Contacts of the helix formed by residues 348 - 368 (chain B) in PDB entry 4S15
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 CYS 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346B GLU 3.7 2.0 + - - -
347B LEU* 1.3 76.8 - - - +
349B GLN* 1.3 68.0 + - - +
350B ASN* 3.9 4.5 - - - -
351B ASP* 3.1 48.9 + - - +
352B GLN* 3.1 9.2 + - - +
437B GLN* 4.0 19.3 - - - +
438B GLU* 3.6 25.4 + - - +
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Residues in contact with GLN 349 (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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347B LEU 4.5 0.4 - - - +
348B CYS* 1.3 73.6 - - - +
350B ASN* 1.3 63.0 + - - +
352B GLN* 3.4 4.5 + - - +
353B ILE* 3.2 31.4 + - + +
501D GLN* 4.9 6.6 + - - -
506D HIS* 3.4 61.3 + - + +
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Residues in contact with ASN 350 (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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348B CYS* 3.2 4.8 - - - +
349B GLN* 1.3 79.1 - - - +
351B ASP* 1.3 80.7 + - - +
353B ILE* 3.3 6.4 + - - +
354B VAL* 2.9 36.3 + - - +
435B TRP* 3.2 22.7 + - - +
437B GLN* 3.4 32.0 + - - +
516B GLU 5.8 0.2 - - - +
518B ALA* 4.4 9.2 - - - +
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Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 4.3 12.5 - - + +
348B CYS* 3.1 19.3 + - - +
350B ASN* 1.3 89.1 + - - +
352B GLN* 1.3 67.7 + - - +
354B VAL* 3.8 0.4 - - - +
355B LEU* 2.9 32.3 + - - +
436B LEU* 3.5 16.5 - - + -
437B GLN* 2.8 24.6 + - - +
438B GLU* 2.8 37.1 + - - +
442B ILE* 3.9 11.0 - - + +
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B PHE* 3.4 47.9 + - + +
345B MET* 3.3 30.2 + - - +
347B LEU* 2.7 25.2 + - + +
348B CYS 3.1 12.2 + - - +
349B GLN* 3.8 6.8 - - - +
350B ASN 3.4 0.2 - - - -
351B ASP* 1.3 75.6 - - - +
353B ILE* 1.3 59.0 + - - +
355B LEU* 3.4 1.4 + - - +
356B LEU* 3.0 34.3 + - - +
504D LEU* 3.9 15.2 - - + +
506D HIS* 2.7 32.2 + - - -
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Residues in contact with ILE 353 (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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349B GLN* 3.2 18.4 + - + +
350B ASN* 3.7 5.2 - - - +
352B GLN* 1.3 75.4 - - - +
354B VAL* 1.3 67.4 + - + +
356B LEU* 3.2 5.4 + - - +
357B LYS* 2.9 53.6 + - + +
500D LEU* 4.1 17.9 - - + -
501D GLN* 4.4 20.9 - - + +
504D LEU* 4.0 17.9 - - + -
506D HIS* 4.2 13.2 - - + +
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Residues in contact with VAL 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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350B ASN* 2.9 40.0 + - - +
351B ASP 3.4 3.8 + - - +
353B ILE* 1.3 79.3 - - + +
355B LEU* 1.3 62.5 + - - +
357B LYS* 3.9 7.6 - - + +
358B ALA* 3.1 25.1 + - + +
433B ARG* 4.2 8.3 - - + -
434B SER 3.3 23.8 - - - +
435B TRP* 4.1 20.2 - - + +
436B LEU* 3.6 19.3 - - + -
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Residues in contact with LEU 355 (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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344B PHE* 4.1 15.7 - - + -
347B LEU* 3.6 31.4 - - + -
351B ASP 2.9 19.6 + - - +
352B GLN 3.8 4.0 - - - +
354B VAL* 1.3 76.9 - - - +
356B LEU* 1.3 59.8 + - - +
358B ALA* 3.9 2.5 - - - +
359B GLY* 2.9 27.7 + - - -
428B LEU* 3.4 33.3 - - + +
429B MET* 4.4 9.9 - - + -
430B SER 3.5 24.9 - - - +
433B ARG* 3.9 14.0 + - + +
436B LEU* 4.0 11.9 - - + -
