Contacts of the helix formed by residues 345 - 365 (chain C) in PDB entry 5NTI
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343C GLU 4.0 0.2 + - - -
344C LEU* 1.3 78.1 - - - +
346C GLN* 1.3 66.2 - - - +
347C ASN 4.2 0.9 - - - +
348C ASP* 3.2 38.1 + - - +
349C GLN* 3.2 19.5 + - - +
434C GLN* 4.1 19.5 - - - +
435C GLU* 3.7 32.3 + - - +
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Residues in contact with GLN 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C CYS* 1.3 74.2 - - - +
347C ASN* 1.3 63.9 + - - +
349C GLN* 3.2 18.2 + - - +
350C ILE* 3.3 29.4 + - + +
502R GLN* 6.0 4.0 - - + +
506R GLY 4.4 15.7 + - - +
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Residues in contact with ASN 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C CYS* 3.3 1.4 - - - +
346C GLN* 1.3 78.3 - - - +
348C ASP* 1.3 76.3 + - - +
350C ILE* 3.3 9.4 + - - +
351C VAL* 3.1 28.0 + - - +
432C GLY 3.1 25.9 + - - +
434C GLN* 3.5 39.7 + - - +
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Residues in contact with ASP 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 4.5 12.9 - - + +
345C CYS* 3.2 18.7 + - - +
347C ASN* 1.3 79.7 + - - +
349C GLN* 1.3 66.1 + - - +
351C VAL* 3.4 2.5 + - - +
352C LEU* 2.9 32.1 + - + +
433C LEU* 3.7 18.6 - - + +
434C GLN* 2.7 27.6 + - - +
435C GLU* 2.9 36.4 + - - +
439C VAL* 4.0 9.6 - - + +
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Residues in contact with GLN 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C PHE* 3.6 43.1 + - + +
342C MET* 2.8 53.7 + - - +
344C LEU* 3.9 11.5 - - + +
345C CYS 3.2 9.1 + - - +
346C GLN* 3.2 33.0 + - - +
348C ASP* 1.3 77.1 - - - +
350C ILE* 1.3 61.7 + - - +
352C LEU* 3.7 0.4 - - - +
353C LEU* 3.0 24.3 + - - +
505R LEU* 4.1 18.9 - - + +
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Residues in contact with ILE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C GLN* 3.3 15.2 + - + +
347C ASN* 3.3 10.0 + - - +
349C GLN* 1.3 77.0 - - - +
351C VAL* 1.3 59.4 + - + +
353C LEU* 3.3 1.8 + - - -
354C LYS* 2.8 46.5 + - + +
499R THR* 4.9 6.7 - - + +
501R LEU* 3.8 21.5 - - + +
502R GLN* 3.5 48.2 - - + +
505R LEU* 3.6 21.8 - - + -
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Residues in contact with VAL 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ASN* 3.1 22.8 + - - +
348C ASP* 3.4 7.4 + - - +
350C ILE* 1.3 77.2 - - + +
352C LEU* 1.3 63.3 + - - +
354C LYS* 3.9 4.5 - - - +
355C ALA* 3.1 25.6 + - + +
430C ARG* 3.9 18.8 - - + -
431C PRO 3.4 23.3 - - - +
432C GLY* 3.7 21.5 - - - +
433C LEU* 4.1 12.3 - - + -
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Residues in contact with LEU 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C PHE* 4.1 11.0 - - + -
344C LEU* 3.8 28.3 - - + -
348C ASP 2.9 20.3 + - - +
349C GLN 3.7 3.6 - - - +
351C VAL* 1.3 76.2 - - - +
353C LEU* 1.3 56.8 + - - +
355C ALA* 3.8 1.2 - - - +
356C GLY* 2.8 28.6 + - - -
425C LEU* 3.6 24.1 - - + +
426C ILE* 3.9 21.8 - - + -
427C ASN 3.3 27.6 - - - +
430C ARG* 3.9 14.7 + - + -
433C LEU* 4.1 13.9 - - + -
439C VAL* 4.3 12.3 - - + -
