Contacts of the strand formed by residues 278 - 284 (chain D) in PDB entry 1JXQ
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 LYS 278 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D CYS* 3.9 7.2 - - + -
265D PHE* 2.8 38.8 - - + +
266D ASN* 5.1 4.9 - - - +
267D GLY 5.6 0.9 - - - +
273D LEU* 2.9 46.1 + - + -
274D GLY* 4.5 1.8 - - - +
275D GLY 4.5 3.2 - - - +
276D LYS 2.7 26.4 + - - +
277D PRO* 1.3 73.1 - - - +
279D LEU* 1.3 62.9 + - - +
280D PHE* 3.6 19.8 - - + -
325D SER* 3.6 24.0 + - - -
326D ASP* 2.9 15.3 + - - +
327D ILE* 4.1 8.5 - - + -
328D PHE 2.9 28.1 + - - +
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D CYS* 4.1 14.6 - - - -
230D CYS 3.0 11.9 + - - +
231D VAL* 3.4 7.0 - - + +
232D VAL* 2.9 26.7 + - - +
277D PRO* 4.2 8.3 - - + -
278D LYS* 1.3 79.5 - - - +
280D PHE* 1.3 67.1 + - - +
281D PHE* 4.1 19.5 - - + -
328D PHE* 3.4 23.8 - - + +
366D LEU* 3.8 14.6 - - + -
394D LEU* 4.5 2.2 - - + -
398D LEU* 3.8 25.6 - - + -
400D PHE* 3.6 34.3 - - + -
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Residues in contact with PHE 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D VAL* 3.4 20.9 - - + +
258D VAL* 6.2 0.9 - - + -
261D ILE* 3.6 34.8 - - + -
262D VAL* 4.1 13.7 - - + -
265D PHE* 3.6 43.3 - + + -
278D LYS* 3.6 28.3 - - + -
279D LEU* 1.3 78.9 - - - +
281D PHE* 1.3 58.1 + - - +
282D ILE* 4.0 15.3 - - + -
327D ILE* 4.4 13.0 - - + -
328D PHE* 2.7 21.6 + - - +
329D VAL* 3.3 18.2 - - + +
330D SER* 2.7 33.8 + - - +
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Residues in contact with PHE 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D LEU* 6.1 1.1 - - + -
193D PHE* 3.3 40.6 - + - -
231D VAL* 4.3 4.3 - - + -
232D VAL 2.8 11.5 + - - -
233D VAL* 3.2 25.1 - - + +
234D ILE 3.0 24.6 + - - -
279D LEU* 4.1 24.7 - - + -
280D PHE* 1.3 73.7 - - - +
282D ILE* 1.3 64.0 + - - +
283D GLN 4.2 0.2 - - - -
328D PHE* 5.6 2.2 - + - -
330D SER* 3.6 26.2 - - - -
349D TYR* 5.2 0.7 - + - -
353D LEU* 4.5 14.8 - - + -
357D PHE* 4.5 14.4 - + - -
366D LEU* 4.0 27.8 - - + -
370D LEU* 4.6 6.3 - - + -
400D PHE* 4.8 0.4 - + - -
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Residues in contact with ILE 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D VAL* 5.2 1.8 - - + +
234D ILE* 3.8 24.2 - - + +
243D VAL* 3.8 24.2 - - + -
258D VAL* 5.0 11.2 - - + -
261D ILE* 5.7 5.4 - - + -
280D PHE* 4.0 19.3 - - + +
281D PHE* 1.3 89.4 - - - +
283D GLN* 1.3 58.1 + - - +
284D ALA 4.0 7.6 - - - +
329D VAL* 4.4 10.5 - - + -
330D SER* 2.8 12.7 + - - +
331D TYR* 3.3 37.2 - - + -
332D SER* 2.7 34.7 + - - -
349D TYR* 5.2 1.5 + - - -
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Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D ARG* 4.9 2.5 + - - +
185D ASP* 5.3 2.9 - - - +
189D LEU* 6.3 0.2 - - + -
234D ILE 3.2 9.5 + - - +
235D LEU* 3.7 21.5 - - + -
236D SER 3.4 22.7 + - - +
243D VAL* 5.5 0.4 - - - +
281D PHE 4.2 0.4 - - - -
282D ILE* 1.3 73.8 - - - +
284D ALA* 1.3 56.7 + - - +
285D CYS* 2.9 35.0 + - + +
332D SER* 2.6 33.3 + - - -
334D PHE 3.2 20.6 + - - +
347D SER* 3.5 13.0 + - - +
349D TYR* 3.0 21.9 - - + +
350D VAL* 4.5 13.2 - - + -
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Residues in contact with ALA 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D SER 3.2 7.9 - - - +
237D HIS 4.4 0.2 - - - -
238D GLY* 3.4 28.5 - - - -
243D VAL* 4.5 3.6 - - + -
282D ILE* 3.9 5.5 - - + -
283D GLN* 1.3 69.7 - - - +
285D CYS* 1.3 59.3 + - - +
286D GLY 3.5 6.7 + - - +
331D TYR* 3.9 12.8 - - + +
332D SER 2.7 8.8 + - - +
333D THR* 3.2 41.8 - - + -
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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