Contacts of the helix formed by residues 353 - 374 (chain B) in PDB entry 4D1Q
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 ASN 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B PRO* 4.9 8.7 - - + +
351B HIS 3.4 5.7 + - - +
352B ILE* 1.3 70.3 - - - +
354B LYS* 1.3 66.6 + - - +
355B SER* 3.4 18.8 + - - -
356B ILE* 2.8 57.2 + - + +
357B ILE* 3.1 12.0 + - - +
403B VAL* 5.3 5.5 - - - +
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Residues in contact with LYS 354 (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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330B LEU* 4.7 7.5 + - + -
333B TRP* 3.2 69.9 - - + +
334B GLU* 4.3 9.1 + - - -
352B ILE 3.0 8.7 + - - +
353B ASN* 1.3 71.5 + - - +
355B SER* 1.3 58.6 + - - +
357B ILE* 3.0 6.1 + - - +
358B GLN* 2.8 52.9 + - + +
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Residues in contact with SER 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ASN* 3.1 18.9 + - - -
354B LYS* 1.3 77.8 - - - +
356B ILE* 1.3 61.2 + - - +
358B GLN* 3.5 7.8 - - - +
359B THR* 2.7 37.8 + - - -
403B VAL* 4.4 14.2 - - - +
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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
----------------------------------------------------------
284B LEU* 3.8 25.1 - - + -
287B PRO* 5.2 11.4 - - + -
353B ASN* 2.8 42.0 + - + +
355B SER* 1.3 75.0 + - - +
357B ILE* 1.3 73.0 + - + +
359B THR* 3.3 5.3 + - - -
360B MET* 2.8 27.7 + - - +
403B VAL* 4.8 10.3 - - + -
405B ASP* 3.9 35.4 - - + +
406B ILE* 4.0 17.7 - - + -
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Residues in contact with ILE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B PRO* 4.6 15.7 - - + +
288B ILE* 5.9 0.4 - - + -
291B CYS* 3.9 21.8 - - - -
326B LEU* 4.1 23.1 - - + +
329B ILE* 4.9 5.4 - - + -
330B LEU* 3.2 35.0 - - + -
333B TRP* 4.8 2.0 - - + -
352B ILE* 3.5 27.4 - - + -
353B ASN 3.1 7.5 + - - +
354B LYS* 3.0 10.0 + - - +
356B ILE* 1.3 81.4 - - + +
358B GLN* 1.3 65.2 + - - +
360B MET* 3.0 18.7 + - - +
361B VAL* 3.1 17.2 + - + +
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Residues in contact with GLN 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 3.5 26.8 - - + +
354B LYS* 2.8 41.3 + - + +
355B SER* 3.5 11.4 - - - +
357B ILE* 1.3 73.5 - - - +
359B THR* 1.3 63.9 + - - +
361B VAL* 3.0 15.4 + - - +
362B ASN* 3.1 29.8 + - - +
493G SER* 5.7 1.0 + - - -
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B SER* 2.7 24.9 + - - -
356B ILE* 3.6 4.0 - - - -
358B GLN* 1.3 77.1 - - - +
360B MET* 1.3 63.2 + - - +
362B ASN* 3.0 11.0 + - + +
363B ILE* 2.9 34.5 + - + +
402B ASP* 6.2 0.2 - - - +
403B VAL* 5.9 1.2 - - - +
406B ILE* 3.5 39.6 - - + +
410B LYS* 5.6 1.8 - - - +
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Residues in contact with MET 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 3.5 25.8 - - + -
284B LEU* 3.2 49.1 - - + -
287B PRO* 5.7 1.8 - - - -
288B ILE* 4.2 11.9 - - + -
326B LEU* 4.2 24.2 - - + -
356B ILE* 2.8 29.0 + - + +
357B ILE* 3.4 13.2 - - - +
359B THR* 1.3 71.7 - - - +
361B VAL* 1.3 58.7 + - - +
363B ILE* 3.1 9.3 + - - +
364B LEU* 2.7 38.6 + - + +
406B ILE* 4.3 9.0 - - + -
409B LEU* 4.4 8.1 - - + -
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B TYR* 3.7 11.7 - - + -
