Contacts of the helix formed by residues 506 - 524 (chain A) in PDB entry 5DO7
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 506 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ASN* 4.5 0.3 + - - -
426A PHE* 3.9 26.5 - - + -
427A VAL* 4.5 1.1 - - + +
430A THR* 3.9 26.4 - - + +
479A THR* 3.3 18.6 - - + +
482A PHE* 3.6 28.9 - - + -
502A PHE* 3.4 38.0 + - + +
503A SER 4.1 0.4 + - - -
505A ALA* 1.3 79.0 - - - +
507A LEU* 1.3 61.4 + - - +
508A ALA 3.4 0.9 - - - -
509A PRO* 3.7 5.2 - - + -
510A HIS* 3.7 16.1 + - - +
571A CYS* 4.6 4.5 - - - -
575A LEU* 3.7 26.5 - - + -
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Residues in contact with LEU 507 (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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472A LEU* 5.2 1.6 - - + +
475A SER* 3.9 5.4 - - - -
476A VAL* 3.6 43.3 - - + +
479A THR* 3.3 24.0 - - + +
503A SER 3.7 13.4 + - - +
504A ALA* 3.5 1.7 + - - -
505A ALA 3.4 0.4 - - - -
506A LEU* 1.3 79.4 - - - +
508A ALA* 1.3 68.8 + - - +
510A HIS* 3.5 2.1 + - + +
511A LEU* 3.2 39.6 + - + +
628A TYR* 3.6 22.2 - - + +
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Residues in contact with ALA 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ALA 3.7 2.6 + - - +
507A LEU* 1.3 77.1 - - - +
509A PRO* 1.3 75.7 - - + +
511A LEU* 2.8 9.8 + - - +
512A ILE* 2.8 25.9 + - + +
627A LEU* 3.7 34.8 - - + +
628A TYR* 3.8 29.8 - - + -
631A ILE* 5.0 2.2 - - + -
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Residues in contact with PRO 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 4.8 2.7 - - + +
430A THR* 3.3 26.7 - - - +
431A PRO* 3.6 18.7 - - + +
505A ALA 2.9 28.7 - - - +
506A LEU* 3.7 8.1 - - + -
508A ALA* 1.3 85.8 - - + +
510A HIS* 1.3 52.0 + - - +
512A ILE* 2.8 17.1 + - + +
513A GLY 2.8 30.8 + - - -
567A PHE* 4.5 10.8 - - + -
571A CYS* 4.1 19.5 - - + -
627A LEU* 4.7 1.8 - - + -
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Residues in contact with HIS 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG 4.3 4.8 + - - -
392A GLN* 4.3 8.7 - - - -
393A ASN* 3.2 29.6 + - + +
430A THR* 2.6 18.1 + - - +
431A PRO* 4.5 0.4 - - - -
433A THR* 2.6 38.2 + - - -
434A GLY* 3.6 13.1 - - - -
437A ASN* 3.5 17.0 + - - -
475A SER* 2.9 35.4 + - - -
478A ALA* 4.6 2.2 - - + -
479A THR* 4.7 3.6 - - - +
506A LEU 3.7 17.6 + - - +
507A LEU* 3.5 7.1 + - - +
508A ALA 3.3 0.6 - - - -
509A PRO* 1.3 74.9 - - - +
511A LEU* 1.3 57.5 + - - +
513A GLY 4.4 1.1 - - - -
514A GLU* 3.8 6.4 - - - +
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Residues in contact with LEU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A VAL* 4.1 13.0 - - + -
472A LEU* 4.4 22.0 - - + -
475A SER* 4.0 21.5 - - - -
507A LEU* 3.2 38.3 + - + +
508A ALA* 2.8 11.0 + - - +
510A HIS* 1.3 71.0 - - - +
512A ILE* 1.3 66.7 - - - +
513A GLY 3.1 1.6 - - - -
514A GLU* 2.8 6.1 + - + +
515A PHE* 2.8 55.5 + - + -
628A TYR* 5.1 1.3 - - + -
631A ILE* 3.9 26.0 - - + -
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Residues in contact with ILE 512 (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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508A ALA 2.8 20.9 + - - +
509A PRO* 3.3 7.4 - - + +
511A LEU* 1.3 75.1 - - - +
