Contacts of the helix formed by residues 418 - 438 (chain B) in PDB entry 1N8T
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 GLY 418 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B THR* 6.1 0.2 - - - -
414B PRO* 3.7 16.0 + - - +
415B ILE 3.1 9.1 + - - -
417B LYS* 1.3 76.1 - - - +
419B LEU* 1.3 58.9 + - - +
420B HIS 3.6 2.0 - - - -
421B HIS* 3.4 11.3 + - - +
422B LYS* 2.9 31.2 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR* 4.0 21.8 - - + +
222A GLU* 5.7 0.7 - - - +
415B ILE 3.7 1.2 + - - -
416B ARG* 3.2 50.8 + - + +
417B LYS 3.5 0.6 + - - -
418B GLY* 1.3 74.4 - - - +
420B HIS* 1.3 69.2 + - + +
422B LYS* 3.1 30.3 + - - +
423B ILE* 3.1 28.1 + - + +
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Residues in contact with HIS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 2.9 41.3 + - + +
188A GLY* 3.6 17.2 - - - +
191A ILE* 4.2 5.8 - - + -
219A THR* 3.9 21.1 - - + +
220A ASN* 3.3 27.2 + - - -
223A THR* 2.6 33.7 + - - -
413B HIS 5.7 0.4 - - - +
415B ILE* 3.5 27.5 + - + +
416B ARG* 4.4 9.4 - - + -
418B GLY 3.6 0.4 - - - -
419B LEU* 1.3 79.3 - - + +
421B HIS* 1.3 59.1 + - - +
423B ILE* 3.3 3.3 + - - +
424B LEU* 2.9 28.5 + - - +
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Residues in contact with HIS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 4.9 3.0 + - - -
188A GLY 5.1 1.7 - - - +
407B ILE* 4.6 4.3 - - + -
408B PRO* 3.1 22.7 + - + -
409B VAL 2.8 30.3 + - - -
410B GLN* 4.7 0.2 - - - -
411B THR* 3.5 44.6 + - + -
413B HIS 5.8 1.3 + - - +
414B PRO* 5.9 0.4 - - + -
415B ILE 5.6 0.2 + - - -
418B GLY* 3.4 11.0 + - - +
419B LEU 3.2 0.8 - - - -
420B HIS* 1.3 81.5 - - - +
422B LYS* 1.3 56.8 + - - +
424B LEU* 3.6 24.5 - - + +
425B LEU* 2.9 51.7 + - + +
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Residues in contact with LYS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLU* 3.7 36.0 + - - +
526A PRO* 5.5 0.2 - - - -
528A LEU* 3.7 22.0 - - + +
529A ASP* 4.0 20.6 - - - +
552A ARG* 6.3 0.2 - - - +
418B GLY 2.9 18.6 + - - +
419B LEU* 3.1 24.8 + - - +
421B HIS* 1.3 75.1 - - - +
423B ILE* 1.3 72.0 + - - +
425B LEU* 3.2 10.6 + - - +
426B ALA* 2.9 22.7 + - - +
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.7 28.3 - - + -
215A GLN* 3.7 37.0 - - + +
216A GLU* 5.6 2.7 - - + +
219A THR* 4.0 25.1 - - + +
525A GLU* 4.0 9.6 - - - +
419B LEU* 3.1 34.9 + - + +
420B HIS 3.7 4.7 - - - +
422B LYS* 1.3 80.1 - - - +
424B LEU* 1.3 64.0 + - - +
426B ALA* 3.3 6.8 + - - +
427B ASN* 2.8 39.1 + - - +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASN* 4.0 4.0 - - - +
186A ILE* 3.6 25.3 - - + +
187A ASP* 3.5 27.8 - - + +
340B TYR* 3.2 44.8 - - + +
383B GLY 3.9 9.9 - - - +
384B THR* 3.8 7.2 - - + -
407B ILE* 4.1 10.5 - - + -
420B HIS 2.9 18.2 + - - +
421B HIS* 3.6 22.4 - - + +
422B LYS 3.2 0.2 - - - -
423B ILE* 1.3 77.9 - - - +
425B LEU* 1.3 63.0 + - - +
427B ASN* 3.2 4.2 + - - +
428B PHE* 3.0 20.4 + - - +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A LEU* 4.2 12.1 - - + -
548A ILE* 3.8 44.9 - - + -
552A ARG* 5.5 4.3 - - - +
407B ILE* 3.9 28.9 - - + -
408B PRO 4.2 11.9 - - - +
409B VAL* 4.3 7.2 - - + +
421B HIS* 2.9 41.6 + - + +
422B LYS* 3.7 7.2 - - - +
424B LEU* 1.3 76.0 - - - +
426B ALA* 1.3 62.6 + - - +
428B PHE* 3.1 3.3 + - + +
429B LEU* 3.0 29.0 + - - +