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Residues in contact with LEU 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C VAL* 4.3 18.8 - - + -
332C VAL* 4.2 25.6 - - + -
335C ALA* 4.0 15.7 - - + -
341C PHE* 4.1 13.2 - - + -
349C GLN 3.0 13.6 + - - +
350C ILE 3.9 2.2 - - - +
352C LEU* 1.3 74.1 - - - +
354C LYS* 1.3 62.3 + - - +
357C ALA* 2.8 39.3 + - + +
425C LEU* 3.8 18.6 - - + -
505C LEU* 5.2 0.2 - - - -
501R LEU* 4.0 16.4 - - + -
505R LEU* 3.9 38.1 - - + -
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Residues in contact with LYS 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ILE* 2.8 31.5 + - + +
351C VAL* 3.9 4.9 - - - +
353C LEU* 1.3 73.0 - - - +
355C ALA* 1.3 58.7 + - - +
357C ALA* 4.8 1.6 + - - +
358C MET* 5.6 1.2 + - - +
504C GLU* 3.8 25.7 + - + +
505C LEU* 4.0 39.9 - - + +
506C PHE* 5.4 5.9 - - - -
501R LEU* 3.8 8.8 - - + +
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Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C VAL* 3.1 16.9 + - + +
352C LEU 4.3 0.2 - - - +
354C LYS* 1.3 76.7 - - - +
356C GLY* 1.3 58.4 + - - +
358C MET* 5.2 2.3 + - - +
359C GLU* 3.9 14.9 + - - +
430C ARG* 3.7 40.2 + - + +
431C PRO* 6.4 0.7 - - + -
476C CYS* 5.2 3.6 - - - -
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Residues in contact with GLY 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C LEU 2.8 18.3 + - - -
355C ALA* 1.3 78.8 - - - +
357C ALA* 1.3 65.6 + - - +
358C MET 3.3 2.2 - - - -
359C GLU* 3.0 6.4 + - - +
360C VAL* 2.9 31.6 + - - +
424C VAL 5.0 2.9 - - - -
425C LEU* 4.6 6.3 - - - -
430C ARG* 3.7 15.9 - - - +
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Residues in contact with ALA 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ILE* 4.1 27.6 - - + +
331C VAL* 4.1 19.4 - - + +
332C VAL* 5.7 0.7 - - + -
353C LEU* 2.8 33.0 + - + +
354C LYS 4.7 1.3 - - - +
355C ALA 3.8 0.4 - - - -
356C GLY* 1.3 72.9 - - - +
358C MET* 1.3 63.1 + - - +
360C VAL* 3.3 3.8 + - - +
361C VAL* 3.2 26.6 + - - +
505C LEU* 4.7 9.6 - - + -
506C PHE* 5.8 0.2 - - + -
501R LEU* 6.4 1.3 - - + -
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Residues in contact with MET 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C LEU* 3.7 44.9 - - + -
328C ILE* 4.8 2.6 - - - +
354C LYS 5.6 2.1 + - - +
355C ALA 5.2 2.2 + - - +
356C GLY 3.3 0.6 - - - +
357C ALA* 1.3 78.2 - - - +
359C GLU* 1.3 62.5 + - - +
361C VAL* 3.2 7.2 + - - +
362C LEU* 3.1 48.0 + - + +
400C ILE* 5.0 4.3 - - + -
475C LEU 5.6 1.1 - - - +
476C CYS* 3.7 24.2 - - + -
479C HIS* 4.2 25.6 - - + +
506C PHE* 3.7 30.6 - - + -
601C C3S 4.8 9.9 - - + -
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Residues in contact with GLU 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ALA 3.9 8.1 + - - +
356C GLY 3.0 9.5 + - - +
358C MET* 1.3 79.1 - - - +
360C VAL* 1.3 63.0 + - - +
362C LEU* 3.5 0.4 + - - -
363C VAL* 3.3 19.2 + - - +
424C VAL* 3.5 19.0 - - + +
427C ASN* 5.3 1.0 + - - -
430C ARG* 2.7 40.6 + - - -
472C LEU* 3.4 41.2 - - + +
473C ARG* 4.0 20.5 + - - +
476C CYS* 3.5 21.8 - - - +
