Contacts of the helix formed by residues 501 - 520 (chain C) in PDB entry 1JFZ
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 ASN 501 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C LYS* 3.7 22.5 + - + -
500C ILE* 1.3 76.9 - - - +
502C GLU* 1.3 54.0 + - + +
503C THR* 2.9 40.0 + - - +
504C ILE* 2.9 32.2 + - - +
505C ILE* 2.9 41.5 + - - +
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Residues in contact with GLU 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C GLU* 3.3 23.8 - - + +
478C GLU* 5.4 5.4 - - + +
481C ASN* 2.8 59.8 + - + +
501C ASN* 1.3 74.7 - - + +
503C THR* 1.3 59.8 + - + +
505C ILE* 4.3 3.0 - - - +
506C GLY 3.1 12.5 + - - -
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Residues in contact with THR 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C GLU* 2.8 28.3 - - - +
501C ASN* 2.9 14.4 + - - +
502C GLU* 1.3 75.0 - - + +
504C ILE* 1.3 64.7 + - - +
506C GLY* 3.6 0.8 - - - +
507C ASP* 2.7 45.8 + - - +
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Residues in contact with ILE 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C HIS* 3.8 20.2 - - + +
436C TYR* 3.6 21.5 - - + +
493C ILE* 4.3 5.6 - - + -
495C ILE* 3.8 26.7 - - + -
499C LYS 4.1 10.8 - - - +
500C ILE* 3.9 20.2 - - + -
501C ASN* 2.9 29.6 - - - +
503C THR* 1.3 80.4 + - - +
505C ILE* 1.3 58.3 + - - +
507C ASP* 3.2 3.3 + - - +
508C VAL* 2.8 40.0 + - + +
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Residues in contact with ILE 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C ASN* 3.3 26.5 - - - +
484C ALA* 3.7 25.1 - - + -
489C LEU* 3.9 8.4 - - + +
490C HIS* 4.6 18.4 - - + +
493C ILE* 4.2 18.6 - - + -
500C ILE* 3.7 24.0 - - + -
501C ASN 2.9 25.7 + - - +
502C GLU* 4.0 2.9 - - - +
504C ILE* 1.3 78.4 - - - +
506C GLY* 1.3 54.8 + - - +
508C VAL* 3.5 2.3 + - - +
509C PHE* 3.0 26.7 + - - +
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Residues in contact with GLY 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C GLU* 5.4 3.8 - - - -
480C PHE* 4.3 15.1 - - - -
481C ASN* 4.2 7.2 - - - +
502C GLU 3.1 15.5 + - - -
503C THR* 3.6 4.7 - - - -
504C ILE 3.2 0.2 - - - -
505C ILE* 1.3 75.7 - - - +
507C ASP* 1.3 66.4 + - - +
509C PHE* 3.2 15.8 + - - +
510C GLU* 3.3 21.6 + - - +
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Residues in contact with ASP 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C TYR* 3.8 20.1 + - + +
440C GLU* 3.0 29.0 - - - +
503C THR* 2.7 34.2 + - - +
504C ILE* 3.2 4.1 + - - +
506C GLY* 1.3 73.6 - - - +
508C VAL* 1.3 62.9 + - - +
510C GLU* 3.4 10.4 + - - +
511C ALA* 3.3 21.7 + - - +
763C MN 2.5 25.1 + - - -
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Residues in contact with VAL 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ALA 3.2 17.7 - - - +
425C LEU* 3.7 25.1 - - + +
436C TYR* 3.4 31.0 - - + -
489C LEU* 4.0 13.7 - - + -
493C ILE* 3.7 25.8 - - + -
504C ILE* 2.8 23.7 + - + +
505C ILE 3.8 4.0 - - - +
507C ASP* 1.3 75.9 - - - +
509C PHE* 1.3 56.8 + - - +
511C ALA* 3.9 3.1 - - - +
