Contacts of the helix formed by residues 479 - 494 (chain C) in PDB entry 1Z6T
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 ASP 479 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C PRO* 4.2 8.1 - - + -
398C LYS* 3.5 22.8 - - + +
399C VAL* 3.8 17.9 - - + -
402C ILE* 3.2 12.5 - - - +
468C HIS* 2.9 24.4 + - - -
477C GLN* 3.7 20.6 - - - +
478C GLU* 1.3 73.1 + - - +
480C CYS* 1.3 64.7 + - - +
481C MET 3.4 2.9 - - - -
482C TYR* 3.2 7.0 + - - +
483C TRP* 3.0 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C LEU* 4.4 5.7 - - - +
474C SER 3.4 36.1 - - - +
475C PRO* 3.7 6.1 - - + +
477C GLN* 3.2 23.0 + - + +
478C GLU 3.4 0.6 - - - -
479C ASP* 1.3 80.2 + - - +
481C MET* 1.3 81.6 + - + +
483C TRP* 3.2 9.5 + - - +
484C TYR* 3.1 44.8 + - - -
516C LEU* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LEU* 5.9 2.9 - - - -
475C PRO* 4.8 8.7 - - + -
477C GLN 5.0 0.2 + - - -
478C GLU 5.0 2.3 + - - +
479C ASP 3.4 0.4 - - - -
480C CYS* 1.3 110.2 - - + +
482C TYR* 1.3 60.3 + - - +
483C TRP 3.2 0.2 - - - -
484C TYR* 3.5 18.6 - - + +
485C ASN* 2.9 48.9 + - - +
516C LEU* 3.6 17.9 - - + -
517C VAL* 4.7 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ILE 5.0 1.6 + - - -
389C LEU* 5.3 5.4 - - - +
390C GLN* 4.0 6.6 + - - -
393C VAL* 4.0 9.4 - - + -
394C LYS 5.5 0.7 - - - -
395C VAL* 3.6 31.9 - - + +
396C PRO* 4.6 10.8 - - + -
399C VAL* 3.8 35.7 - - + +
460C ILE* 4.5 3.2 - - + +
478C GLU 5.5 0.6 + - - -
479C ASP* 3.2 14.6 + - - +
481C MET* 1.3 78.4 - - - +
483C TRP* 1.3 81.8 + + - +
485C ASN* 4.8 0.7 - - - +
486C PHE* 2.9 55.6 + + + +
490C HIS* 2.7 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C VAL* 4.3 14.8 - - + -
402C ILE* 4.1 20.4 - - + -
460C ILE* 3.8 35.0 - - + -
461C ILE* 5.5 1.1 - - + -
464C PHE* 3.5 43.5 - + + -
468C HIS* 3.8 10.5 - + - -
473C LEU* 4.0 22.7 - - + -
479C ASP* 3.0 49.9 + - - +
480C CYS 3.2 4.9 + - - +
482C TYR* 1.3 97.3 - + - +
484C TYR* 1.3 61.9 + - - +
487C LEU* 2.8 52.8 + - + +
490C HIS* 4.6 7.4 - + - -
509C TRP* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C PRO 4.4 3.1 + - - -
473C LEU* 3.8 31.9 + - + +
474C SER* 5.6 0.2 - - - -
480C CYS* 3.1 47.2 + - - +
481C MET* 3.5 17.9 - - + +
483C TRP* 1.3 76.1 - - - +
485C ASN* 1.3 60.5 + - - +
487C LEU* 4.7 0.9 + - - +
488C ALA 5.6 0.2 + - - -
509C TRP* 3.4 38.5 - + - -
512C ALA* 3.5 19.9 + - + +
513C LYS* 2.6 67.1 + - + +
516C LEU* 3.5 19.1 - - + +
517C VAL* 5.9 4.5 - - + -
525C GLU* 4.2 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C MET* 3.6 33.7 - - - +
481C MET* 2.9 37.5 + - - +
482C TYR* 4.8 0.4 - - - +
484C TYR* 1.3 83.0 - - - +
486C PHE* 1.3 87.2 + - + +
489C TYR* 4.8 2.6 - - - +
513C LYS* 5.0 1.6 + - - -
517C VAL* 5.2 10.6 - - - +
521C HIS* 3.1 28.5 + - - -
525C GLU* 3.7 6.0 - - - +
529C TYR* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C MET* 4.5 18.8 - - + -
390C GLN* 3.4 31.6 - - - +
393C VAL* 3.7 35.7 - - + -
482C TYR* 2.9 53.8 + + + +