326B LEU* 4.1 25.4 - - + -
327B ARG* 4.2 13.2 - - - +
330B LEU* 3.3 32.1 - - + -
357B ILE 3.3 7.0 - - - +
358B GLN* 3.0 8.4 + - - +
360B MET* 1.3 75.8 - - - +
362B ASN* 1.3 63.4 + - - +
364B LEU* 4.0 6.7 - - - -
365B ASP* 2.6 32.8 + - - +
493G SER* 3.5 24.7 - - - +
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Residues in contact with ASN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLN* 3.1 33.0 + - - +
359B THR* 3.0 11.8 + - + +
361B VAL* 1.3 79.9 - - - +
363B ILE* 1.3 68.4 + - + +
365B ASP* 3.2 15.0 + - - +
366B GLY* 3.7 2.8 + - - -
395B ILE* 4.9 4.5 - - - +
493G SER 3.6 25.5 - - - +
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Residues in contact with ILE 363 (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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359B THR* 2.9 28.4 + - + +
360B MET* 3.4 6.7 - - - +
362B ASN* 1.3 80.2 - - + +
364B LEU* 1.3 66.2 + - + +
366B GLY* 3.2 10.2 + - - -
367B PHE* 3.3 29.8 - - + -
395B ILE* 4.2 24.5 - - + +
396B CYS* 4.8 6.1 - - - -
406B ILE* 4.6 3.4 - - + -
409B LEU* 4.5 17.0 - - + -
410B LYS* 3.9 35.9 - - + +
413B ILE* 4.4 14.8 - - + -
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 4.3 17.0 - - + -
278B PHE* 4.1 24.9 - - + -
320B ASN* 3.7 11.9 + - - +
322B THR* 4.5 3.4 - - - +
323B TYR* 3.4 49.8 - - + +
326B LEU* 5.1 6.7 - - + -
360B MET* 2.7 23.5 + - + +
361B VAL* 4.0 1.1 - - - -
363B ILE* 1.3 82.1 - - + +
365B ASP* 1.3 63.5 + - - +
366B GLY 3.0 2.2 - - - -
367B PHE* 2.8 36.1 + - + +
368B GLU 3.1 8.8 + - - -
409B LEU* 6.3 1.6 - - + -
413B ILE* 5.5 3.4 - - + -
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Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B TYR* 2.6 36.2 + - - -
361B VAL 2.6 21.3 + - - +
362B ASN* 3.2 10.9 + - - +
364B LEU* 1.3 71.6 - - - +
366B GLY* 1.3 61.2 + - - +
368B GLU* 3.3 17.3 + - - +
369B ARG* 3.4 4.9 + - - +
493G SER* 3.6 18.2 + - - +
494G HIS 3.2 10.1 + - - -
495G SER* 2.8 47.8 + - - +
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Residues in contact with GLY 366 (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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362B ASN 3.7 2.0 + - - -
363B ILE 3.2 9.1 + - - -
364B LEU 3.0 0.8 - - - -
365B ASP* 1.3 79.4 - - - +
367B PHE* 1.3 67.3 + - - +
369B ARG* 3.1 5.2 + - - +
370B ILE* 2.9 29.4 + - - +
395B ILE* 4.1 18.4 - - - -
495G SER* 4.5 6.9 + - - -
503G PHE* 3.8 10.2 - - - -
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Residues in contact with PHE 367 (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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270B LEU* 3.7 26.5 - - + -
273B VAL* 5.1 2.9 - - + -
274B LEU* 3.7 34.3 - - + -
320B ASN* 4.1 13.7 - - - +
363B ILE* 3.3 33.9 - - + -
364B LEU* 2.8 15.3 + - + +
366B GLY* 1.3 78.1 - - - +
368B GLU* 1.3 50.9 + - - +
370B ILE* 3.1 10.4 + - + +
371B PHE* 2.6 45.2 + - + +
392B VAL* 3.5 35.4 - - + -
395B ILE* 5.4 5.6 - - + -
396B CYS* 5.3 1.6 - - - -
413B ILE* 3.7 22.0 - - + -
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TRP 4.7 2.4 - - - +
320B ASN* 3.0 34.1 + - - +
323B TYR* 3.1 35.6 - - + +
324B THR* 4.7 8.9 - - - +
364B LEU 3.1 5.4 + - - +
365B ASP* 3.3 12.8 - - - +
366B GLY 3.1 0.4 - - - -
367B PHE* 1.3 74.5 - - - +
369B ARG* 1.3 63.8 + - - +