513A GLY* 1.3 57.7 + - - +
515A PHE* 4.6 0.7 - - - +
516A LEU* 2.8 40.3 + - + +
567A PHE* 3.6 61.2 - - + -
627A LEU* 4.0 20.4 - - + +
630A PHE* 4.1 4.9 - - + -
631A ILE* 3.3 21.8 - - + -
634A LEU* 3.9 24.3 - - + +
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Residues in contact with GLY 513 (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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431A PRO* 3.5 29.3 - - - +
434A GLY* 4.2 0.4 - - - -
435A MET 3.9 4.0 - - - -
509A PRO 2.8 12.0 + - - -
512A ILE* 1.3 76.0 - - - +
514A GLU* 1.3 59.4 + - - +
516A LEU* 3.8 4.2 - - - +
517A THR* 2.4 39.4 + - - -
534A VAL* 5.2 5.2 - - - -
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Residues in contact with GLU 514 (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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389A ARG* 3.1 11.7 + - - -
434A GLY* 3.1 27.7 - - - +
437A ASN* 3.0 37.6 + - - +
438A ALA* 3.2 6.3 + - + +
467A TYR* 2.3 42.2 + - + +
471A VAL* 3.8 19.3 - - + +
510A HIS 3.8 7.6 - - - +
511A LEU* 2.8 20.1 + - - +
513A GLY* 1.3 71.6 - - - +
515A PHE* 1.3 64.0 + - + +
517A THR* 3.4 3.1 - - - -
518A LEU* 2.8 27.1 + - - +
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Residues in contact with PHE 515 (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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468A ALA* 3.4 50.5 - - + -
471A VAL* 3.5 17.3 - - + -
472A LEU* 4.9 7.9 - - + -
511A LEU* 2.8 51.5 + - + +
512A ILE* 4.3 1.1 - - - +
514A GLU* 1.3 74.2 - - + +
516A LEU* 1.3 61.1 + - - +
518A LEU* 3.1 11.4 - - + +
519A VAL* 2.8 32.2 + - - +
631A ILE* 4.1 32.3 - - + -
634A LEU* 3.9 18.8 - - + -
635A VAL* 4.5 11.9 - - + +
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Residues in contact with LEU 516 (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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512A ILE* 2.8 28.5 + - + +
513A GLY* 3.8 3.1 - - - +
515A PHE* 1.3 69.6 - - - +
517A THR* 1.3 66.7 + - - +
519A VAL* 2.8 18.0 + - + +
520A LEU* 2.8 40.8 + - + +
534A VAL* 4.1 17.7 - - + -
537A LEU* 3.8 29.8 - - + -
538A SER* 6.2 1.3 - - - -
567A PHE* 6.1 3.8 - - + -
634A LEU* 3.4 24.7 - - + +
565C PHE* 4.9 12.8 - - + -
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Residues in contact with THR 517 (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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435A MET* 3.0 30.6 - - + +
438A ALA* 3.6 21.1 - - + -
439A VAL* 3.9 4.9 - - + +
513A GLY 2.4 29.2 + - - -
514A GLU 3.4 4.3 - - - -
516A LEU* 1.3 73.3 - - - +
518A LEU* 1.3 57.1 + - - +
520A LEU* 3.4 3.0 + - - +
521A LEU* 2.8 47.4 + - + +
530A VAL* 3.7 14.8 - - + -
534A VAL* 3.6 17.4 - - + +
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Residues in contact with LEU 518 (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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438A ALA* 4.6 1.7 - - + +
442A PHE* 3.6 28.5 - - + -
464A MET* 3.4 44.4 - - + +
467A TYR* 3.1 35.9 - - + -
468A ALA* 3.8 15.5 - - + -
514A GLU 2.8 13.1 + - - +
515A PHE* 3.1 19.1 - - + +
517A THR* 1.3 72.7 - - - +
519A VAL* 1.3 70.7 + - + +
521A LEU* 2.7 18.5 + - - +
522A GLY 3.2 6.6 + - - -
635A VAL* 5.4 1.8 - - + -
642A PHE* 3.9 5.6 - - - -
