Contacts of the strand formed by residues 265 - 273 (chain C) in PDB entry 1JZ3
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 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261C TRP* 3.2 5.4 - - - -
262C GLN* 2.8 48.3 + - - +
263C GLY 3.3 0.2 - - - -
264C GLU* 1.3 80.0 + - - +
266C GLN* 1.3 76.5 + - - +
267C VAL* 3.4 5.9 + - + +
8602C DMS 5.6 0.7 - - + -
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Residues in contact with GLN 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C SER* 3.9 8.4 - - - -
260C LEU 3.7 9.9 - - - +
261C TRP* 3.5 39.4 - - + +
264C GLU 4.0 0.2 + - - -
265C THR* 1.3 82.7 - - - +
267C VAL* 1.3 59.9 + - - +
268C ALA 3.9 7.2 - - - +
269C SER* 3.8 22.3 + - - -
8602C DMS 2.7 57.0 + - + +
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Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C LEU* 2.8 25.4 + - + +
262C GLN* 3.8 27.1 - - + +
265C THR* 3.8 17.0 - - + +
266C GLN* 1.3 76.2 - - - +
268C ALA* 1.3 66.2 + - + +
295C VAL* 4.0 27.4 - - + -
309C TYR* 4.1 7.9 - - + -
8601C DMS 3.3 36.9 - - + +
8602C DMS 3.8 7.4 + - - +
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Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C SER* 3.3 2.3 - - - -
260C LEU* 2.7 34.4 + - + +
266C GLN* 3.6 3.7 - - - +
267C VAL* 1.3 88.4 - - + +
269C SER* 1.3 66.4 + - - +
293C LEU* 4.1 29.2 - - + -
294C ASN 4.1 14.1 - - - +
8601C DMS 5.2 0.4 - - + -
8602C DMS 3.6 9.4 - - - -
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Residues in contact with SER 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C THR* 3.7 13.7 - - - +
258C VAL 3.4 7.9 - - - -
259C SER* 3.7 11.7 - - - -
266C GLN* 3.8 21.7 + - - -
268C ALA* 1.3 82.2 - - - +
270C GLY* 1.3 60.0 + - - +
271C THR* 5.0 0.9 + - - -
293C LEU* 3.6 7.3 - - - +
8602C DMS 4.2 4.1 + - - -
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Residues in contact with GLY 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C THR* 3.3 3.3 - - - +
258C VAL 2.9 33.9 + - - +
269C SER* 1.3 75.6 + - - +
271C THR* 1.3 62.8 + - - -
291C LEU* 3.5 10.2 - - - +
293C LEU* 3.6 11.8 - - - +
8405C DMS 4.2 13.5 - - - -
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ARG* 4.0 26.5 - - + +
256C VAL 3.1 9.4 - - - +
257C THR* 2.5 30.9 + - - +
269C SER* 5.0 1.0 + - - -
270C GLY* 1.3 72.7 - - - -
272C ALA* 1.3 69.3 + - - +
291C LEU* 3.8 2.7 - - - +
316C HIS* 4.2 4.5 - - + -
8405C DMS 3.4 14.2 - - - +
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ARG* 3.4 6.0 - - - +
256C VAL* 2.9 34.3 + - - +
271C THR* 1.3 80.0 - - - +
273C PRO* 1.3 83.1 - - + +
289C VAL* 3.8 18.7 - - + +
290C THR 5.6 0.4 - - - +
291C LEU* 4.0 10.5 - - + +
8405C DMS 4.7 4.9 - - + -
8412C DMS 5.8 2.5 - - + -
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Residues in contact with PRO 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C ASP* 4.8 4.0 - - - +
254C LEU 3.5 17.9 - - - +
255C ARG* 3.8 19.7 - - - +
272C ALA* 1.3 93.3 - - + +
274C PHE* 1.4 71.4 + - - +
275C GLY 4.7 1.2 - - - +
289C VAL* 3.4 15.6 - - - +
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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