Contacts of the helix formed by residues 507 - 532 (chain A) in PDB entry 4RIB
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 ARG 507 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A LEU* 3.1 47.2 - - - +
503A LEU* 3.0 13.4 + - - +
504A ALA 3.7 2.5 - - - -
506A GLN* 1.3 106.4 - - + +
508A SER* 1.3 52.5 + - - +
509A VAL* 3.2 3.8 - - - -
519A ILE* 2.7 68.9 + - + +
520A GLY 3.2 1.2 + - - -
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Residues in contact with SER 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ALA 3.0 20.2 + - - -
505A LYS 5.4 2.7 - - - -
506A GLN 3.4 5.6 + - - -
507A ARG* 1.3 73.2 - - - +
509A VAL* 1.3 65.4 + - - +
520A GLY* 2.8 11.5 + - - +
521A ALA* 3.0 13.2 + - - +
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Residues in contact with VAL 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ARG 3.1 1.3 + - - +
508A SER* 1.3 78.8 + - - +
519A ILE* 1.3 62.7 + - - +
521A ALA* 3.3 16.2 + - - +
522A VAL* 3.2 16.1 - - + +
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Residues in contact with ILE 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PHE* 4.6 20.0 - - + -
486A LEU* 4.6 9.2 - - + -
503A LEU* 4.2 20.9 - - + +
507A ARG* 2.7 71.7 + - + +
509A VAL* 1.3 75.0 - - + +
520A GLY* 1.3 63.1 + - - +
522A VAL* 3.0 22.3 + - + +
523A ILE* 3.1 19.3 + - + +
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Residues in contact with GLY 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 4.8 4.4 - - - +
504A ALA* 3.5 29.2 - - - -
507A ARG 3.2 6.3 + - - -
508A SER 2.8 9.1 + - - -
519A ILE* 1.3 77.7 - - - +
521A ALA* 1.3 55.5 + - - +
523A ILE* 3.1 11.6 + - - +
524A LEU* 2.9 30.7 + - - +
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Residues in contact with ALA 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A SER 3.0 9.0 + - - +
509A VAL* 3.3 14.8 - - - +
520A GLY* 1.3 77.0 - - - +
522A VAL* 1.3 56.4 + - + +
524A LEU* 3.5 12.7 + - + +
525A LYS* 2.9 28.6 + - - +
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Residues in contact with VAL 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PHE* 4.2 15.4 - - + -
509A VAL* 3.2 22.7 - - + +
519A ILE* 3.0 18.6 + - + +
521A ALA* 1.3 74.8 - - + +
523A ILE* 1.3 58.0 + - - +
525A LYS* 3.4 13.6 - - + +
526A ARG* 3.1 33.9 + - - +
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Residues in contact with ILE 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 4.9 11.0 - - + -
469A LEU* 5.5 1.1 - - + -
480A LEU* 3.8 18.4 - - + -
484A PHE* 3.4 28.9 - - + -
500A PHE* 3.7 33.7 - - + +
503A LEU* 3.8 30.7 - - + -
504A ALA* 5.1 5.2 - - + -
519A ILE* 3.1 20.2 - - + +
520A GLY* 3.1 14.1 + - - +
522A VAL* 1.3 72.8 - - - +
524A LEU* 1.3 57.8 + - - +
526A ARG* 3.1 1.7 + - - +
527A ALA* 2.8 37.1 + - + +
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU 4.6 0.7 - - - +
463A GLN* 3.1 32.3 - - - +
465A LEU* 4.1 24.1 - - + +
468A VAL* 3.6 30.1 - - + -
520A GLY 2.9 16.4 + - - +
521A ALA* 3.6 11.4 - - - +
523A ILE* 1.3 76.7 - - - +
525A LYS* 1.3 63.0 + - - +
527A ALA* 3.3 2.8 + - - +
528A LYS* 3.1 47.1 + - + +