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Residues in contact with VAL 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C VAL* 3.8 29.2 - - + -
334C PHE* 5.2 6.5 - - + -
356C GLY 2.9 20.8 + - - +
357C ALA 3.6 7.0 - - - +
358C MET 3.2 0.2 - - - -
359C GLU* 1.3 74.3 - - - +
361C VAL* 1.3 60.2 + - - +
363C VAL* 3.2 4.3 + - - +
364C ARG* 2.8 37.6 + - + +
421C THR* 3.8 43.1 - - + +
424C VAL* 4.1 10.8 - - + -
425C LEU* 4.2 13.2 - - + -
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Residues in contact with VAL 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C LEU* 3.8 25.1 - - + -
327C ALA* 4.2 21.8 - - + -
328C ILE* 3.9 20.9 - - + -
331C VAL* 3.8 17.5 - - + -
357C ALA 3.2 16.8 + - - +
358C MET* 3.2 8.7 + - - +
360C VAL* 1.3 75.6 - - - +
362C LEU* 1.3 65.4 + - + +
364C ARG* 3.2 11.4 + - + +
365C MET* 3.1 21.7 + - - +
601C C3S 4.2 20.7 - - + +
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Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C LEU* 6.2 0.2 - - + -
358C MET* 3.1 44.2 + - + +
359C GLU 3.7 4.7 - - - +
360C VAL 3.3 0.2 - - - -
361C VAL* 1.3 77.2 - - + +
363C VAL* 1.3 60.7 + - - +
365C MET* 3.4 21.0 - - - +
366C CYS 4.7 0.3 + - - -
400C ILE* 3.8 42.3 - - + +
403C PHE* 3.8 19.4 - - + -
404C SER* 4.7 2.8 + - - -
407C LEU* 4.8 1.0 - - - +
472C LEU* 4.1 13.2 - - + -
475C LEU* 3.8 31.2 - - + -
476C CYS* 4.2 9.9 - - - +
601C C3S 5.4 7.2 - - + -
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Residues in contact with VAL 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C GLU 3.3 13.9 + - - +
360C VAL* 3.2 7.7 + - - +
362C LEU* 1.3 73.9 - - - +
364C ARG* 1.3 61.9 + - - +
365C MET 3.0 5.3 + - - -
366C CYS* 3.4 22.3 + - - -
403C PHE* 3.9 19.1 - - + -
407C LEU* 3.9 15.1 - - + +
412C PHE* 4.8 3.8 - - + -
417C ILE* 4.4 9.0 - - + +
420C TYR* 3.6 40.2 - - + -
421C THR* 3.7 18.4 - - + -
424C VAL* 4.5 5.8 - - + -
472C LEU* 4.0 8.3 - - + -
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Residues in contact with ARG 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C TYR* 4.1 26.6 + - + -
284C THR* 2.8 49.0 + - - -
285C CYS* 4.3 1.3 - - - +
327C ALA* 4.7 2.3 + - - -
330C TYR* 4.0 13.5 - - - +
331C VAL* 4.2 15.7 - - - +
334C PHE* 3.7 22.2 - - - +
360C VAL* 2.8 40.7 + - + +
361C VAL* 3.2 10.0 + - - +
363C VAL* 1.3 71.5 - - - +
365C MET* 1.3 62.0 + - - +
366C CYS* 3.2 1.3 + - - -
367C ARG* 3.2 22.4 + - - +
417C ILE* 4.4 8.0 - - - +
421C THR* 4.2 8.8 + - + +
601C C3S 3.3 44.5 + - + +
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Residues in contact with MET 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C VAL 3.1 9.6 + - - +
362C LEU* 3.4 17.9 - - - +
363C VAL 3.0 0.8 - - - -
364C ARG* 1.3 76.3 - - - +
366C CYS* 1.3 57.4 + - - +
367C ARG 3.2 0.2 - - - -
368C ALA* 2.9 20.0 + - - -
369C TYR* 3.0 15.6 + - + +
376C VAL* 3.8 28.9 - - + -
400C ILE* 3.6 25.6 - - + -
401C PHE* 4.0 28.3 - - + -
404C SER* 3.5 23.8 - - - +
601C C3S 3.8 39.0 - - + -
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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