Contacts of the helix formed by residues 280 - 286 (chain P) 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 LEU 280 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234P ASN* 4.2 7.0 - - + +
236P GLY 3.4 25.4 - - - +
237P THR 3.4 26.0 - - - +
238P GLY* 3.8 11.7 - - - +
278P ALA* 3.6 17.4 + - + -
279P ASP* 1.3 74.0 + - - +
281P THR* 1.3 64.5 + - - +
282P ASN 3.4 2.2 - - - -
283P LEU* 3.3 21.7 + - + -
284P ARG* 2.9 58.2 + - + +
292P PHE* 4.0 4.0 - - + -
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Residues in contact with THR 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279P ASP* 2.6 28.4 + - - -
280P LEU* 1.3 76.7 - - - +
282P ASN* 1.3 65.8 + - - +
284P ARG* 3.3 4.8 + - - +
285P ALA* 2.9 33.8 + - + +
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Residues in contact with ASN 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P ILE* 4.7 8.3 - - - +
129P GLU* 2.6 45.4 + - - +
232P ILE 5.0 1.5 + - - +
233P PHE* 3.7 17.0 - - + -
279P ASP* 4.7 1.6 + - - -
280P LEU 3.4 0.2 - - - -
281P THR* 1.3 82.2 - - - +
283P LEU* 1.3 58.4 + - - +
285P ALA* 3.1 8.5 + - - +
286P ALA* 2.8 30.7 + - - +
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Residues in contact with LEU 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P GLU* 4.7 1.8 + - - +
165P PHE* 5.5 0.4 - - + -
220P VAL* 4.6 7.6 - - + -
224P PHE* 3.7 30.5 - - + -
233P PHE* 3.8 15.3 - - + -
234P ASN 3.8 25.6 - - - +
235P LEU* 5.0 4.3 - - + -
280P LEU* 3.3 31.9 + - + +
282P ASN* 1.3 80.4 - - - +
284P ARG* 1.3 66.0 + - - +
286P ALA* 3.3 10.9 + - - +
288P TYR* 3.5 31.9 + - + +
292P PHE* 3.9 27.4 - - + -
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Residues in contact with ARG 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237P THR 5.1 1.0 + - - -
280P LEU* 2.9 43.4 + - + +
281P THR* 3.8 4.9 - - - +
283P LEU* 1.3 74.6 - - - +
285P ALA* 1.3 59.8 + - - +
287P GLY* 2.8 24.9 + - - -
288P TYR* 3.1 31.5 + - - +
289P ASP* 3.4 15.3 - - + +
290P LYS 2.7 29.6 + - - +
291P PRO* 4.6 3.6 - - - +
292P PHE* 3.4 25.5 - - - -
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Residues in contact with ALA 285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281P THR* 2.9 22.8 + - + +
282P ASN* 3.1 9.4 + - - +
284P ARG* 1.3 77.2 - - - +
286P ALA* 1.3 61.6 + - - +
287P GLY* 3.1 1.6 + - - -
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Residues in contact with ALA 286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223P TRP* 3.6 12.3 - - - -
224P PHE* 4.2 15.3 - - + -
229P VAL* 4.0 23.8 - - + +
233P PHE* 3.8 25.1 - - + -
282P ASN 2.8 12.5 + - - +
283P LEU 3.5 10.5 - - - +
284P ARG 3.1 0.2 - - - -
285P ALA* 1.3 76.8 - - - +
287P GLY* 1.3 56.9 + - - +
288P TYR 3.7 0.7 - - - +
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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