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Residues in contact with ALA 426 (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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521A ALA* 3.7 14.6 - - + +
524A ILE* 3.8 21.9 - - + +
525A GLU* 3.6 29.4 - - + +
528A LEU* 3.8 3.9 - - + +
422B LYS 2.9 17.1 + - - +
423B ILE 3.7 4.3 - - - +
425B LEU* 1.3 76.0 - - - +
427B ASN* 1.3 58.8 + - - +
429B LEU* 3.5 1.9 + - - +
430B ALA* 2.8 32.0 + - - +
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Residues in contact with ASN 427 (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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186A ILE* 5.6 0.4 - - - +
215A GLN* 4.6 6.1 - - - +
216A GLU* 4.8 6.5 + - - +
517A GLY 5.1 2.6 - - - +
518A LYS* 5.7 2.9 + - - -
521A ALA* 3.9 22.9 - - - +
525A GLU* 4.8 0.6 + - - -
340B TYR* 4.2 2.5 - - + -
384B THR* 4.2 13.3 - - + +
387B GLN* 2.7 35.9 - - - +
423B ILE* 2.8 40.8 + - - +
424B LEU 3.6 7.2 - - - +
425B LEU 3.2 0.2 - - - -
426B ALA* 1.3 75.7 - - - +
428B PHE* 1.3 59.6 + - - +
430B ALA* 4.3 1.1 - - - -
431B GLN* 2.8 37.9 + - - +
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Residues in contact with PHE 428 (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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544A LEU* 4.9 0.4 - - + -
548A ILE* 5.1 4.3 - - + -
340B TYR* 3.8 26.6 - + + -
405B PHE* 3.4 42.4 - - + -
406B LEU 3.6 5.8 - - - -
407B ILE* 3.5 38.8 - - + -
424B LEU 3.0 12.5 + - - +
425B LEU* 3.1 6.3 + - - +
427B ASN* 1.3 78.9 - - - +
429B LEU* 1.3 84.3 + - + +
432B THR* 3.7 22.2 + - - +
475B SER* 3.9 23.1 - - - -
476B ILE 4.4 0.4 - - - -
477B VAL* 3.6 29.2 - - + -
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ILE* 3.9 26.9 - - + -
528A LEU* 4.1 7.6 - - + -
541A THR* 4.5 8.3 + - + +
544A LEU* 3.3 37.9 - - + -
545A ILE* 3.8 24.9 - - + +
548A ILE* 3.9 24.5 - - + -
56B LYS* 5.2 0.2 + - - -
425B LEU 3.0 21.3 + - - +
426B ALA 3.9 2.2 - - - +
428B PHE* 1.3 87.8 - - + +
430B ALA* 1.3 65.6 + - - +
432B THR* 3.4 7.9 + - - -
433B GLU* 3.1 23.0 + - - +
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Residues in contact with ALA 430 (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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517A GLY 3.7 9.6 - - - +
520A LEU* 3.5 11.5 - - + +
521A ALA* 3.4 32.5 - - + +
524A ILE* 4.1 7.0 - - + -
426B ALA 2.8 19.5 + - - +
427B ASN* 3.9 2.2 - - - +
429B LEU* 1.3 75.6 - - - +
431B GLN* 1.3 56.8 + - + +
433B GLU* 3.1 4.9 + - - +
434B ALA* 2.7 37.9 + - - +
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Residues in contact with GLN 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A VAL* 5.4 2.2 + - - +
517A GLY* 3.7 25.2 - - - -
340B TYR* 3.7 4.7 - - - +
387B GLN* 3.4 38.1 + - - +
391B TYR* 3.1 16.8 - - + +
395B HIS* 2.6 34.0 + - - -
405B PHE* 3.7 21.1 - - + -
427B ASN* 2.8 24.9 + - - +
428B PHE 4.3 0.4 - - - +
430B ALA* 1.3 73.6 - - + +
432B THR* 1.3 57.5 + - - +
434B ALA* 3.2 4.3 + - - +
435B LEU* 2.9 34.4 + - - +
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Residues in contact with THR 432 (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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544A LEU* 4.7 1.2 - - - +
56B LYS* 3.0 34.0 + - - +
405B PHE* 3.6 38.4 - - + -