371B PHE* 3.0 11.1 + - - +
372B LYS* 2.9 45.9 + - + +
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Residues in contact with ARG 369 (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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365B ASP 3.4 5.0 + - - +
366B GLY 3.1 7.9 + - - +
368B GLU* 1.3 78.8 - - - +
370B ILE* 1.3 55.8 + - - +
372B LYS* 3.1 4.3 + - - +
373B GLU* 2.8 49.0 + - + +
495G SER* 2.9 39.3 + - - +
496G LYS* 3.5 32.9 + - - +
498G ILE* 2.7 33.5 + - - +
499G SER 3.4 1.4 - - - -
500G THR* 3.0 35.3 + - - +
503G PHE* 3.5 36.1 - - + +
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Residues in contact with ILE 370 (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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270B LEU* 3.9 18.2 - - + -
366B GLY 2.9 18.3 + - - +
367B PHE* 3.5 13.0 - - + +
369B ARG* 1.3 75.2 - - - +
371B PHE* 1.3 58.4 + - - +
373B GLU* 3.2 6.4 + - - +
374B LEU* 2.9 42.8 + - + +
388B SER* 3.4 39.0 - - - +
391B LYS* 4.2 13.7 - - + -
392B VAL* 3.5 31.2 - - + -
395B ILE* 5.7 1.1 - - + -
421B TRP* 4.3 1.6 - - + -
503G PHE* 3.9 17.5 - - + -
504G PHE* 5.1 0.2 - - - -
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Residues in contact with PHE 371 (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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267B SER* 3.2 36.8 + - - -
270B LEU* 3.4 32.8 - - + -
271B SER* 3.7 17.0 - - - -
274B LEU* 4.0 13.9 - - + -
319B TRP* 3.9 30.1 - + + -
320B ASN* 3.9 31.0 - - + -
367B PHE* 2.6 28.5 + - + +
368B GLU* 3.0 12.5 + - - +
370B ILE* 1.3 74.6 - - - +
372B LYS* 1.3 62.1 + - + +
374B LEU* 3.3 13.0 + - - +
375B GLN* 3.3 23.5 + - - +
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Residues in contact with LYS 372 (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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368B GLU* 2.9 39.5 + - + +
369B ARG 3.8 3.1 - - - +
371B PHE* 1.3 75.7 - - + +
373B GLU* 1.3 66.3 - - - +
375B GLN* 3.4 22.8 + - - +
376B THR* 3.3 13.5 + - - -
1E A 3.5 49.2 + - - +
496G LYS* 3.7 37.2 - - + +
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Residues in contact with GLU 373 (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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369B ARG* 2.8 41.9 + - - +
370B ILE 3.7 4.0 - - - +
372B LYS* 1.3 78.9 - - - +
374B LEU* 1.3 65.6 + - + +
375B GLN 3.2 1.4 + - - -
376B THR* 3.3 23.8 + - - -
381B SER* 4.1 10.0 - - - -
384B PHE* 4.3 10.9 - - + +
1E A 6.0 1.5 + - - -
496G LYS* 4.5 5.4 + - - -
500G THR* 3.2 34.3 + - - +
504G PHE* 3.8 29.2 - - + -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B SER* 3.7 30.5 - - - -
267B SER* 3.7 12.6 - - - +
270B LEU* 5.0 3.6 - - + -
370B ILE* 2.9 31.1 + - + +
371B PHE* 3.3 7.2 + - - +
372B LYS 3.2 0.4 - - - -
373B GLU* 1.3 81.4 - - + +
375B GLN* 1.3 53.1 + - - +
376B THR 3.4 2.9 + - - +
381B SER* 4.6 5.6 - - - +
384B PHE* 4.6 8.1 - - + +
385B VAL* 4.3 11.9 - - + -
388B SER* 4.3 11.0 - - - +
421B TRP* 4.0 19.1 - - + -
566B ALA* 3.7 30.8 - - + +
567B SER* 2.6 25.8 + - - +
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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
------------------------------------------------------------
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