Contacts of the helix formed by residues 345 - 365 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343D GLU 3.9 0.4 + - - -
344D LEU* 1.3 77.1 - - - +
346D GLN* 1.3 66.6 - - - +
347D ASN 4.1 3.4 - - - -
348D ASP* 3.1 38.5 + - - +
349D GLN* 3.0 19.1 + - - +
434D GLN* 4.1 25.1 - - - +
435D GLU* 3.8 28.7 + - - +
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Residues in contact with GLN 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D LEU 3.8 0.8 + - - -
345D CYS* 1.3 71.8 - - - +
347D ASN* 1.3 63.4 + - - +
349D GLN* 3.2 4.6 + - - +
350D ILE* 3.0 28.4 + - - +
502S GLN* 5.4 4.2 - - - +
507S HIS* 3.4 63.5 + - + +
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Residues in contact with ASN 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D CYS* 3.3 3.4 - - - -
346D GLN* 1.3 77.3 - - - +
348D ASP* 1.3 80.2 + - - +
350D ILE* 3.3 8.8 + - - +
351D VAL* 3.0 39.9 + - - +
432D GLY 3.2 23.3 + - - +
434D GLN* 3.5 29.3 - - - +
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Residues in contact with ASP 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D LEU* 4.6 12.5 - - + +
345D CYS* 3.1 18.9 + - - +
347D ASN* 1.3 82.0 + - - +
349D GLN* 1.3 60.4 + - - +
351D VAL* 3.9 0.4 - - - +
352D LEU* 3.0 38.0 + - + +
433D LEU* 3.7 17.5 - - + -
434D GLN* 2.8 28.5 + - - +
435D GLU* 3.0 36.2 + - - +
439D VAL* 3.9 10.9 - - + +
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Residues in contact with GLN 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D PHE* 3.2 48.5 + - + +
342D MET* 3.2 34.3 + - - +
344D LEU* 2.8 23.9 + - + +
345D CYS 3.0 16.7 + - - +
346D GLN* 3.4 9.1 - - - +
348D ASP* 1.3 76.9 - - - +
350D ILE* 1.3 59.8 + - - +
353D LEU* 3.1 26.7 + - - +
505S LEU* 4.0 15.1 - - + +
507S HIS* 2.9 23.6 + - + -
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Residues in contact with ILE 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D GLN 3.0 15.1 + - - +
347D ASN* 3.5 9.4 - - - +
349D GLN* 1.3 76.6 - - - +
351D VAL* 1.3 59.7 + - + +
354D LYS* 2.9 45.0 + - + +
499S THR* 4.8 2.5 - - - +
501S LEU* 4.0 20.9 - - + +
502S GLN* 3.9 31.4 - - + +
505S LEU* 3.8 12.1 - - + -
507S HIS* 3.6 26.9 - - + +
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Residues in contact with VAL 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D ASN* 3.0 31.7 + - - +
348D ASP* 3.9 4.5 - - - +
350D ILE* 1.3 78.4 - - + +
352D LEU* 1.3 61.4 + - - +
354D LYS* 4.0 4.8 - - - +
355D ALA* 3.2 25.3 + - + +
430D ARG* 4.1 11.7 - - + -
431D PRO 3.4 23.1 - - - +
432D GLY* 3.9 20.9 - - - +
433D LEU* 3.9 19.5 - - + -
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Residues in contact with LEU 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D PHE* 4.3 10.3 - - + -
344D LEU* 3.7 29.2 - - + -
348D ASP 3.0 21.9 + - - +
349D GLN 4.2 2.0 - - - +
351D VAL* 1.3 75.8 - - - +
353D LEU* 1.3 52.6 + - - +
355D ALA* 4.2 0.3 - - - +
356D GLY* 2.8 34.3 + - - -
425D LEU* 3.4 29.8 - - + +
426D ILE* 4.2 11.0 - - + -
427D ASN 3.3 29.2 - - - +
430D ARG* 3.8 15.6 + - + -
433D LEU* 4.1 12.3 - - + -