428B PHE 3.7 11.2 + - - +
429B LEU* 3.4 10.1 + - - -
430B ALA 3.3 0.4 - - - -
431B GLN* 1.3 76.0 - - - +
433B GLU* 1.3 63.3 + - - +
435B LEU* 3.5 7.6 + - - +
436B MET* 3.2 17.0 + - - +
473B THR* 3.5 20.0 + - - +
475B SER* 3.8 15.8 + - - +
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Residues in contact with GLU 433 (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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520A LEU* 3.7 26.4 - - + +
524A ILE* 3.7 17.0 - - - +
537A HIS* 2.8 37.0 + - - +
538A ASP* 3.7 8.7 + - - +
541A THR* 3.4 22.9 - - + +
56B LYS* 4.3 4.9 - - - +
429B LEU 3.1 17.1 + - - +
430B ALA 3.1 3.7 + - - +
432B THR* 1.3 77.9 + - - +
434B ALA* 1.3 57.5 - - - +
436B MET* 3.4 3.7 + - + +
437B LYS* 2.9 51.8 + - + +
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Residues in contact with ALA 434 (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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516A LEU* 3.8 25.4 - - + +
517A GLY* 4.2 10.1 - - - +
520A LEU* 3.6 12.1 - - + +
395B HIS* 3.7 21.1 + - + -
430B ALA 2.7 20.4 + - - +
431B GLN 3.4 4.5 - - - +
433B GLU* 1.3 71.7 - - - +
435B LEU* 1.3 65.7 + - - +
437B LYS* 4.5 0.4 - - - +
438B GLY* 3.0 26.0 + - - -
467B PHE* 5.5 0.5 - - - +
469B GLY* 4.5 0.7 - - - -
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Residues in contact with LEU 435 (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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391B TYR* 5.9 0.9 - - + -
394B ILE* 3.7 32.1 - - + -
395B HIS* 3.4 31.9 - - + +
403B CYS* 5.1 1.1 - - - -
405B PHE* 3.8 20.4 - - + -
431B GLN* 2.9 20.7 + - - +
432B THR 3.5 4.2 + - - +
433B GLU 3.4 0.2 - - - -
434B ALA* 1.3 75.5 - - - +
436B MET* 1.3 57.9 + - - +
469B GLY* 3.2 7.8 - - - -
470B ASN 3.1 8.0 + - - -
471B ARG* 3.0 54.2 + - + +
473B THR* 3.7 23.1 - - + -
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Residues in contact with MET 436 (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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538A ASP* 3.7 37.2 - - + +
25B LEU* 4.0 23.2 - - + +
26B ARG* 4.0 35.2 + - + +
29B PHE* 4.1 13.2 - - + -
56B LYS* 3.8 29.2 - - + -
432B THR 3.2 9.2 + - - +
433B GLU* 3.8 7.9 - - + +
434B ALA 3.1 0.4 - - - -
435B LEU* 1.3 80.0 - - - +
437B LYS* 1.3 81.1 + - + +
470B ASN 3.5 14.1 + - - +
471B ARG 4.3 6.1 - - - +
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Residues in contact with LYS 437 (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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516A LEU* 6.0 0.9 - - + -
520A LEU* 4.7 20.6 - - + +
26B ARG* 2.9 61.3 + - + +
433B GLU* 2.9 39.5 + - + +
434B ALA* 4.2 2.7 - - - +
436B MET* 1.3 93.2 - - + +
438B GLY* 1.3 66.5 + - - +
443B GLU* 5.2 2.6 + - - -
468B GLU 5.1 1.7 - - - +
469B GLY* 4.4 2.2 - - - -
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Residues in contact with GLY 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU* 3.5 18.1 - - - +
26B ARG* 3.6 6.8 + - - -
434B ALA 3.0 12.4 + - - -
436B MET 3.8 0.6 - - - -
437B LYS* 1.3 88.6 - - - +
439B LYS* 1.3 62.6 + - - +
443B GLU* 4.1 1.0 - - - +
467B PHE* 3.2 24.9 - - - -
469B GLY* 3.8 8.9 - - - -
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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