Contacts of the strand formed by residues 273 - 278 (chain A) in PDB entry 4J2X
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LEU* 3.5 6.6 - - - +
251A LEU* 2.9 53.1 + - + +
252A ASP 4.6 1.8 - - - -
253A ASP* 3.4 16.0 + - - -
271A GLY 3.9 0.4 + - - -
272A GLN* 1.4 71.5 - - - +
274A VAL* 1.3 67.0 + - - +
287A ARG* 3.9 13.9 - - + -
288A LEU 3.4 12.8 - - - +
289A ILE* 3.9 5.0 - - - +
317A LYS* 2.9 46.1 + - + +
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Residues in contact with VAL 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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248A ILE* 4.0 15.9 - - + -
249A HIS 3.1 7.9 - - - +
250A LEU* 4.8 0.2 - - - -
251A LEU* 4.4 2.7 - - - -
268A ILE* 3.7 42.8 - - + -
272A GLN* 3.5 3.6 + - + +
273A THR* 1.3 82.4 - - - +
275A LYS* 1.3 63.1 + - - +
276A LEU* 4.8 5.6 - - + -
287A ARG* 4.0 2.8 - - - -
288A LEU* 2.9 44.8 + - + +
290A ILE* 3.9 13.5 - - + -
314A PHE* 4.2 25.1 - - + -
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Residues in contact with LYS 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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247A TYR 3.2 4.3 - - - +
248A ILE* 3.5 2.3 - - - -
249A HIS* 2.8 33.2 + - + +
251A LEU* 3.7 24.2 - - + -
257A GLU* 3.5 16.5 + - - -
258A GLY 4.3 8.3 - - - -
261A PHE* 3.4 43.7 - - + -
274A VAL* 1.3 72.0 - - - +
276A LEU* 1.3 64.0 + - - +
277A VAL* 4.0 1.7 + - + -
284A ALA* 4.1 7.6 - - + +
285A LEU 2.5 30.7 + - - +
286A PRO 3.6 2.3 - - - -
287A ARG* 3.9 21.8 - - + -
288A LEU* 5.4 1.3 - - - +
188B ALA 5.5 0.2 - - - -
190B VAL* 3.3 21.3 - - - +
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Residues in contact with LEU 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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213A VAL* 4.3 13.7 - - + -
215A LEU* 3.7 27.1 - - + -
229A LEU* 4.7 1.1 - - + -
236A PHE* 4.7 2.5 - - + -
246A PHE* 4.3 12.8 - - + -
247A TYR 3.3 7.2 - - - +
248A ILE* 3.9 36.6 - - + -
274A VAL* 4.8 4.3 - - + -
275A LYS* 1.3 72.8 - - - +
277A VAL* 1.3 61.6 + - - +
278A CYS 4.2 0.2 - - - -
283A MET 3.9 0.5 - - - +
284A ALA* 3.2 22.0 - - - +
285A LEU* 3.4 26.4 + - + +
286A PRO 5.7 0.4 + - - -
288A LEU* 3.7 29.7 - - + +
314A PHE* 4.2 12.3 - - + -
324A LEU* 5.0 0.7 - - + -
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Residues in contact with VAL 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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246A PHE* 4.1 2.9 - - - +
247A TYR* 2.8 48.6 + - + +
249A HIS* 3.8 24.0 - - + +
261A PHE* 4.0 11.4 - - + -
275A LYS* 4.6 1.3 - - + -
276A LEU* 1.3 76.9 - - - +
278A CYS* 1.4 71.8 + - - +
279A SER 3.4 0.3 + - - -
282A GLY* 3.8 14.8 - - - +
283A MET 3.5 3.6 - - - +
284A ALA* 3.9 12.3 - - + -
186B VAL* 4.5 4.7 - - + -
188B ALA* 3.7 27.1 - - + -
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Residues in contact with CYS 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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231A VAL* 4.0 12.8 - - + -
244A GLY* 5.7 3.6 - - - -
245A ALA 3.8 5.6 - - - -
246A PHE* 3.6 30.7 - - + -
247A TYR* 4.9 0.3 - - - -
277A VAL* 1.4 71.3 - - - +
279A SER* 1.3 58.3 + - - +
280A VAL* 3.4 12.3 - - - -
281A THR* 3.1 47.6 - - - +
282A GLY* 3.1 27.9 + - - -
283A MET 2.9 14.7 + - - +
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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