Contacts of the helix formed by residues 263 - 272 (chain A) in PDB entry 2JZB
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LEU* 5.9 0.3 - - - +
261A GLU 3.7 0.8 + - - -
262A LEU* 1.3 80.7 - - - +
264A VAL* 1.3 64.3 + - - +
265A ARG* 2.9 26.7 + - - +
266A SER* 2.9 15.2 + - - -
267A ALA* 3.9 1.6 + - - +
302A GLU* 3.8 11.2 + - - +
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ASP* 4.5 24.2 - - + +
262A LEU 3.7 0.6 + - - -
263A THR* 1.3 74.0 - - - +
265A ARG* 1.3 51.8 + - - +
267A ALA* 3.0 7.1 + - - +
268A ASN* 2.5 73.1 + - - +
271A LYS* 6.1 0.9 - - + +
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A THR* 2.9 16.0 + - - +
264A VAL* 1.3 78.7 - - - +
266A SER* 1.3 62.6 + - - +
268A ASN* 3.3 16.3 - - + +
269A CYS* 3.1 31.9 + - - -
298A LYS* 5.1 15.5 - - - -
299A SER* 5.8 2.7 - - - +
302A GLU* 4.3 13.0 - - - +
465B ASP* 5.9 1.6 + - - -
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 4.8 10.1 - - - +
262A LEU* 3.6 20.1 - - - +
263A THR 2.9 12.0 + - - -
265A ARG* 1.3 79.5 - - - +
267A ALA* 1.3 61.2 + - - +
269A CYS* 3.4 16.2 + - - +
270A LEU* 3.7 10.4 + - - +
299A SER* 5.1 1.6 + - - +
302A GLU* 2.7 45.5 + - - +
303A ILE* 4.6 6.1 + - - +
306A VAL* 4.8 2.6 - - - +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A VAL* 3.1 43.4 + - + +
258A ASP* 3.2 25.6 - - - +
260A LEU* 4.6 3.3 - - + +
263A THR 3.9 1.3 + - - +
264A VAL* 3.0 10.1 + - - +
266A SER* 1.3 77.4 - - - +
268A ASN* 1.3 57.9 + - - +
269A CYS 3.1 0.2 + - - -
270A LEU* 3.3 1.5 + - - +
271A LYS* 2.5 39.0 + - - +
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Residues in contact with ASN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A VAL* 2.5 61.6 + - - +
265A ARG* 3.2 15.7 + - + +
267A ALA* 1.3 73.9 - - - +
269A CYS* 1.3 58.1 + - - +
271A LYS* 4.0 12.3 - - - +
272A ALA* 2.8 31.2 + - - +
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Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ARG* 3.1 22.1 + - - -
266A SER 3.5 9.0 - - - +
267A ALA 3.1 0.6 - - - -
268A ASN* 1.3 80.4 - - - +
270A LEU* 1.3 66.5 + - + +
272A ALA* 3.1 15.4 - - - +
273A GLU* 3.9 3.8 + - - +
294A ASN* 4.2 15.9 - - - +
295A LEU* 3.8 24.6 - - + +
296A GLY* 4.3 3.1 - - - -
299A SER* 3.0 36.3 - - - -
303A ILE* 6.1 1.8 - - + -
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A VAL* 4.7 17.9 - - + -
260A LEU* 6.0 2.9 - - + -
266A SER 3.7 9.5 + - - +
267A ALA* 3.3 4.3 + - - +
269A CYS* 1.3 73.1 - - + +
271A LYS* 1.3 61.7 + - - +
273A GLU* 2.7 35.1 + - - +
275A ILE* 3.5 19.9 - - + +
281A LEU* 3.4 31.4 - - + -
289A LEU* 3.4 30.1 - - + -
295A LEU* 4.1 18.2 - - + -
303A ILE* 4.7 21.3 - - + -
312A LEU* 6.1 2.7 - - + -
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A VAL* 4.4 6.4 - - + +
258A ASP* 3.0 34.8 + - - +
264A VAL* 6.2 0.6 - - - +
267A ALA 2.5 26.6 + - - +
268A ASN* 4.0 11.9 - - - +
270A LEU* 1.3 73.4 - - - +
272A ALA* 1.3 52.5 + - - +
274A ALA* 2.7 26.9 + - - -
275A ILE* 3.1 27.8 + - - +
276A HIS* 5.5 7.9 - - - +
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN 2.8 21.8 + - - +
269A CYS* 3.1 11.4 - - - +
270A LEU 2.9 0.2 + - - -
271A LYS* 1.3 76.5 - - - +
273A GLU* 1.3 56.0 + - - +
274A ALA 3.2 3.6 + - - -
294A ASN* 4.6 19.5 - - + +
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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