Contacts of the strand formed by residues 272 - 278 (chain A) in PDB entry 5JAX
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A ASP* 1.3 87.8 + - + +
273A PHE* 1.3 60.4 + - - +
274A PHE* 3.6 14.7 - - - -
306A GLY 3.4 3.1 - - - +
310A LEU* 3.9 5.9 - - - +
316A ARG* 2.9 40.8 + - - +
330A VAL* 3.7 26.5 - - + -
331A ILE 3.4 7.6 - - - +
332A ASP* 4.3 9.9 - - + -
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Residues in contact with PHE 273 (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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237A PHE* 4.0 12.6 - + - -
272A THR* 1.3 73.4 - - - +
274A PHE* 1.3 61.4 + - - +
275A ILE* 3.9 18.6 - - + -
304A TRP* 3.5 45.8 - + + -
305A PHE 3.5 15.3 - - - -
307A GLU* 3.9 22.0 - - + -
310A LEU* 3.6 13.9 - - + +
329A LEU 3.7 0.7 - - - +
330A VAL* 3.3 5.7 - - - +
331A ILE* 2.8 55.1 + - + +
336A PHE* 3.7 20.2 - + + -
340A ILE* 4.1 22.2 - - + -
346A VAL* 4.7 3.4 - - + -
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Residues in contact with PHE 274 (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 TYR* 3.8 11.7 - - - -
263A ILE* 3.5 26.9 - - + -
264A ILE* 3.8 21.1 - - + -
272A THR* 3.6 36.1 - - - -
273A PHE* 1.3 77.2 - - - +
275A ILE* 1.3 63.9 + - - +
304A TRP* 3.1 7.8 - - - +
305A PHE* 2.9 76.1 + + + +
316A ARG* 3.8 2.7 - - - -
328A CYS* 3.9 10.8 - - + -
329A LEU 3.4 4.5 - - - -
330A VAL* 3.8 24.5 - - + -
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Residues in contact with ILE 275 (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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230A PHE* 3.7 27.4 - - + -
231A LEU* 3.9 18.8 - - + -
234A VAL* 4.9 0.7 - - + -
237A PHE* 3.6 38.1 - - + -
248A LEU* 6.3 0.7 - - + -
252A LEU* 6.2 0.4 - - + -
273A PHE* 3.9 13.7 - - + -
274A PHE* 1.3 79.2 - - - +
276A ILE* 1.3 65.2 + - - +
277A SER 3.4 0.9 + - - -
302A GLY 4.5 5.6 - - - +
303A ASP 3.6 9.9 - - - +
304A TRP* 4.2 1.3 - - + -
328A CYS* 3.3 3.2 - - - -
329A LEU* 2.8 47.0 + - + +
331A ILE* 3.6 25.8 - - + -
340A ILE* 5.2 0.2 - - + -
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Residues in contact with ILE 276 (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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230A PHE* 3.2 6.6 - - - -
275A ILE* 1.3 72.5 - - - +
277A SER* 1.3 58.8 + - - +
278A LYS 3.6 23.3 - - - +
279A GLY 3.6 17.7 - - - +
280A THR 4.8 0.2 - - - +
281A VAL* 3.8 21.8 - - + -
299A LEU* 3.8 29.4 - - + +
300A GLY 3.5 24.0 - - - +
301A LYS* 3.5 1.0 - - - -
302A GLY* 2.8 29.3 + - - -
303A ASP 2.9 15.8 + - - +
305A PHE* 3.7 23.1 - - + -
326A VAL* 4.8 3.1 - - + -
327A THR 3.7 4.9 - - - +
328A CYS* 4.4 6.5 - - - +
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Residues in contact with SER 277 (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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230A PHE* 3.6 28.3 - - - -
275A ILE 3.4 2.2 + - - -
276A ILE* 1.3 72.8 - - - +
278A LYS* 1.3 61.6 + - - +
301A LYS* 2.8 28.2 - - - -
327A THR* 2.9 35.9 + - - +
329A LEU* 3.8 18.6 - - - +
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Residues in contact with LYS 278 (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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276A ILE* 3.6 6.9 - - - +
277A SER* 1.3 80.4 - - - +
279A GLY* 1.3 65.5 + - - +
301A LYS* 4.6 6.7 - - - -
325A ALA* 4.1 15.0 - - + +
326A VAL* 3.2 4.9 - - - +
327A THR* 3.0 49.3 + - - +
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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