Contacts of the helix formed by residues 410 - 427 (chain B) in PDB entry 5J1T
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 GLY 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B PHE* 3.8 2.9 - - - -
408B SER 3.3 5.2 + - - -
409B VAL* 1.3 77.7 - - - +
411B PRO* 1.3 76.3 - - - +
412B ARG 3.4 2.7 - - - -
413B GLU* 3.4 8.3 + - - +
414B THR* 2.8 28.4 + - - -
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Residues in contact with PRO 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.7 36.8 - - + -
276B ARG* 3.4 41.3 - - - +
410B GLY* 1.3 86.0 - - - +
412B ARG* 1.3 66.5 + - + +
414B THR* 3.4 3.8 + - - +
415B GLU* 3.1 24.1 + - - +
454B VAL 4.5 5.0 - - - +
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLU* 2.9 50.9 + - - +
303A MET 2.8 28.2 + - - -
304A THR* 3.9 21.3 - - + +
305A PHE* 4.4 4.6 - - - +
324A LYS* 6.2 0.2 - - - +
405A BTB 4.2 6.1 + - - -
410B GLY 3.4 0.4 - - - -
411B PRO* 1.3 82.7 - - + +
413B GLU* 1.3 59.0 + - - +
415B GLU* 3.3 5.6 + - - +
416B GLU* 2.9 36.4 + - - +
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B VAL* 3.7 27.5 - - + +
410B GLY* 3.4 8.4 + - - +
411B PRO 3.4 0.2 - - - -
412B ARG* 1.3 78.3 - - - +
414B THR* 1.3 63.9 + - - +
416B GLU* 3.2 17.4 + - + +
417B LYS* 3.0 45.4 + - + +
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Residues in contact with THR 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B THR* 3.4 29.6 - - + -
405B LEU* 5.4 2.0 - - + -
409B VAL* 3.5 24.3 - - + +
410B GLY 2.8 21.6 + - - -
411B PRO 3.7 4.5 - - - -
413B GLU* 1.3 77.6 - - - +
415B GLU* 1.3 62.6 + - - +
417B LYS* 3.3 9.9 + - - +
418B VAL* 3.2 22.5 + - - +
454B VAL* 3.8 15.3 - - + +
456B PRO* 3.6 27.6 - - + +
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 5.8 2.3 - - - +
304A THR* 3.6 25.1 + - + +
316A LYS* 2.7 37.7 + - - -
411B PRO 3.1 18.3 + - - +
412B ARG* 3.3 7.3 + - - +
414B THR* 1.3 76.7 - - - +
416B GLU* 1.4 57.0 + - - +
418B VAL* 3.3 1.9 + - - -
419B ARG* 2.9 28.3 + - + +
447B TRP* 3.7 17.5 + - + +
451B SER* 4.3 8.1 + - - +
452B HIS 5.7 0.5 - - - +
454B VAL* 4.0 23.6 + - + +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A THR* 4.1 16.5 - - + +
305A PHE 5.2 0.2 - - - +
311A ARG* 3.1 32.0 + - - -
412B ARG* 2.9 23.5 + - - +
413B GLU* 3.2 20.6 + - + +
415B GLU* 1.4 74.7 - - - +
417B LYS* 1.3 58.6 + - + +
419B ARG* 3.4 37.8 + - - +
420B ASP* 2.9 39.6 + - - +
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Residues in contact with LYS 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 4.1 17.7 - - + +
402B GLU* 3.4 21.6 + - - +
405B LEU* 3.7 32.5 - - + -
406B GLU 6.0 0.9 - - - +
409B VAL* 4.3 3.8 - - - -
413B GLU* 3.0 48.2 + - + +
414B THR* 3.3 10.3 + - + +
416B GLU* 1.3 77.2 - - + +
418B VAL* 1.3 61.3 + - - +
420B ASP* 4.0 5.0 - - - +
421B LEU* 3.1 24.4 + - - +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 4.5 8.3 - - + -
299B THR* 3.6 31.0 - - + +
398B VAL* 4.0 27.4 - - + -
400B LEU* 4.4 7.6 - - + -
414B THR 3.2 13.6 + - - +
415B GLU 3.8 5.6 - - - +
417B LYS* 1.3 73.3 - - - +
419B ARG* 1.3 66.3 + - - +
421B LEU* 3.2 3.5 + - - +
422B LEU* 2.9 27.0 + - + +
447B TRP* 3.6 25.1 - - + -
454B VAL* 3.6 17.7 - - + -
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A THR* 4.3 4.4 - - - -
305A PHE 4.6 9.3 + - - -
306A PHE* 5.4 0.2 - - - +
308A LYS* 5.7 7.9 - - - +
311A ARG* 6.0 0.2 - - - +
315A ASP* 2.8 40.3 + - - -
404A BTB 3.3 29.1 + - - -
415B GLU* 2.9 19.3 + - + +
416B GLU* 3.5 36.0 + - - +
418B VAL* 1.3 77.2 - - - +
420B ASP* 1.3 94.9 + - - +
