Contacts of the helix formed by residues 469 - 493 (chain C) in PDB entry 3J8B
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 LEU 469 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433C LYS* 5.9 8.5 - - + -
467C ILE 3.5 4.0 + - - +
468C ASN* 1.3 72.7 - - - +
470C GLU* 1.3 62.0 + - - +
472C LEU* 3.2 7.7 + - - +
473C GLU* 2.9 32.1 + - + +
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Residues in contact with GLU 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ASN* 3.4 4.7 - - + +
469C LEU* 1.3 78.7 - - - +
471C LEU* 1.3 62.7 + - - +
473C GLU* 3.9 4.4 - - - +
474C CYS* 2.9 28.1 + - - +
523C MET* 6.1 4.9 - - + +
553C GLY* 5.1 14.8 - - - +
555C VAL* 4.9 6.1 - - + -
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Residues in contact with LEU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ASN* 3.8 18.5 + - + +
469C LEU 3.3 0.4 - - - -
470C GLU* 1.3 77.5 - - - +
472C LEU* 1.3 57.1 + - - +
474C CYS* 3.8 1.6 - - - +
475C VAL* 2.9 32.2 + - - +
555C VAL* 4.3 27.7 - - - +
558C LEU* 5.0 11.0 - - + -
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Residues in contact with LEU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C VAL* 6.0 5.8 - - + -
468C ASN 3.7 10.0 + - - +
469C LEU* 3.2 11.3 + - - +
471C LEU* 1.3 77.6 - - - +
473C GLU* 1.3 56.7 + - - +
475C VAL* 3.2 8.1 + - - +
476C TYR* 2.9 30.6 + - - +
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Residues in contact with GLU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C LEU* 2.9 20.5 + - + +
470C GLU* 3.9 4.5 - - - +
472C LEU* 1.3 74.3 - - - +
474C CYS* 1.3 57.6 + - - +
476C TYR* 3.4 4.8 + - - +
477C LEU* 2.9 32.0 + - - +
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Residues in contact with CYS 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C GLU 2.9 19.3 + - - +
471C LEU 3.8 2.2 - - - +
473C GLU* 1.3 75.1 - - - +
475C VAL* 1.3 58.0 + - - +
477C LEU* 3.4 5.6 + - - +
478C VAL* 2.9 31.9 + - - +
523C MET* 5.4 11.0 - - + -
555C VAL* 4.0 21.1 - - + -
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Residues in contact with VAL 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ILE* 6.3 2.9 - - - -
411C PHE* 5.3 13.7 - - + -
471C LEU 2.9 18.4 + - - +
472C LEU* 3.2 8.3 + - - +
474C CYS* 1.3 75.4 - - - +
476C TYR* 1.3 63.9 + - - +
478C VAL* 3.1 8.9 + - - +
479C SER* 3.0 21.2 + - - -
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Residues in contact with TYR 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ALA* 6.5 0.2 - - - -
420C HIS* 5.9 1.1 - - - +
423C LEU* 4.8 18.8 - - + -
427C GLN* 5.1 11.9 - - + -
472C LEU 2.9 16.3 + - - +
473C GLU* 3.9 5.8 - - - +
475C VAL* 1.3 76.6 - - - +
477C LEU* 1.3 58.1 + - - +
479C SER* 3.3 8.8 - - - -
480C ALA* 2.9 28.8 + - - +
503C GLN* 4.2 6.5 - - + +
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Residues in contact with LEU 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C GLU 2.9 18.8 + - - +
474C CYS* 3.9 5.2 - - - +
476C TYR* 1.3 73.3 - - - +
478C VAL* 1.3 62.1 + - - +
480C ALA* 3.8 7.2 - - - +
481C MET* 2.9 29.8 + - - +
503C GLN* 4.3 6.3 - - - +
504C PHE* 4.1 20.4 - - + +
524C ARG* 6.6 0.4 - - - -
527C VAL* 5.1 15.4 - - + +
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Residues in contact with VAL 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C CYS 2.9 19.4 + - - +
475C VAL* 3.1 7.8 + - - +
477C LEU* 1.3 77.2 - - - +
479C SER* 1.3 61.6 + - - +
481C MET* 3.3 7.4 - - - +
482C LEU* 3.2 22.5 + - - +
527C VAL* 5.8 3.5 - - - +
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Residues in contact with SER 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C THR* 4.6 18.7 - - - -
419C ALA* 4.9 7.4 - - - -
420C HIS* 4.4 23.6 - - - -
475C VAL 3.0 12.0 + - - -
476C TYR* 3.3 13.0 - - - -
478C VAL* 1.3 76.5 - - - +
480C ALA* 1.3 62.3 + - - -
482C LEU* 2.9 18.8 + - - +
483C LEU* 2.9 15.3 + - - +
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Residues in contact with ALA 480 (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 HIS* 5.2 5.6 - - + +
476C TYR 2.9 12.5 + - - +
477C LEU 3.9 1.1 - - - +
479C SER* 1.3 73.3 - - - +
481C MET* 1.3 53.8 + - - +
483C LEU* 3.9 6.1 - - - -
484C GLU 2.9 10.6 + - - -
501C SER 5.4 0.7 - - - +
502C LYS* 2.6 30.4 - - - +
503C GLN* 2.5 62.4 - - + +
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Residues in contact with MET 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C LEU 2.9 17.7 + - - +
478C VAL* 3.3 9.9 - - - +
480C ALA* 1.3 74.4 - - - +
482C LEU* 1.3 67.2 + - - +
485C ILE* 2.9 34.0 + - + +
502C LYS* 4.7 2.5 - - - -
503C GLN 4.5 2.0 + - - +
527C VAL* 5.9 4.7 - - + +
531C SER* 5.6 11.4 - - - -
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Residues in contact with LEU 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C THR* 5.1 11.9 - - - -
478C VAL 3.2 7.5 + - - +