442B ILE* 4.1 8.7 - - + -
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Residues in contact with LEU 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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334B VAL* 4.9 2.2 - - + +
335B VAL* 4.5 19.3 - - + -
338B ALA* 3.8 23.6 - - + -
344B PHE* 3.8 15.7 - - + -
352B GLN 3.0 20.7 + - - +
353B ILE* 3.9 4.7 - - - +
355B LEU* 1.3 76.3 - - - +
357B LYS* 1.3 63.7 + - - +
360B SER* 2.8 43.5 + - - +
428B LEU* 4.3 13.7 - - + -
510B LEU* 4.1 12.0 - - + +
500D LEU* 4.3 13.5 - - + -
504D LEU* 3.9 30.3 - - + -
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Residues in contact with LYS 357 (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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353B ILE* 2.9 41.9 + - + +
354B VAL* 3.9 7.2 - - + +
356B LEU* 1.3 77.7 - - - +
358B ALA* 1.3 61.8 + - - +
360B SER* 4.6 0.7 + - - -
361B LEU* 5.5 0.7 + - - +
509B GLU 3.7 18.8 - - - -
510B LEU* 3.7 36.3 - - + +
511B PHE* 4.3 17.8 - - - -
513B SER* 4.3 18.1 + - - -
514B GLU 5.3 3.2 + - - -
515B PHE* 6.1 2.0 - - - +
500D LEU* 5.2 3.4 - - - -
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Residues in contact with ALA 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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354B VAL* 3.1 17.4 + - + +
355B LEU 4.2 0.4 - - - +
357B LYS* 1.3 80.4 - - + +
359B GLY* 1.3 58.5 + - - +
360B SER 3.8 0.2 - - - -
361B LEU* 5.1 1.8 + - - +
362B GLU* 3.5 22.0 + - - +
433B ARG* 3.6 36.2 + - + +
481B CYS* 4.9 6.1 - - - +
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Residues in contact with GLY 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU 2.9 16.5 + - - -
358B ALA* 1.3 78.5 - - - +
360B SER* 1.3 63.8 + - - +
361B LEU 3.3 2.9 - - - -
362B GLU* 3.1 8.6 + - - +
363B VAL* 3.1 25.3 + - - +
427B VAL* 5.1 0.8 - - - +
428B LEU* 3.9 11.9 - - - -
433B ARG* 3.6 16.6 - - - -
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Residues in contact with SER 360 (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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331B ILE* 4.1 23.1 - - - +
334B VAL* 3.9 20.1 - - - +
335B VAL* 5.4 1.8 - - - -
355B LEU 4.2 0.4 + - - -
356B LEU* 2.8 33.1 + - - -
357B LYS 4.6 0.3 + - - -
358B ALA 3.8 0.4 - - - -
359B GLY* 1.3 76.4 - - - +
361B LEU* 1.3 64.0 + - - +
363B VAL* 3.3 5.7 + - - +
364B VAL* 3.1 24.8 + - - +
428B LEU* 4.3 2.8 - - - +
510B LEU* 4.0 16.5 - - - +
511B PHE* 4.3 6.4 - - - -
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Residues in contact with LEU 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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327B ILE* 3.9 31.6 - - + -
331B ILE* 4.5 1.1 - - + +
357B LYS 5.5 0.8 + - - +
358B ALA 5.1 1.7 + - - +
359B GLY 3.3 0.6 - - - +
360B SER* 1.3 79.0 + - - +
362B GLU* 1.3 66.9 + - - +
364B VAL* 3.2 18.8 + - + +
365B PHE* 3.0 46.3 + - + -
481B CYS* 3.8 16.6 - - + +
484B HIS* 3.4 46.2 - - + +
511B PHE* 4.0 20.2 - - + -
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Residues in contact with GLU 362 (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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358B ALA 3.5 11.5 - - - +
359B GLY 3.1 7.5 + - - +
361B LEU* 1.3 77.5 - - - +
363B VAL* 1.3 61.6 + - - +
365B PHE 3.3 1.2 + - - -
366B ILE* 3.0 27.1 + - - +
427B VAL* 3.9 21.8 - - + +
433B ARG* 2.8 43.9 + - - -
474B VAL* 5.2 1.9 - - - +
477B LEU* 3.5 26.4 - - + +