512C LEU* 3.1 25.6 + - - +
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Residues in contact with PHE 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C VAL* 4.5 5.4 - - + -
480C PHE* 4.0 28.9 - + + +
483C LEU* 3.7 28.9 - - + -
484C ALA* 3.6 35.7 - - + -
487C LEU* 5.0 4.9 - - + -
489C LEU* 3.7 11.9 - - + -
505C ILE 3.0 15.1 + - - +
506C GLY* 3.3 13.0 - - - +
507C ASP 3.1 0.2 - - - -
508C VAL* 1.3 76.2 - - - +
510C GLU* 1.3 68.5 + - - +
512C LEU* 3.3 11.8 + - + +
513C TRP* 3.2 52.0 + + - -
531C PHE* 4.0 12.1 - + - -
535C PHE* 3.8 17.0 - + - -
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Residues in contact with GLU 510 (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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440C GLU* 3.0 16.1 - - - +
443C GLY* 2.9 43.4 - - - +
444C ASP* 3.8 15.7 - - - +
447C VAL* 4.4 6.5 - - + -
480C PHE* 3.6 32.0 - - + -
506C GLY 3.3 13.0 + - - +
507C ASP* 3.7 4.8 - - - +
509C PHE* 1.3 79.3 - - - +
511C ALA* 1.3 59.5 + - - +
513C TRP* 3.2 4.9 + - - +
514C ALA 3.1 8.8 + - - -
763C MN 2.5 33.6 + - - -
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Residues in contact with ALA 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ALA* 3.3 25.8 - - + +
436C TYR* 3.9 14.1 - - + -
439C LEU* 3.4 17.7 + - + +
440C GLU 3.7 16.6 - - - +
507C ASP 3.3 14.3 + - - +
508C VAL 3.9 3.4 - - - +
510C GLU* 1.3 76.8 - - - +
512C LEU* 1.3 60.2 + - - +
514C ALA* 3.2 2.3 + - - +
515C ALA* 2.9 24.6 + - - +
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Residues in contact with LEU 512 (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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407C LEU* 4.3 9.6 - - + -
411C LEU* 4.2 22.4 - - + -
415C PHE* 4.6 1.6 - - + -
421C LEU* 3.5 31.6 - - + -
424C ALA* 3.7 8.9 - - + +
425C LEU* 5.3 2.5 - - + -
487C LEU* 3.9 27.6 - - + -
489C LEU* 4.1 22.2 - - + -
508C VAL* 3.1 18.8 + - + +
509C PHE* 3.5 7.4 - - + +
510C GLU 3.3 0.4 - - - -
511C ALA* 1.3 76.6 - - - +
513C TRP* 1.3 66.4 + - + +
515C ALA* 3.3 3.2 + - + +
516C VAL* 2.9 38.5 + - + +
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Residues in contact with TRP 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C LEU* 3.9 21.3 - - + -
446C LEU* 3.6 19.4 - - + +
447C VAL* 4.0 7.9 - - + -
450C PHE* 4.6 0.7 - + + -
487C LEU* 5.2 0.6 - - + +
509C PHE* 3.2 56.1 + + - -
510C GLU 3.2 7.7 + - - +
511C ALA 3.1 0.4 - - - -
512C LEU* 1.3 82.7 - - + +
514C ALA* 1.3 55.4 + - - +
515C ALA 3.1 1.1 - - - -
516C VAL* 3.7 15.2 - - + +
517C TYR* 2.6 36.4 + - - +
527C THR* 3.5 39.0 - - + +
530C LEU* 4.0 12.6 - - + -
531C PHE* 3.4 42.5 - + - -
534C LEU* 3.8 13.0 - - + -
535C PHE* 3.7 15.3 - + - -
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Residues in contact with ALA 514 (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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439C LEU* 3.0 37.2 - - + +
442C LEU* 3.9 17.0 - - + -
443C GLY* 3.4 15.8 - - - +
446C LEU* 4.6 1.6 - - - -
510C GLU 3.1 6.1 + - - -
511C ALA 3.5 4.7 - - - +
513C TRP* 1.3 76.4 - - - +