483C TRP* 4.9 0.9 - - - -
485C ASN* 1.3 106.6 - - + +
487C LEU* 1.3 68.7 + - - +
488C ALA 3.3 2.2 - - - -
489C TYR* 3.2 12.3 + - + -
490C HIS* 3.0 29.1 + - + -
521C HIS* 5.7 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ILE* 3.6 24.3 - - + +
464C PHE* 3.6 44.2 - - + -
470C PRO* 4.5 5.2 - - + -
473C LEU* 5.1 0.9 - - + -
482C TYR 4.2 0.2 + - - -
483C TRP* 2.8 37.0 + - + +
484C TYR 4.7 0.6 + - - +
486C PHE* 1.3 77.5 - - - +
488C ALA* 1.3 62.1 + - - +
490C HIS* 3.3 1.0 + - - -
491C MET* 3.1 41.6 + - + +
503C LEU* 3.9 31.2 - - + -
509C TRP* 4.5 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C TYR 5.6 0.6 + - - -
486C PHE 3.3 0.4 - - - -
487C LEU* 1.3 76.0 - - - +
489C TYR* 1.3 61.3 + - - +
491C MET* 3.3 1.8 + - - -
492C ALA* 2.9 32.6 + - - +
500C LEU* 3.7 19.9 - - + +
503C LEU* 4.0 11.8 - - + +
504C MET* 4.1 10.1 - - + -
509C TRP* 6.2 1.5 - - + +
525C GLU* 3.4 26.4 + - - +
529C TYR* 3.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ILE 4.8 0.7 + - - -
390C GLN* 3.6 48.3 - - + +
457C HIS* 3.8 28.3 + + - -
485C ASN 4.8 0.7 - - - +
486C PHE* 3.2 21.7 + + + +
488C ALA* 1.3 79.6 - - - +
490C HIS* 1.3 67.1 + + - +
492C ALA* 3.8 1.2 - - - +
493C SER* 2.7 51.0 + - - -
525C GLU* 4.6 0.6 + - - -
529C TYR* 3.2 33.4 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ILE* 3.7 36.6 - - + -
390C GLN* 4.4 0.4 + - - -
457C HIS* 2.9 33.7 + + - +
460C ILE* 3.6 20.8 - - + +
461C ILE* 3.7 20.0 - - + -
482C TYR* 2.7 39.5 + + - -
483C TRP* 4.6 5.2 - + - -
486C PHE* 3.0 28.4 + - + +
489C TYR* 1.3 87.0 - + - +
491C MET* 1.3 58.5 + - - +
494C ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ILE* 3.5 28.9 - - + -
464C PHE* 5.8 2.7 - - + -
465C GLN* 4.7 5.8 - - + +
470C PRO* 5.9 2.7 - - + -
487C LEU* 3.1 37.3 + - + +
488C ALA 3.7 3.6 - - - +
490C HIS* 1.3 74.4 - - - +
492C ALA* 1.3 59.1 + - - +
494C ALA* 3.4 3.4 + - - -
495C LYS 3.2 2.6 + - - -
496C MET* 2.8 42.7 + - + +
499C GLU* 3.6 43.7 - - + +
500C LEU* 3.7 13.0 - - + -
503C LEU* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C ALA 2.9 17.5 + - - +
489C TYR 3.8 2.5 - - - +
491C MET* 1.3 73.4 - - - +
493C SER* 1.3 60.7 + - - +
495C LYS* 3.0 29.5 + - - +
500C LEU* 4.4 4.2 - - + +
529C TYR* 3.6 39.9 - - + -
531C HIS* 6.3 0.2 - - - +
532C ILE* 3.9 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C GLN* 4.0 16.1 - - - +
457C HIS* 3.4 34.3 - - - -
489C TYR* 2.7 43.9 + - - -
490C HIS 3.8 0.2 - - - -
492C ALA* 1.3 77.7 - - - +
494C ALA* 1.3 58.2 + - - +
495C LYS* 3.2 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 494 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C GLN* 3.5 26.5 + - - +
457C HIS* 3.7 1.1 - - - +
458C LYS* 3.3 39.2 - - + +
490C HIS 2.9 19.0 + - - +
491C MET 3.4 0.9 + - - +
492C ALA 3.2 0.6 - - - -
493C SER* 1.3 73.9 - - - +
495C LYS* 1.3 67.4 + - - +
496C MET* 3.3 21.8 + - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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