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Residues in contact with LYS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ALA 2.9 18.5 + - - +
522A VAL* 3.4 14.4 - - + +
524A LEU* 1.3 78.7 - - - +
526A ARG* 1.3 75.2 + - - +
528A LYS* 3.7 9.0 + - - +
529A ALA* 3.5 26.1 + - - +
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Residues in contact with ARG 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 4.2 13.9 - - + -
483A THR* 4.1 26.1 + - - -
484A PHE* 3.6 32.3 - - + -
522A VAL* 3.1 18.9 + - - +
523A ILE 3.1 5.1 + - - +
525A LYS* 1.3 90.7 - - - +
527A ALA* 1.3 61.5 + - - +
529A ALA* 3.2 8.8 + - + +
530A LEU* 2.9 30.0 + - + +
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Residues in contact with ALA 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A LEU* 5.5 0.9 - - + -
468A VAL* 3.7 21.5 - - + -
469A LEU* 5.2 4.9 - - + -
472A LEU* 4.2 17.1 - - + +
480A LEU* 4.1 17.2 - - + +
523A ILE* 2.8 21.7 + - + +
524A LEU* 3.7 4.3 - - - +
526A ARG* 1.3 72.0 - - - +
528A LYS* 1.3 51.0 + - - +
530A LEU* 2.8 11.8 + - - +
531A ALA* 2.7 35.7 + - - +
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Residues in contact with LYS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLU* 2.9 39.6 + - + +
460A SER* 4.0 4.8 + - - +
462A LEU* 3.2 27.2 + - + +
463A GLN* 3.9 10.1 + - - +
468A VAL* 3.7 15.2 - - + +
524A LEU* 3.1 35.6 + - + +
525A LYS* 3.8 7.2 - - - +
527A ALA* 1.3 74.6 - - - +
529A ALA* 1.3 63.7 + - - +
531A ALA* 3.3 4.0 + - - +
532A GLY* 3.0 26.7 + - - +
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Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LYS* 3.5 21.5 + - - +
526A ARG* 3.2 12.9 + - + +
528A LYS* 1.3 77.7 - - - +
530A LEU* 1.3 63.4 + - - +
532A GLY* 3.2 14.4 + - - -
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Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 4.2 5.8 - - + -
476A GLU* 3.8 50.6 - - + +
479A SER* 4.2 16.6 - - - +
480A LEU* 4.3 20.4 - - + +
526A ARG* 2.9 15.0 + - + +
527A ALA* 2.8 15.3 + - - +
529A ALA* 1.3 74.1 - - - +
531A ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LYS* 3.7 26.4 - - - +
462A LEU* 5.9 0.7 - - + -
468A VAL* 5.0 3.6 - - + -
471A LEU* 4.2 27.4 - - + -
472A LEU* 3.8 22.0 - - + +
527A ALA 2.7 18.5 + - - +
528A LYS* 3.8 7.0 - - - +
529A ALA 3.2 0.2 - - - -
530A LEU* 1.3 74.3 - - - +
532A GLY* 1.3 63.1 + - - +
533A GLN 4.1 0.7 + - - +
534A SER* 4.6 0.4 + - - -
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Residues in contact with GLY 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLU* 4.2 13.4 - - - +
528A LYS 3.0 15.7 + - - +
529A ALA* 3.2 11.3 + - - -
531A ALA* 1.3 81.3 - - - +
533A GLN* 1.3 65.4 + - - -
534A SER* 3.7 5.4 + - - -
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Residues in contact with GLN 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A LYS* 3.7 2.4 - - - +
431A MET* 3.0 58.9 + - + +
432A THR* 5.8 1.2 - - + +
444A THR* 5.3 2.3 + - - +
459A GLU* 3.5 21.5 + - - +
531A ALA 4.1 1.4 + - - +
532A GLY* 1.3 67.5 - - - -
534A SER* 1.3 69.0 + - - +
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Residues in contact with SER 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A TRP* 4.2 11.9 - - - -
429A ILE 3.3 14.5 + - - -