478B ARG* 3.4 26.7 + - - +
481B CYS* 3.4 22.2 - - - +
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Residues in contact with VAL 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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334B VAL* 3.7 29.4 - - + -
337B PHE* 4.6 5.4 - - + -
359B GLY 3.1 13.4 + - - +
360B SER 3.7 7.0 - - - +
361B LEU 3.2 0.2 - - - -
362B GLU* 1.3 72.4 - - - +
364B VAL* 1.3 61.8 + - - +
366B ILE* 3.2 7.9 + - - +
367B ARG* 2.8 40.4 + - - +
424B SER* 3.7 44.0 - - - +
427B VAL* 4.0 8.3 - - + -
428B LEU* 4.3 13.2 - - + -
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Residues in contact with VAL 364 (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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327B ILE* 4.8 5.4 - - + +
330B ALA* 4.0 19.7 - - + -
331B ILE* 3.8 22.2 - - + -
334B VAL* 3.8 17.5 - - + -
360B SER 3.1 15.9 + - - +
361B LEU* 3.2 20.8 + - + +
363B VAL* 1.3 77.7 - - - +
365B PHE* 1.3 59.2 + - + +
367B ARG* 3.2 7.8 + - - +
368B MET* 2.8 26.5 + - - +
601B 4D8 3.8 31.5 - - + +
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Residues in contact with PHE 365 (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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327B ILE* 6.0 2.7 - - + -
361B LEU* 3.0 52.4 + - + +
364B VAL* 1.3 75.2 - - + +
366B ILE* 1.3 65.8 + - - +
368B MET* 3.3 34.8 - - + +
369B CYS* 3.9 1.6 + - - +
399B PHE* 4.4 19.3 - + - -
403B VAL* 4.2 22.0 - - + -
406B PHE* 3.5 15.7 - - + -
410B LEU* 4.5 0.3 - - - +
477B LEU* 3.7 18.4 - - + -
480B LEU* 4.0 35.2 - - + -
481B CYS* 4.0 12.6 - - - -
484B HIS* 5.2 1.6 - + + -
601B 4D8 4.4 21.1 - - + -
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Residues in contact with ILE 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 GLU 3.0 16.4 + - - +
363B VAL* 3.2 7.8 + - - +
365B PHE* 1.3 76.1 - - - +
367B ARG* 1.3 64.1 + - - +
369B CYS* 3.0 27.4 + - - +
370B ARG* 5.0 0.3 - - - +
410B LEU* 4.0 12.1 - - + -
415B LEU* 6.1 0.4 - - + -
420B ILE* 4.0 18.8 - - + +
423B PHE* 3.6 37.2 - - + -
424B SER* 3.6 26.0 - - - +
427B VAL* 3.6 30.7 - - + -
477B LEU* 3.7 16.8 - - + -
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Residues in contact with ARG 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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284B HIS* 3.6 29.8 + - - +
287B THR* 2.9 47.2 + - - -
288B CYS* 4.2 1.3 - - - -
289B GLN* 5.4 1.1 - - - +
330B ALA* 4.9 1.3 + - - -
333B TYR* 3.8 18.2 - - - +
334B VAL* 4.2 13.8 - - - +
337B PHE* 3.7 18.2 - - - +
363B VAL* 2.8 33.6 + - + +
364B VAL* 3.6 6.3 - - - +
366B ILE* 1.3 75.0 - - - +
368B MET* 1.3 65.8 + - - +
370B ARG* 3.0 24.6 + - - +
371B ALA 3.8 0.7 + - - -
420B ILE* 5.0 1.8 - - + -
424B SER* 4.8 6.0 + - - +
601B 4D8 3.9 4.9 - - + +
602B GOL 3.0 51.3 + - - -
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Residues in contact with MET 368 (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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364B VAL 2.8 14.0 + - - +
365B PHE* 3.3 26.0 - - + +
367B ARG* 1.3 77.6 - - - +
369B CYS* 1.3 55.8 + - - +
371B ALA* 2.8 27.2 + - - -
372B PHE* 3.3 8.9 + - + +
379B VAL* 3.7 26.7 - - + -
403B VAL* 3.6 44.9 - - + +
404B PHE* 6.5 0.2 - - - -
406B PHE* 4.1 7.0 - - + -
407B GLY* 3.9 22.2 - - - +
601B 4D8 3.7 34.7 - - + +
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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