Contacts of the helix formed by residues 345 - 365 (chain B) in PDB entry 5NTN
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 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B GLU 3.9 0.4 + - - -
344B LEU* 1.3 79.0 - - - +
346B GLN* 1.3 66.8 + - - +
347B ASN 4.0 2.2 - - - -
348B ASP* 3.2 41.5 + - - +
349B GLN* 3.1 19.3 + - - +
434B GLN* 3.5 32.8 - - - +
435B GLU* 3.5 21.3 + - - +
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Residues in contact with GLN 346 (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 LEU 3.9 0.6 + - - -
345B CYS* 1.3 72.6 - - - +
347B ASN* 1.3 63.9 + - - +
349B GLN* 3.3 19.4 + - - +
350B ILE* 3.1 28.8 + - + +
502Q GLN* 2.8 34.2 + - - +
505Q LEU* 6.3 0.2 - - - -
506Q GLY 5.5 4.0 + - - -
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Residues in contact with ASN 347 (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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345B CYS* 3.3 2.0 - - - +
346B GLN* 1.3 77.1 - - - +
348B ASP* 1.3 80.3 + - - +
350B ILE* 3.2 8.6 + - - +
351B VAL* 3.0 39.9 + - - +
432B GLY 3.1 23.5 + - - +
434B GLN* 3.7 26.5 - - - +
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Residues in contact with ASP 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 4.4 12.6 - - + +
345B CYS* 3.2 20.1 + - - +
347B ASN* 1.3 81.3 + - - +
349B GLN* 1.3 64.9 + - - +
351B VAL* 3.7 0.9 - - - +
352B LEU* 3.0 33.4 + - + +
433B LEU* 3.3 19.8 - - + -
434B GLN* 2.6 26.1 + - - +
435B GLU* 2.9 38.5 + - - +
439B VAL* 4.0 8.6 - - + +
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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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341B PHE* 3.5 45.9 + - + +
342B MET* 3.5 37.3 + - - +
344B LEU* 2.8 26.1 + - + +
345B CYS 3.1 11.9 + - - +
346B GLN* 3.5 18.6 - - - +
348B ASP* 1.3 77.6 - - - +
350B ILE* 1.3 57.1 + - - +
352B LEU* 3.9 0.2 - - - +
353B LEU* 3.1 30.3 + - - +
505Q LEU* 3.5 25.6 - - + +
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Residues in contact with ILE 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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346B GLN* 3.1 18.1 + - + +
347B ASN* 3.5 8.5 - - - +
349B GLN* 1.3 74.7 - - - +
351B VAL* 1.3 60.6 + - + +
353B LEU* 3.8 0.4 - - - -
354B LYS* 2.8 44.6 + - + +
499Q THR* 4.4 13.7 - - + +
501Q LEU* 3.8 20.6 - - + +
502Q GLN* 3.6 46.2 - - + +
505Q LEU* 3.6 18.8 - - + -
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ASN* 3.0 41.9 + - - +
348B ASP 3.4 4.7 + - - +
350B ILE* 1.3 76.8 - - + +
352B LEU* 1.3 63.1 + - - +
354B LYS* 3.9 4.0 - - - +
355B ALA* 3.2 25.4 + - + +
430B ARG* 4.0 11.6 - - + +
431B PRO 3.3 24.2 - - - +
432B GLY* 3.9 10.8 - - - +
433B LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 352 (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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341B PHE* 4.2 10.1 - - + -
344B LEU* 3.7 29.2 - - + -
348B ASP 3.0 19.0 + - - +
349B GLN 3.9 3.6 - - - +
351B VAL* 1.3 77.2 - - - +
353B LEU* 1.3 52.5 + - - +
355B ALA* 3.8 0.9 - - - +
356B GLY* 2.8 34.3 + - - -
425B LEU* 3.5 25.5 - - + +
426B ILE* 4.0 20.2 - - + -
427B ASN 3.4 27.1 - - - +
430B ARG* 3.8 14.6 + - + -
433B LEU* 4.0 13.7 - - + -
439B VAL* 4.1 13.7 - - + -
