP* 3.1 6.2 + + - +
306B LEU* 2.9 56.5 + - + +
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Residues in contact with MET 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ALA* 3.6 34.1 - - + +
189B ASN* 3.6 28.7 - - + +
250B THR* 3.6 28.5 - - + +
253B TYR* 3.5 37.0 + - + -
254B HIS* 3.9 9.0 - - - -
299B VAL* 2.8 36.8 + - + +
300B THR 3.1 3.8 + - - +
302B TYR* 1.3 75.2 - - + +
304B ALA* 1.3 61.8 + - - +
306B LEU* 3.3 11.6 + - + -
307B ASN* 2.6 28.9 + - - +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 3.4 21.2 + - + +
300B THR 3.0 11.2 + - - +
301B GLU* 3.5 11.4 - - - +
303B MET* 1.3 76.7 - - - +
305B TRP* 1.3 62.5 + - - +
307B ASN 3.1 21.3 + - - -
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PRO* 3.6 48.1 - - + +
174B ARG* 4.0 29.8 - - + +
213B TYR* 5.7 0.7 - - - +
301B GLU* 3.1 9.6 + - + +
302B TYR* 3.1 8.8 + + - +
304B ALA* 1.3 80.0 - - - +
306B LEU* 1.3 88.0 + - + +
307B ASN 3.1 3.7 + - - +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B PHE* 4.1 25.1 - - + -
189B ASN* 3.6 37.9 + - + +
193B ASN* 5.2 0.9 + - - -
302B TYR* 2.9 53.4 + - + +
303B MET* 3.7 13.5 - - + +
304B ALA 3.2 0.4 - - - -
305B TRP* 1.3 90.0 - - + +
307B ASN* 1.3 75.9 + - - +
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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