422B LEU* 3.3 1.7 + - - -
423B TRP* 3.0 52.0 + - + -
447B TRP* 3.6 25.5 - - + +
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Residues in contact with ASP 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LYS* 6.1 0.7 - - - +
404A BTB 4.4 9.0 + - - -
416B GLU* 2.9 23.2 + - - +
417B LYS* 4.0 5.0 - - - +
419B ARG* 1.3 111.3 + - - +
421B LEU* 1.3 63.0 + - - +
423B TRP* 3.5 5.4 + - - +
424B ALA* 3.0 24.8 + - - +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 4.3 11.0 - - + -
398B VAL* 3.9 18.4 - - + -
399B LEU 3.5 24.9 - - - +
400B LEU* 3.9 17.3 - - + -
401B GLU* 3.7 35.2 - - + +
417B LYS 3.1 17.2 + - - +
418B VAL* 3.2 4.5 + - - +
420B ASP* 1.3 78.1 - - - +
422B LEU* 1.3 58.5 + - - +
424B ALA* 3.2 7.5 + - + +
425B LYS* 2.9 42.5 + - + +
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 5.5 0.4 - - + -
367B PHE* 4.3 18.8 - - + -
368B GLU* 3.9 36.8 - - + +
398B VAL* 4.5 10.5 - - + -
418B VAL* 2.9 24.2 + - + +
419B ARG* 3.9 3.6 - - - +
421B LEU* 1.3 77.7 - - - +
423B TRP* 1.3 60.3 + - + +
425B LYS* 4.5 2.0 - - + +
426B PHE* 2.9 54.8 + - + +
443B LEU* 4.0 11.7 - - + -
446B LEU* 6.3 0.2 - - + -
447B TRP* 3.8 32.8 - - + -
450B ILE* 4.4 7.4 - - + -
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Residues in contact with TRP 423 (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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404A BTB 3.2 49.0 - - - +
419B ARG* 3.0 50.0 + - + +
420B ASP* 4.0 5.6 - - - +
422B LEU* 1.3 78.4 - - + +
424B ALA* 1.3 62.4 + - - +
427B THR* 2.8 42.3 + - + +
430B ASP* 5.4 1.3 - - - -
440B SER* 2.9 31.9 + - - +
443B LEU* 3.4 24.9 - - + +
444B SER* 3.7 30.5 - - - -
447B TRP* 3.7 45.1 - + + -
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Residues in contact with ALA 424 (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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420B ASP 3.0 18.6 + - - +
421B LEU* 3.2 11.4 + - + +
423B TRP* 1.3 77.9 - - - +
425B LYS* 1.3 62.3 + - + +
427B THR 3.2 14.3 - - - +
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Residues in contact with LYS 425 (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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336B THR* 5.1 8.9 + - - +
368B GLU* 3.3 37.8 + - + +
369B SER* 4.7 5.7 + - - +
372B ALA* 4.9 1.7 - - - +
401B GLU* 3.4 25.4 - - - +
421B LEU* 2.9 35.1 + - + +
422B LEU* 4.1 2.0 - - - +
424B ALA* 1.3 80.1 - - + +
426B PHE* 1.3 75.9 + - + +
427B THR 3.5 1.4 + - - +
428B ASN* 5.7 0.5 - - - +
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Residues in contact with PHE 426 (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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367B PHE* 3.5 37.0 - + - -
368B GLU* 3.6 21.1 - - - -
370B PHE 3.7 15.3 - - - -
372B ALA* 3.6 26.7 - - + +
375B THR* 3.8 26.2 - - + -
422B LEU* 2.9 37.1 + - + +
425B LYS* 1.3 86.2 - - + +
427B THR* 1.3 59.1 + - - +
438B MET* 3.5 32.8 - - + +
443B LEU* 4.0 24.5 - - + -
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B TRP* 2.8 28.7 + - + +
424B ALA* 3.2 18.2 - - - +
425B LYS 3.5 1.4 - - - -
426B PHE* 1.3 84.3 - - - +
428B ASN* 1.3 66.0 + - - +
429B SER 3.8 18.4 + - - -
430B ASP* 5.5 0.5 + - - -
438B MET* 4.4 2.7 - - + -
439B ASP* 3.8 11.2 - - - +
440B SER* 3.8 26.9 - - - +
443B LEU* 4.0 18.6 - - + -
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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
------------------------------------------------------------
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