515C ALA* 1.3 52.5 + - - +
517C TYR* 3.3 7.7 - - - +
518C ILE* 2.8 40.6 + - - +
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Residues in contact with ALA 515 (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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415C PHE* 3.8 19.7 - - + -
420C LEU* 3.5 29.4 - - + +
421C LEU* 4.8 0.9 - - - -
424C ALA* 4.2 7.0 - - + -
439C LEU* 4.5 6.9 - - + +
511C ALA 2.9 12.8 + - - +
512C LEU* 3.4 10.5 - - + +
514C ALA* 1.3 75.1 - - - +
516C VAL* 1.3 57.4 + - - +
518C ILE 4.3 0.2 - - - +
519C ASP* 2.7 38.1 + - - +
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Residues in contact with VAL 516 (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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411C LEU* 3.7 30.3 - - + -
413C TYR* 4.2 11.4 - - + -
415C PHE* 3.7 15.7 - - + -
512C LEU* 2.9 23.5 + - + +
513C TRP* 3.8 17.7 - - + +
515C ALA* 1.3 73.9 - - - +
517C TYR* 1.3 62.1 + - - +
519C ASP* 4.0 2.1 - - - +
520C SER* 2.8 29.6 + - - -
526C PHE* 4.6 5.8 - - + -
527C THR* 4.0 15.7 - - + +
530C LEU* 3.9 24.9 - - + -
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Residues in contact with TYR 517 (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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442C LEU* 4.0 19.5 - - + -
446C LEU* 4.1 19.5 - - + -
513C TRP 2.6 22.5 + - - +
514C ALA* 3.3 5.6 - - - +
516C VAL* 1.3 75.2 - - - +
518C ILE* 1.3 67.0 + - + +
520C SER* 3.2 5.7 + - - -
522C ARG* 3.0 59.0 + - + +
523C ASP 3.9 9.0 - - - -
524C ALA* 3.6 16.6 - - + -
527C THR* 3.3 11.3 + - - +
649D PHE* 3.6 16.2 - + - -
653D ASP* 2.8 39.8 + - - -
728D ARG* 2.7 26.8 + - - -
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Residues in contact with ILE 518 (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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420C LEU* 4.1 18.8 - - + -
439C LEU* 3.8 26.5 - - + -
442C LEU* 4.1 12.3 - - + -
514C ALA 2.8 22.4 + - - +
515C ALA* 4.0 2.2 - - - +
517C TYR* 1.3 75.6 - - + +
519C ASP* 1.3 67.7 + - - +
521C GLY* 3.0 14.0 + - - -
522C ARG* 3.3 52.0 + - + +
656D VAL* 5.9 3.4 - - + -
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Residues in contact with ASP 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C TYR* 2.6 22.6 + - + +
415C PHE* 3.3 20.8 - - + -
416C LYS* 2.6 44.6 + - - +
417C ASP* 2.9 34.0 + - - +
420C LEU* 3.4 11.1 - - + +
515C ALA 2.7 21.7 + - - +
516C VAL 4.0 1.8 - - - +
518C ILE* 1.3 73.6 - - - +
520C SER* 1.3 56.6 + - - +
521C GLY* 3.0 6.2 + - - -
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Residues in contact with SER 520 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C TYR* 3.5 13.5 - - - -
416C LYS* 3.4 18.8 + - - +
516C VAL 2.8 21.3 + - - -
517C TYR 3.2 7.1 + - - -
518C ILE 3.1 0.4 + - - -
519C ASP* 1.3 74.7 - - - +
521C GLY* 1.3 54.9 + - - +
523C ASP* 3.3 24.4 - - - +
526C PHE* 4.0 21.0 - - - -
527C THR* 3.4 12.8 + - - -
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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