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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
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331B VAL* 4.3 12.3 - - + +
332B VAL* 4.2 22.2 - - + -
335B ALA* 3.8 15.7 - - + -
341B PHE* 3.8 16.8 - - + -
349B GLN 3.1 15.0 + - - +
350B ILE 4.1 1.8 - - - +
352B LEU* 1.3 75.3 - - - +
354B LYS* 1.3 60.0 + - - +
357B ALA* 2.8 38.1 + - + +
425B LEU* 3.8 18.2 - - + -
505B LEU* 4.5 0.3 - - - +
501Q LEU* 4.2 25.1 - - + -
505Q LEU* 3.7 35.2 - - + -
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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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350B ILE* 2.8 34.9 + - + +
351B VAL* 3.9 5.4 - - - +
353B LEU* 1.3 75.0 - - - +
355B ALA* 1.3 60.1 + - - +
357B ALA* 4.6 2.1 + - - +
358B MET* 5.4 2.6 + - - +
504B GLU* 3.4 28.1 + - + -
505B LEU* 3.9 38.0 + - + +
501Q LEU* 4.0 7.1 - - + +
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Residues in contact with ALA 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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351B VAL* 3.2 17.8 + - + +
352B LEU 4.2 0.2 - - - +
354B LYS* 1.3 77.8 - - - +
356B GLY* 1.3 58.9 + - - +
357B ALA 3.8 0.2 - - - -
358B MET* 5.0 1.7 + - - +
359B GLU* 3.9 15.6 + - - +
430B ARG* 3.6 39.6 + - + +
431B PRO* 6.3 0.9 - - + -
476B CYS* 5.1 4.0 - - - -
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Residues in contact with GLY 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 LEU 2.8 17.7 + - - -
355B ALA* 1.3 79.1 - - - +
357B ALA* 1.3 65.3 + - - +
358B MET 3.4 2.5 - - - -
359B GLU* 3.1 5.3 + - - +
360B VAL* 2.9 30.8 + - - +
424B VAL* 4.5 4.0 - - - +
425B LEU* 4.7 7.9 - - - -
430B ARG* 3.7 15.3 - - - -
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Residues in contact with ALA 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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328B ILE* 4.2 26.0 - - + -
331B VAL* 4.1 19.3 - - + +
332B VAL* 5.7 1.1 - - + -
353B LEU* 2.8 32.3 + - + +
354B LYS 4.6 1.1 + - - +
355B ALA 3.8 0.6 - - - -
356B GLY* 1.3 73.4 - - - +
358B MET* 1.3 62.0 + - - +
360B VAL* 3.3 3.5 + - - +
361B VAL* 3.1 26.7 + - - +
505B LEU* 4.8 10.1 - - + -
506B PHE* 6.2 0.2 - - + -
501Q LEU* 6.1 1.1 - - + -
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Residues in contact with MET 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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324B LEU* 3.6 36.8 - - + -
328B ILE* 4.9 1.9 - - - +
354B LYS 5.4 2.8 + - - +
355B ALA 5.0 2.4 + - - +
356B GLY 3.4 0.4 - - - +
357B ALA* 1.3 75.1 - - - +
359B GLU* 1.3 65.4 + - - +
361B VAL* 3.3 8.0 + - + +
362B LEU* 2.9 44.1 + - + +
400B ILE* 5.3 6.1 - - + -
475B LEU 5.9 0.4 - - - +
476B CYS* 3.7 24.7 - - + -
479B HIS* 3.7 36.6 - - + +
506B PHE* 3.9 25.5 - - + -
601B 98H 5.4 6.5 - - + -
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Residues in contact with GLU 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 ALA 3.9 8.5 + - - +
356B GLY 3.1 8.8 + - - +
358B MET* 1.3 76.9 - - - +
360B VAL* 1.3 62.3 + - - +
362B LEU* 3.3 4.6 + - - +
363B VAL* 3.1 25.8 + - - +
424B VAL* 3.6 19.9 - - + +
430B ARG* 2.7 41.7 + - - -
469B LYS 5.1 0.9 - - - +
472B LEU* 3.7 29.6 - - + +
473B ARG* 3.9 23.6 + - - +
476B CYS* 3.6 20.3 - - - +
