Contacts of the strand formed by residues 273 - 278 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250C LEU* 3.7 2.8 - - - +
251C LEU* 2.9 50.6 + - + +
252C ASP 4.5 5.2 - - - +
253C ASP* 4.1 10.5 + - - -
255C GLU 5.6 0.2 - - - +
271C GLY 4.3 0.7 + - - -
272C GLN* 1.3 72.2 - - - +
274C VAL* 1.3 66.3 + - - +
287C ARG* 3.8 20.4 - - + -
288C LEU 3.3 10.5 - - - +
289C ILE* 3.7 7.3 - - - +
317C LYS* 2.9 45.6 + - + +
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE* 3.9 23.6 - - + -
249C HIS 3.1 11.7 - - - +
250C LEU* 4.4 3.6 - - + -
251C LEU* 4.5 3.8 - - - -
268C ILE* 3.8 34.3 - - + -
272C GLN* 3.6 2.9 + - + +
273C THR* 1.3 80.3 - - - +
275C LYS* 1.3 60.9 + - - +
276C LEU* 4.9 4.7 - - + -
287C ARG* 3.8 5.5 - - - -
288C LEU* 2.8 44.2 + - + +
290C ILE* 4.3 23.6 - - + -
314C PHE* 4.5 10.1 - - + -
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Residues in contact with LYS 275 (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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247C TYR 3.3 2.9 - - - +
248C ILE* 3.5 1.7 - - - -
249C HIS* 2.8 37.8 + - + +
251C LEU* 4.0 23.3 - - + -
257C GLU* 2.7 30.9 + - - -
258C GLY 4.4 1.7 + - - +
261C PHE* 3.4 50.0 - - + -
274C VAL* 1.3 73.3 - - - +
276C LEU* 1.3 64.4 + - - +
277C VAL* 3.9 6.9 + - + -
284C ALA* 4.3 4.5 - - + -
285C LEU 3.1 25.4 + - - +
286C PRO* 3.3 1.8 - - - +
287C ARG* 3.2 18.5 - - + +
190D VAL* 3.6 12.7 - - - +
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Residues in contact with LEU 276 (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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213C VAL* 4.3 14.1 - - + -
215C LEU* 3.8 24.9 - - + -
229C LEU* 4.6 4.5 - - + -
236C PHE* 4.8 2.8 - - + -
246C PHE* 4.5 14.1 - - + -
247C TYR 3.2 3.6 - - - +
248C ILE* 3.9 37.2 - - + -
274C VAL* 4.9 2.7 - - + -
275C LYS* 1.3 73.6 - - - +
277C VAL* 1.4 58.3 + - - +
278C CYS 4.3 0.2 - - - -
283C MET 4.1 0.5 - - - +
284C ALA* 3.3 22.5 - - - +
285C LEU* 3.4 23.6 + - + -
288C LEU* 3.6 31.0 - - + +
314C PHE* 4.1 13.9 - - + -
324C LEU* 5.0 1.1 - - + -
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Residues in contact with VAL 277 (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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246C PHE* 4.1 2.9 - - - +
247C TYR* 2.8 45.7 + - + -
249C HIS* 3.7 32.1 - - + +
261C PHE* 3.9 10.8 - - + -
275C LYS* 4.3 2.9 - - + -
276C LEU* 1.4 76.0 - - - +
278C CYS* 1.3 68.2 + - - +
279C SER 3.2 0.9 + - - -
282C GLY* 3.6 26.0 - - - +
283C MET 3.8 2.7 - - - -
284C ALA* 3.8 13.0 - - + -
186D VAL* 4.6 4.9 - - + -
187D LYS 5.4 1.1 - - - +
188D ALA* 3.8 14.1 - - + -
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Residues in contact with CYS 278 (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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231C VAL* 3.8 24.9 - - + -
244C GLY* 5.6 4.5 - - - -
245C ALA 3.9 3.8 - - - -
246C PHE* 3.8 19.4 - - + -
247C TYR* 4.7 0.6 - - - -
277C VAL* 1.3 69.6 - - - +
279C SER* 1.3 57.7 + - - +
280C VAL* 2.9 15.1 + - - -
281C THR* 3.2 42.6 - - - +
282C GLY* 2.8 30.9 + - - +
283C MET 3.0 17.5 + - - +
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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