Contacts of the helix formed by residues 270 - 274 (chain D) in PDB entry 1JXQ
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 CYS 270 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D ALA* 3.7 33.0 - - + -
224D HIS* 3.7 8.7 - - - -
265D PHE* 4.2 11.6 - - - +
266D ASN 2.8 17.3 + - - +
267D GLY* 3.4 4.2 - - - +
269D SER* 1.3 81.2 - - - +
271D PRO* 1.3 68.0 - - - +
272D SER* 3.0 5.2 - - - -
273D LEU* 3.0 47.6 + - - +
274D GLY 3.7 4.3 + - - -
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Residues in contact with PRO 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C PHE* 5.7 5.3 - - + -
219D ALA 5.9 0.2 - - - +
267D GLY* 3.0 17.3 - - - +
268D THR 3.7 7.9 - - - +
269D SER 3.7 6.7 - - - +
270D CYS* 1.3 88.0 - - - +
272D SER* 1.3 66.3 + - - +
274D GLY* 2.9 17.3 + - - +
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Residues in contact with SER 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA 5.2 0.4 - - - -
221D GLN 3.7 14.1 - - - -
222D ASP* 3.2 11.7 + - - -
224D HIS* 2.4 44.9 + - - +
225D GLY* 3.1 10.3 + - - +
270D CYS* 4.1 4.0 - - - -
271D PRO* 1.3 84.5 - - - +
273D LEU* 1.3 57.6 + - - +
274D GLY 3.7 0.3 + - - -
276D LYS* 3.3 21.7 - - - +
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D HIS* 3.4 42.2 - - + +
227D LEU* 5.8 0.2 - - + -
229D CYS 4.5 4.3 - - - +
230D CYS* 3.6 35.7 - - + +
265D PHE* 4.1 11.2 - - + -
270D CYS* 3.0 26.4 + - - +
272D SER* 1.3 74.6 - - - +
274D GLY* 1.3 67.7 + - - +
276D LYS* 2.9 31.5 + - + +
277D PRO 5.4 0.2 - - - +
278D LYS* 2.9 44.0 + - + +
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Residues in contact with GLY 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C PHE* 3.7 27.6 - - - -
296C VAL* 4.7 11.4 - - - +
267D GLY* 5.3 2.5 - - - -
270D CYS 3.7 2.7 + - - -
271D PRO* 2.9 18.4 + - - -
272D SER 3.4 0.8 - - - +
273D LEU* 1.3 77.2 - - - +
275D GLY* 1.3 57.5 + - - -
276D LYS* 3.1 13.9 + - - +
278D LYS* 4.6 2.0 - - - -
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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