479C SER* 2.9 10.6 + - - +
481C MET* 1.3 79.2 - - - +
483C LEU* 1.3 61.8 + - - +
485C ILE* 4.4 2.9 + - - +
486C PRO* 4.8 6.4 - - - +
572C LYS* 6.0 6.1 - - + +
573C ILE* 6.4 1.3 - - - -
576C GLU* 4.3 24.3 - - + +
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Residues in contact with LEU 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C THR* 6.4 1.6 - - - -
417C LYS* 6.6 0.2 - - - -
420C HIS* 5.5 8.3 - - + -
479C SER 2.9 14.6 + - - +
480C ALA* 4.1 6.5 - - - +
482C LEU* 1.3 81.5 - - - +
484C GLU* 1.3 62.2 + - + +
485C ILE 3.7 0.2 + - - -
486C PRO* 4.4 5.9 - - - +
487C TYR* 4.4 9.5 + - - +
500C ILE* 4.7 4.6 - - - +
501C SER 5.2 5.2 - - - +
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Residues in contact with GLU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C ALA 2.9 4.9 + - - -
483C LEU* 1.3 76.5 - - - +
485C ILE* 1.3 60.0 + - - +
486C PRO 3.6 0.4 - - - -
487C TYR* 3.9 1.7 - - - +
488C MET* 3.0 30.6 + - - +
500C ILE* 4.7 11.0 - - - +
501C SER* 3.5 6.3 - - - -
502C LYS* 1.8 63.3 - - + +
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Residues in contact with ILE 485 (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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481C MET* 2.9 21.3 + - + +
482C LEU* 5.0 2.2 - - - +
483C LEU 3.5 0.4 - - - -
484C GLU* 1.3 74.5 - - - +
486C PRO* 1.3 68.3 - - - +
488C MET* 3.2 7.0 + - - +
489C ALA* 2.9 24.3 + - - +
502C LYS* 4.5 0.2 - - - +
531C SER* 5.9 6.5 - - - +
534C MET* 5.3 13.7 - - + -
576C GLU* 6.4 1.6 - - + -
580C THR* 5.3 7.0 - - - -
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Residues in contact with PRO 486 (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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482C LEU 4.8 6.0 - - - +
483C LEU 4.4 4.9 - - - +
484C GLU 3.6 0.2 - - - -
485C ILE* 1.3 78.3 - - - +
487C TYR* 1.3 58.1 + - - +
489C ALA* 3.3 7.7 + - + +
490C ALA* 2.9 30.1 + - - +
576C GLU* 4.6 10.7 - - + +
579C ARG* 4.4 23.8 - - + -
580C THR* 4.6 7.8 - - - +
583C PHE* 4.5 3.0 - - + +
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Residues in contact with TYR 487 (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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483C LEU 4.4 6.3 + - - +
484C GLU 3.6 4.9 + - - +
485C ILE 3.2 0.2 - - - -
486C PRO* 1.3 76.1 - - - +
488C MET* 1.3 63.5 + - - +
490C ALA* 3.8 6.5 + - - +
491C HIS* 3.2 21.3 + - - +
498C ARG* 4.7 13.3 - - + +
500C ILE* 3.4 39.4 + - + +
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Residues in contact with MET 488 (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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484C GLU 3.0 19.5 + - - +
485C ILE* 3.4 7.4 - - - +
487C TYR* 1.3 74.9 - - - +
489C ALA* 1.3 53.3 + - - +
491C HIS* 2.9 10.9 + - - +
492C GLU* 2.7 32.9 + - - +
500C ILE 5.5 1.9 + - - -
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Residues in contact with ALA 489 (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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485C ILE 2.9 15.9 + - - +
486C PRO* 3.5 7.9 - - + +
488C MET* 1.3 77.0 - - - +
490C ALA* 1.3 51.7 + - - +
492C GLU* 2.8 14.8 + - - +
493C SER* 2.6 32.1 + - - -
535C LYS* 6.3 3.1 - - - -
580C THR* 4.1 16.4 - - - +
583C PHE* 4.0 18.5 - - + +
584C THR* 4.8 8.3 + - - +
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Residues in contact with ALA 490 (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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486C PRO 2.9 17.8 + - - +
487C TYR* 3.9 7.4 - - - +
489C ALA* 1.3 74.6 - - - +
491C HIS* 1.3 50.1 + - - +
493C SER* 2.5 17.7 - - - -
494C ASP 2.4 31.5 + - - -
495C ALA* 3.5 13.3 + - + -
496C ARG 4.8 2.9 - - - +
497C ARG 6.2 0.9 - - - +
583C PHE* 3.9 10.0 - - + +
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Residues in contact with HIS 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C TYR 3.2 11.8 + - - +
488C MET* 2.9 16.0 + - - +
490C ALA* 1.3 77.4 - - - +
492C GLU* 1.3 55.8 + - - +
494C ASP* 2.8 25.6 + - - +
496C ARG* 4.8 11.8 - - + +
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Residues in contact with GLU 492 (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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488C MET 2.7 10.0 + - - +
489C ALA* 2.9 20.0 - - - +
491C HIS* 1.3 75.8 - - - +
493C SER* 1.3 60.6 + - - +
494C ASP* 3.4 3.5 + - - +
584C THR* 6.1 4.3 - - - -
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Residues in contact with SER 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ALA 2.6 9.4 + - - -
490C ALA* 2.5 27.3 + - - -
492C GLU* 1.3 70.5 - - - +
494C ASP* 1.3 67.3 + - - +
495C ALA* 3.3 8.7 + - - -
583C PHE* 3.6 23.8 - - - -
584C THR* 5.6 2.9 - - - +
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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