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Residues in contact with VAL 519 (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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464A MET* 5.6 0.6 - - + +
515A PHE 2.8 17.9 + - - +
516A LEU* 2.8 15.0 + - + +
518A LEU* 1.3 73.6 - - + +
520A LEU* 1.3 75.3 + - + +
522A GLY* 2.8 14.0 + - - -
523A ILE* 3.5 10.0 + - + +
634A LEU* 3.0 32.3 - - + +
635A VAL* 5.1 0.4 - - - -
637A LEU* 3.8 27.8 - - + -
638A GLY* 3.6 18.4 - - - +
641A VAL* 3.9 21.1 - - + +
642A PHE* 4.3 3.3 - - - -
565C PHE* 5.0 2.7 - - + -
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Residues in contact with LEU 520 (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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516A LEU* 2.8 38.9 + - + +
517A THR 3.7 7.4 - - - +
519A VAL* 1.3 85.2 - - + +
521A LEU* 1.3 58.2 + - - +
523A ILE* 2.8 11.3 + - + +
524A VAL* 2.8 30.4 + - + +
530A VAL* 3.8 15.3 - - + -
533A VAL* 3.6 31.2 - - + -
534A VAL* 3.9 12.8 - - + -
537A LEU* 4.4 10.1 - - + -
561C ILE* 4.3 35.2 - - + -
565C PHE* 5.1 3.6 - - + -
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Residues in contact with LEU 521 (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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438A ALA* 4.4 4.0 - - + -
439A VAL* 3.8 20.0 - - - +
442A PHE* 4.4 22.4 - - + -
443A PRO* 5.0 4.0 - - + -
446A ARG* 3.3 47.1 + - - +
517A THR* 2.8 40.9 + - + +
518A LEU* 2.7 16.0 + - - +
520A LEU* 1.3 70.7 - - - +
522A GLY* 1.3 55.4 - - - -
524A VAL 3.2 13.5 - - - +
525A GLN* 4.8 0.2 - - - -
527A PRO* 3.9 29.6 - - + -
530A VAL* 3.9 13.2 - - + -
642A PHE* 4.4 1.6 - - - -
645A ARG* 4.8 0.7 + - - -
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Residues in contact with GLY 522 (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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518A LEU 3.2 4.0 + - - -
519A VAL 2.8 11.2 + - - -
521A LEU* 1.3 77.6 - - - +
523A ILE* 1.3 61.5 + - - +
524A VAL 4.4 0.4 - - - -
525A GLN* 4.5 2.1 - - - +
641A VAL* 3.8 10.3 - - - -
642A PHE* 3.5 27.7 - - - -
645A ARG* 3.3 33.7 + - - +
648A LEU* 4.8 0.2 - - - +
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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
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519A VAL* 4.1 16.4 - - + +
520A LEU* 2.8 16.0 + - + +
522A GLY* 1.3 75.2 - - - +
524A VAL* 1.3 63.7 + - + +
525A GLN* 3.8 9.5 - - - +
641A VAL* 3.4 38.1 - - + -
648A LEU* 4.3 12.1 - - - +
560C LYS* 4.2 22.4 + - + +
561C ILE* 4.4 28.3 - - + -
564C TYR* 3.4 47.3 - - + +
565C PHE* 5.2 3.1 - - + -
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Residues in contact with VAL 524 (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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446A ARG* 3.7 2.3 + - - -
520A LEU* 2.8 16.5 + - + +
521A LEU* 3.2 23.0 - - - +
523A ILE* 1.3 77.5 - - + +
525A GLN* 1.3 63.8 + - - +
526A ASN* 3.7 11.6 + - + +
529A ILE* 3.9 23.3 - - + -
530A VAL* 3.7 24.9 - - + +
533A VAL* 6.3 0.4 - - + -
557C ILE* 4.1 20.2 - - + +
560C LYS* 6.4 0.2 - - + -
561C ILE* 3.8 33.0 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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