Contacts of the helix formed by residues 347 - 361 (chain B) 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 SER 347 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ASP* 2.9 30.7 + - - -
188B LYS* 5.5 0.2 - - - +
283B GLN* 3.3 17.2 + - - -
285B CYS* 4.9 6.1 - - - -
334B PHE 4.6 0.2 + - - -
336B GLY 3.6 6.5 + - - -
337B PHE* 5.6 0.9 - - - -
338B VAL* 3.9 2.3 - - - +
346B GLY* 1.3 70.1 - - - -
348B TRP* 1.3 63.2 + - - +
349B TYR* 3.1 21.0 + - - +
350B VAL* 3.1 30.6 + - - +
351B GLU* 3.1 10.0 + - - +
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Residues in contact with TRP 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE* 3.7 19.3 - + + -
336B GLY* 2.8 22.3 + - - +
337B PHE 3.6 15.0 - - - +
338B VAL* 4.2 21.3 - - + +
346B GLY 3.7 2.0 + - - -
347B SER* 1.3 72.5 - - - +
349B TYR* 1.3 60.1 + - - +
351B GLU* 4.0 4.4 - - + +
352B THR* 2.8 55.6 + - + -
376B ALA* 3.3 30.7 - - + -
377B VAL* 3.7 28.7 - - + -
380B LYS* 3.1 45.0 - - + +
348D TRP* 4.6 27.3 - + - +
351D GLU* 6.3 1.1 - - + +
380D LYS* 6.3 0.7 - - - -
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Residues in contact with TYR 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 5.2 1.0 - - - -
282B ILE 5.1 2.3 + - - -
283B GLN* 2.9 34.3 - - + +
330B SER* 3.4 21.8 + - - -
332B SER* 3.4 28.3 - - - +
334B PHE* 4.3 14.4 - - + -
336B GLY 4.5 0.6 + - - -
347B SER* 3.0 9.1 + - - +
348B TRP* 1.3 83.1 - - - +
350B VAL* 1.3 68.2 + - + +
352B THR* 3.0 4.9 + - - -
353B LEU* 2.8 58.7 + - + +
370B LEU* 5.4 1.6 - - - +
373B VAL* 3.7 25.7 - - + +
377B VAL* 4.2 11.9 - - + -
387B PRO* 3.9 14.2 - - + +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASP* 3.1 42.6 - - + +
188B LYS* 4.2 10.5 - - + +
189B LEU* 4.5 26.2 - - + +
235B LEU* 5.4 1.3 - - + -
283B GLN* 4.6 11.7 - - + -
347B SER* 3.1 26.0 + - - +
349B TYR* 1.3 88.9 - - + +
351B GLU* 1.3 59.2 + - - +
353B LEU* 3.7 5.6 - - - +
354B ASP* 2.7 38.2 + - - +
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Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LYS* 3.1 34.2 + - - +
338B VAL* 4.0 9.0 - - + -
347B SER 3.1 13.3 + - - +
348B TRP* 4.0 7.2 - - + +
350B VAL* 1.3 83.4 - - - +
352B THR* 1.3 61.6 + - - +
354B ASP* 3.7 3.8 - - - +
355B ASP* 2.8 35.6 + - + +
337D PHE 4.6 0.5 - - - +
338D VAL 3.4 20.7 - - - +
339D SER* 3.8 5.8 + - - -
340D TRP* 2.9 43.9 + - - +
348D TRP* 6.0 1.5 - - + +
380D LYS* 5.4 4.3 + - - +
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Residues in contact with THR 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B TRP* 2.8 52.2 + - + -
349B TYR* 3.5 3.6 - - - -
351B GLU* 1.3 76.5 - - - +
353B LEU* 1.3 65.5 + - - +
355B ASP* 3.3 5.4 + - - +
356B ILE* 2.9 35.6 + - + +
373B VAL* 4.4 11.0 - - + -
376B ALA* 3.8 29.4 - - + -
348D TRP* 5.9 0.2 + - - -
380D LYS* 5.3 8.0 + - - +
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.8 17.0 - - + -
192B ARG* 5.0 3.1 - - + -
193B PHE* 6.0 2.7 - - + -
281B PHE* 4.5 22.2 - - + -
349B TYR* 2.8 52.2 + - + +
350B VAL* 3.7 5.4 - - - +
352B THR* 1.3 73.7 - - - +
354B ASP* 1.3 67.9 + - - +
356B ILE* 3.1 1.7 + - - -
357B PHE* 2.9 63.8 + - + -