439D VAL* 4.2 15.7 - - + -
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Residues in contact with LEU 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D VAL* 4.2 21.8 - - + +
332D VAL* 4.4 17.0 - - + -
335D ALA* 4.2 13.2 - - + -
341D PHE* 3.8 21.8 - - + -
349D GLN 3.1 12.0 + - - +
350D ILE 4.1 1.3 - - - +
352D LEU* 1.3 75.4 - - - +
354D LYS* 1.3 61.6 + - - +
357D ALA* 2.8 38.9 + - + +
425D LEU* 3.8 16.6 - - + -
505D LEU* 5.1 0.4 - - - -
501S LEU* 3.8 23.8 - - + -
505S LEU* 3.7 32.1 - - + -
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Residues in contact with LYS 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D ILE* 2.9 34.9 + - + +
351D VAL* 4.0 5.4 - - - +
353D LEU* 1.3 74.0 - - - +
355D ALA* 1.3 58.6 + - - +
357D ALA* 4.9 1.7 + - - +
358D MET 5.7 0.3 + - - -
504D GLU* 4.3 18.5 + - - +
505D LEU* 3.9 42.8 - - + +
506D PHE* 5.2 6.6 - - - -
501S LEU* 4.1 6.9 - - + +
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D VAL* 3.2 18.7 + - + +
352D LEU 4.2 0.2 - - - +
354D LYS* 1.3 76.8 - - - +
356D GLY* 1.3 61.1 + - - +
357D ALA 3.7 0.4 - - - -
358D MET* 4.9 2.4 + - - +
359D GLU* 3.9 15.1 + - - +
430D ARG* 3.7 34.7 + - + +
431D PRO* 6.3 0.7 - - + -
476D CYS* 4.7 7.8 - - - +
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Residues in contact with GLY 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D LEU 2.8 21.0 + - - -
355D ALA* 1.3 75.3 - - - +
357D ALA* 1.3 63.6 + - - +
358D MET 3.3 2.5 - - - -
359D GLU* 2.9 6.2 + - - +
360D VAL* 2.9 30.0 + - - +
424D VAL 4.9 3.1 - - - -
425D LEU* 4.7 6.7 - - - -
430D ARG* 3.6 17.7 - - - +
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Residues in contact with ALA 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D ILE* 3.9 28.0 - - + -
331D VAL* 4.0 19.5 - - + +
332D VAL* 5.7 0.7 - - + -
353D LEU* 2.8 32.4 + - + +
354D LYS 4.7 1.8 - - - +
355D ALA 3.7 0.6 - - - -
356D GLY* 1.3 71.5 - - - +
358D MET* 1.3 62.3 + - - +
360D VAL* 3.3 3.8 + - - +
361D VAL* 3.2 25.5 + - - +
505D LEU* 4.9 9.2 - - + -
506D PHE* 5.6 1.3 - - + -
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Residues in contact with MET 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D LEU* 3.6 44.4 - - + -
328D ILE* 4.8 2.5 - - - -
354D LYS 5.7 0.4 + - - -
355D ALA 4.9 2.4 + - - +
356D GLY 3.3 0.4 - - - -
357D ALA* 1.3 78.4 - - - +
359D GLU* 1.3 57.3 + - - +
361D VAL* 3.1 7.3 + - - +
362D LEU* 3.0 58.0 + - + +
400D ILE* 5.1 4.3 - - + -
475D LEU 5.9 0.7 - - - +
476D CYS* 3.8 24.5 - - + -
479D HIS* 4.4 25.1 - - + +
506D PHE* 3.8 32.4 - - + -
601D C3S 4.6 9.2 - - + -
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Residues in contact with GLU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D ALA 3.9 7.5 - - - +
356D GLY 2.9 9.0 + - - +
358D MET* 1.3 77.0 - - - +
360D VAL* 1.3 62.9 + - - +
362D LEU* 3.4 1.5 + - - -
363D VAL* 3.2 26.3 + - - +
424D VAL* 3.5 21.6 - - + +
427D ASN* 4.8 2.6 + - - -
430D ARG* 2.8 41.9 + - - -
469D LYS 5.0 1.1 - - - +
472D LEU* 3.7 45.4 - - + +
473D ARG* 3.9 9.2 + - - +
476D CYS* 3.5 21.5 - - - +