430A LYS* 3.9 7.3 - - - +
431A MET* 3.7 4.3 - - - +
458A THR* 3.4 6.2 + - - -
459A GLU* 2.7 39.7 + - - +
462A LEU* 5.5 0.7 - - - -
471A LEU* 3.6 28.5 - - - +
531A ALA 4.6 0.5 + - - -
532A GLY 3.7 8.5 + - - -
533A GLN* 1.3 81.9 + - - +
535A VAL* 1.3 68.5 + - - +
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Residues in contact with VAL 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 4.8 7.0 - - + -
428A TRP* 3.3 6.2 - - - -
429A ILE* 2.8 45.3 + - + +
431A MET* 3.8 24.0 - - + -
434A LEU* 3.8 23.1 - - + -
447A ILE* 4.2 21.3 - - + -
456A LEU* 3.9 19.1 - - + -
457A GLN 3.2 11.7 - - - +
458A THR* 4.7 3.1 - - - +
534A SER* 1.3 79.7 - - - +
536A ARG* 1.3 65.4 + - - +
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Residues in contact with ARG 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 6.4 0.2 - - - -
426A LEU* 3.9 15.5 - - + +
427A SER* 3.6 34.0 - - - +
428A TRP* 3.0 44.8 - - + +
429A ILE* 5.5 1.6 - - - -
456A LEU* 3.6 5.1 - - - -
457A GLN* 2.7 58.5 + - + +
461A GLU 5.6 1.0 + - - -
467A GLU* 3.1 21.8 + - - +
535A VAL* 1.3 80.7 - - - +
537A ILE* 1.3 76.3 + - - +
539A LYS* 6.4 0.2 - - - +
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Residues in contact with ILE 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A TYR* 3.5 43.7 - - + +
421A LEU* 3.7 34.7 - - + +
422A PHE* 3.8 15.3 - - - +
426A LEU* 3.6 41.3 - - + +
427A SER 5.1 1.0 + - - +
429A ILE* 5.9 1.8 - - - +
455A PHE 4.1 3.1 - - - +
456A LEU* 4.3 10.8 - - + +
457A GLN* 4.9 0.9 - - - -
536A ARG* 1.3 90.0 + - - +
538A CYS* 1.3 65.4 + - - +
539A LYS* 3.5 2.9 + - - +
542A ARG* 4.3 19.1 - - + +
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Residues in contact with CYS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A TYR* 4.8 0.2 + - - -
454A GLY* 4.3 6.5 - - - -
455A PHE 2.9 20.5 + - - +
456A LEU 3.3 28.7 - - - -
457A GLN* 3.2 30.5 - - - +
461A GLU* 5.5 0.7 - - - -
537A ILE* 1.3 73.2 - - - +
539A LYS* 1.3 60.5 + - - +
540A GLY 3.2 0.8 + - - +
541A PRO* 3.3 20.2 - - + +
542A ARG* 3.1 29.0 + - - +
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Residues in contact with LYS 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 4.7 18.2 - - + -
457A GLN* 5.5 1.0 - - - +
536A ARG* 6.4 0.4 - - - +
537A ILE 3.5 5.1 + - - +
538A CYS* 1.3 68.9 - - - +
540A GLY* 1.3 70.6 + - - +
542A ARG* 4.0 9.0 - - - +
543A ALA* 3.3 20.3 + - - +
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Residues in contact with GLY 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE* 5.6 1.8 - - - -
538A CYS* 4.5 0.4 - - - +
539A LYS* 1.3 87.7 - - - +
541A PRO* 1.4 73.1 - - - +
543A ALA* 3.3 14.4 + - - +
544A VAL* 3.6 8.5 - - - +
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Residues in contact with PRO 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE* 4.0 14.7 - - + +
418A TYR* 4.1 4.9 - - - +
454A GLY 3.4 24.9 - - - +
455A PHE* 3.6 31.0 - - + -
538A CYS* 3.3 22.9 - - + +
540A GLY* 1.4 87.6 - - - +
542A ARG* 1.3 63.8 + - - +
544A VAL* 2.9 27.6 + - + +
545A PHE* 3.6 8.2 + - - -
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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