370B LEU* 4.8 4.3 - - + -
373B VAL* 3.9 22.2 - - + +
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Residues in contact with ASP 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LYS* 3.6 23.8 - - + +
189B LEU* 5.3 4.5 - - + -
192B ARG* 2.6 62.9 + - - +
350B VAL 2.7 24.1 + - - +
351B GLU* 3.7 7.0 - - - +
353B LEU* 1.3 81.3 - - + +
355B ASP* 1.3 57.0 + - - +
357B PHE 3.5 0.2 + - - -
358B GLU* 3.0 15.8 + - - +
340D TRP* 2.3 36.9 + - - -
341D ARG* 4.8 5.7 + - - -
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Residues in contact with ASP 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLU* 2.8 22.6 + - + +
352B THR* 3.5 6.3 - - - +
354B ASP* 1.3 77.7 + - - +
356B ILE* 1.3 64.1 + - + +
358B GLU* 3.3 6.2 + - - +
359B GLN* 3.1 35.9 + - - +
340D TRP* 4.1 32.5 - - + +
380D LYS* 3.0 33.7 + - - +
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B THR* 2.9 27.9 + - + +
353B LEU 3.7 2.9 - - - +
355B ASP* 1.3 75.6 - - + +
357B PHE* 1.3 61.3 + - + +
359B GLN* 3.0 3.0 + - - -
360B TRP* 2.8 45.8 + - + +
369B LEU* 3.8 30.1 - - + +
372B ARG* 3.6 22.0 - - + +
373B VAL* 3.5 38.8 - - + +
376B ALA* 4.6 3.4 - - + -
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Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 3.7 30.1 - - - +
193B PHE* 5.0 3.8 - + - -
196B LEU* 4.1 15.5 - - + -
281B PHE* 4.5 11.2 - + - -
353B LEU* 2.9 47.0 + - + +
354B ASP 3.8 0.4 - - - +
356B ILE* 1.3 76.4 - - + +
358B GLU* 1.3 65.7 + - - +
361B ALA* 2.9 38.2 + - + +
362B HIS 4.7 0.2 + - - -
366B LEU* 4.4 8.5 - - + -
369B LEU* 3.8 34.3 - - + -
370B LEU* 3.8 20.4 - - + -
373B VAL* 4.8 2.2 - - + -
400B PHE* 3.9 22.7 - + - -
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ARG* 2.9 30.1 + - - +
354B ASP 3.0 15.4 + - - +
355B ASP* 3.3 11.9 - - - +
357B PHE* 1.3 76.3 - - - +
359B GLN* 1.3 65.1 + - + +
362B HIS* 5.2 2.9 - - - -
340D TRP* 3.1 45.5 - - + -
341D ARG* 4.8 2.8 + - - -
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Residues in contact with GLN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ASP* 3.1 26.6 + - - +
356B ILE* 3.0 2.0 + - - -
357B PHE 3.0 0.6 - - - -
358B GLU* 1.3 85.3 - - + +
360B TRP* 1.3 90.7 + - + +
362B HIS* 3.2 20.1 + - - -
380D LYS 4.7 9.2 - - - +
384D LYS* 3.7 29.0 + - - +
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Residues in contact with TRP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ILE* 2.8 32.7 + - + +
359B GLN* 1.3 101.7 + - + +
361B ALA* 1.3 58.5 + - - +
362B HIS* 2.9 13.4 + - - -
363B SER* 2.9 13.6 + - - -
364B GLU* 2.8 59.5 + - - +
369B LEU* 3.5 16.8 - - + -
372B ARG* 3.0 39.5 - - - +
382D ILE* 6.0 4.0 - - + -
383D TYR* 5.3 14.4 - + - -
384D LYS* 6.1 2.2 - - - -
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LEU* 4.4 13.5 - - + -
357B PHE* 2.9 26.1 + - + +
360B TRP* 1.3 75.8 - - - +
362B HIS* 1.3 60.1 + - - +
363B SER 3.5 0.3 + - - -
364B GLU 3.7 11.4 + - - +
369B LEU* 3.5 23.2 - - + +
399B PHE* 5.3 2.4 - - - +
400B PHE* 4.0 24.8 + - + +
402B THR* 4.3 16.1 - - + +
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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