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Residues in contact with VAL 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 VAL* 3.6 32.1 - - + -
334B PHE* 5.1 6.1 - - + -
356B GLY 2.9 21.6 + - - +
357B ALA 3.6 6.5 - - - +
359B GLU* 1.3 72.6 - - - +
361B VAL* 1.3 60.6 + - - +
363B VAL* 3.1 7.1 + - - +
364B ARG* 2.8 41.3 + - - +
421B THR* 3.9 37.2 - - - +
424B VAL* 4.0 12.8 - - + -
425B LEU* 4.4 11.0 - - + +
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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
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324B LEU* 3.9 22.4 - - + -
327B ALA* 4.0 32.1 - - + -
328B ILE* 4.1 13.2 - - + +
331B VAL* 3.8 17.7 - - + -
357B ALA 3.1 14.3 + - - +
358B MET* 3.3 10.1 + - + +
360B VAL* 1.3 75.7 - - - +
362B LEU* 1.3 64.6 + - + +
364B ARG* 3.6 8.7 - - - +
365B MET* 3.0 23.4 + - - +
601B 98H 4.2 22.4 - - + +
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Residues in contact with LEU 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 MET* 2.9 37.1 + - + +
359B GLU 3.5 7.0 - - - +
360B VAL 3.2 0.2 - - - -
361B VAL* 1.3 78.0 - - + +
363B VAL* 1.3 60.4 + - - +
365B MET* 3.5 18.1 - - - +
366B CYS 4.3 0.2 + - - -
400B ILE* 3.9 41.7 - - + -
403B PHE* 3.9 18.4 - - + -
404B SER* 4.2 5.0 + - - -
407B LEU* 4.5 0.9 - - - +
472B LEU* 3.9 19.7 - - + -
475B LEU* 3.8 30.1 - - + -
476B CYS* 4.2 16.2 - - - +
601B 98H 5.6 5.2 - - + -
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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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359B GLU 3.1 13.8 + - - +
360B VAL 3.1 7.0 + - - +
362B LEU* 1.3 73.8 - - - +
364B ARG* 1.3 65.5 + - - +
365B MET 3.0 2.6 + - - -
366B CYS* 3.1 30.4 + - - +
403B PHE* 4.2 13.9 - - + -
407B LEU* 3.9 13.5 - - + -
412B PHE* 4.8 5.4 - - + -
417B ILE* 5.1 7.2 - - + +
420B TYR* 3.7 40.8 - - + -
421B THR* 3.7 17.0 - - + -
424B VAL* 4.5 8.1 - - + -
472B LEU* 4.3 11.9 - - + -
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Residues in contact with ARG 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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281B TYR* 3.6 41.2 - - + +
284B THR* 2.8 44.8 + - - -
285B CYS* 4.0 10.0 + - - +
286B GLN* 4.6 5.1 + - - +
327B ALA* 4.8 1.9 + - - -
330B TYR* 3.7 18.2 + - - +
331B VAL* 3.9 15.3 - - - +
334B PHE* 3.7 16.6 - - - +
360B VAL* 2.8 40.4 + - + +
361B VAL* 3.3 8.7 + - - +
363B VAL* 1.3 71.9 - - - +
365B MET* 1.3 62.2 + - - +
367B ARG* 3.3 30.4 + - - +
368B ALA 4.3 1.0 + - - -
417B ILE* 5.1 2.9 - - + -
421B THR* 4.6 5.8 + - + -
601B 98H 4.5 18.7 - - + +
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Residues in contact with MET 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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361B VAL 3.0 13.0 + - - +
362B LEU* 3.5 15.7 - - - +
363B VAL 3.0 0.6 + - - -
364B ARG* 1.3 74.1 - - - +
366B CYS* 1.3 59.4 + - - +
368B ALA* 2.8 21.2 + - - +
369B TYR* 3.2 10.9 + - + +
376B VAL* 3.8 22.0 - - + -
400B ILE* 3.6 32.3 - - + +
401B PHE* 4.2 22.0 - - + -
404B SER* 3.4 21.8 - - - +
601B 98H 3.9 49.6 - - + +
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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
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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