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Residues in contact with VAL 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D VAL* 3.8 31.9 - - + -
334D PHE* 4.8 8.3 - - + -
356D GLY 2.9 17.2 + - - +
357D ALA 3.7 7.0 - - - +
358D MET 3.3 0.4 - - - -
359D GLU* 1.3 75.0 - - - +
361D VAL* 1.3 57.5 + - - +
363D VAL* 3.3 5.8 + - - +
364D ARG* 2.9 39.9 + - - +
421D THR* 3.8 38.8 - - - +
424D VAL* 4.1 9.9 - - + -
425D LEU* 4.2 15.3 - - + -
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Residues in contact with VAL 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D LEU* 3.9 25.6 - - + -
327D ALA* 3.9 22.4 - - + -
328D ILE* 3.9 20.0 - - + -
331D VAL* 3.6 20.0 - - + -
357D ALA 3.2 14.5 + - - +
358D MET* 3.1 10.6 + - - +
360D VAL* 1.3 77.0 - - - +
362D LEU* 1.3 61.9 + - + +
364D ARG* 3.3 9.4 + - - +
365D MET* 3.2 22.9 + - - +
601D C3S 4.2 19.0 - - + +
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Residues in contact with LEU 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D MET* 3.0 51.5 + - + +
359D GLU 3.8 4.9 - - - +
360D VAL 3.4 0.2 - - - -
361D VAL* 1.3 77.4 - - + +
363D VAL* 1.3 60.9 + - - +
365D MET* 3.6 18.6 - - - +
400D ILE* 3.8 36.8 - - + +
403D PHE* 3.8 18.2 - - + -
404D SER* 4.1 5.5 + - - -
407D LEU* 4.7 0.7 - - - +
472D LEU* 4.1 15.5 - - + -
475D LEU* 3.8 35.9 - - + -
476D CYS* 4.5 6.1 - - - -
601D C3S 5.3 7.0 - - + -
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Residues in contact with VAL 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D GLU 3.2 14.3 + - - +
360D VAL* 3.7 7.2 - - - +
361D VAL 3.2 0.6 - - - -
362D LEU* 1.3 75.0 - - - +
364D ARG* 1.3 61.2 + - - +
365D MET 3.0 6.5 + - - -
366D CYS* 3.1 29.1 + - - +
403D PHE* 3.7 22.7 - - + -
407D LEU* 4.0 8.2 - - + +
417D ILE* 4.7 6.5 - - + +
420D TYR* 3.5 39.5 - - + -
421D THR* 3.6 21.1 - - + -
424D VAL* 4.3 6.5 - - + -
472D LEU* 4.2 11.2 - - + -
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Residues in contact with ARG 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D TYR* 4.1 26.8 - - + +
284D THR* 2.9 45.9 + - - -
285D CYS* 4.3 1.7 - - - +
327D ALA* 4.7 1.6 + - - -
330D TYR* 3.9 13.9 - - - +
331D VAL* 4.5 14.1 - - - +
334D PHE* 3.6 24.7 - - - +
360D VAL* 2.9 31.6 + - - +
361D VAL* 3.3 8.5 + - - +
363D VAL* 1.3 74.9 - - - +
365D MET* 1.3 61.7 + - - +
366D CYS* 3.2 0.7 - - - -
367D ARG* 3.2 25.0 + - - +
417D ILE* 4.7 8.1 - - - -
421D THR* 4.2 13.1 + - + +
601D C3S 3.5 44.3 + - + +
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Residues in contact with MET 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D VAL 3.2 12.2 + - - +
362D LEU* 3.6 17.3 - - - +
363D VAL 3.0 0.4 - - - -
364D ARG* 1.3 76.9 - - - +
366D CYS* 1.3 55.6 + - - +
367D ARG 3.1 0.4 - - - -
368D ALA* 2.8 21.1 + - - -
369D TYR* 3.1 12.0 + - + +
376D VAL* 3.7 35.9 - - + -
400D ILE* 3.6 35.2 - - + +
401D PHE* 4.2 20.4 - - + -
404D SER* 3.4 19.7 - - - +
601D C3S 3.9 36.3 - - + -
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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