Contacts of the helix formed by residues 494 - 513 (chain A) in PDB entry 4YOZ
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 GLN 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A VAL* 2.8 41.7 + - - +
491A LEU* 3.7 10.7 + - - +
492A LEU 3.4 2.8 - - - -
493A GLU* 1.3 87.4 + - - +
495A ASP* 1.3 64.7 + - - +
496A ILE* 3.2 10.2 - - + +
497A PHE* 3.2 20.6 + - + +
498A HIS* 3.4 15.4 - - - -
783A LYS* 5.7 2.4 + - - -
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Residues in contact with ASP 495 (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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426A ASN* 5.6 4.5 - - - +
430A ILE* 3.7 25.4 - - + +
493A GLU 3.3 11.8 + - - +
494A GLN* 1.3 71.9 - - - +
496A ILE* 1.3 62.0 + - - +
497A PHE 3.3 0.2 + - - -
498A HIS* 3.3 3.5 + - - +
499A ARG* 3.0 39.2 + - - +
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Residues in contact with ILE 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLN* 4.8 11.0 - - + +
495A ASP* 1.3 79.3 - - - +
497A PHE* 1.3 62.7 + - + +
499A ARG* 3.7 26.9 - - - +
500A SER* 2.8 39.2 + - - +
528A LEU* 3.7 17.3 - - + -
529A GLN 5.5 2.0 - - - +
532A TYR* 3.8 42.2 - - + +
535A LYS* 5.9 5.2 - - - +
784A ARG* 5.9 7.0 - - - +
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Residues in contact with PHE 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 4.1 23.6 - - + -
475A VAL* 4.2 25.4 - - + -
476A MET* 4.8 6.7 - - + -
491A LEU 5.5 5.6 - - - +
494A GLN* 3.2 16.9 + - + +
495A ASP 3.2 0.8 - - - -
496A ILE* 1.3 85.6 - - + +
498A HIS* 1.3 73.6 + + + +
500A SER* 3.3 4.7 + - - -
501A LEU* 2.9 50.4 + - + +
536A VAL* 4.3 19.5 - - + +
539A VAL* 4.4 18.6 - - + -
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Residues in contact with HIS 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 3.6 27.2 - - + +
430A ILE* 4.1 22.8 - - + +
468A TYR* 2.6 37.9 + - + +
472A LEU* 4.0 11.8 - - + +
491A LEU 5.0 0.4 + - - -
492A LEU* 2.7 45.2 + - + -
493A GLU 5.1 0.7 - - - -
494A GLN 3.4 23.5 + - - -
495A ASP* 3.3 7.7 + - - +
497A PHE* 1.3 88.7 - + - +
499A ARG* 1.3 58.8 + - - +
501A LEU 3.3 0.3 + - - -
502A MET* 2.9 30.8 + - - +
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Residues in contact with ARG 499 (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 ILE* 3.8 21.8 - - + -
434A ILE* 3.9 20.5 - - + +
495A ASP* 3.0 33.5 + - - +
496A ILE* 3.7 15.6 - - - +
498A HIS* 1.3 76.6 - - - +
500A SER* 1.3 58.7 + - - +
502A MET* 3.4 1.7 + - - +
503A ALA* 2.9 30.0 + - - +
526A LEU* 3.1 27.1 + - - +
527A ASN* 3.1 21.2 + - - +
528A LEU* 3.5 33.2 - - + +
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Residues in contact with SER 500 (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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496A ILE* 2.8 33.3 + - - +
497A PHE* 3.7 4.3 - - - -
499A ARG* 1.3 76.9 - - - +
501A LEU* 1.3 58.9 + - - +
504A CYS* 2.8 27.2 + - - +
528A LEU* 4.0 7.6 - - - +
532A TYR 4.5 1.8 + - - -
533A PHE* 3.3 44.1 - - - -
536A VAL* 3.6 17.7 - - - +
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Residues in contact with LEU 501 (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 TYR* 3.6 38.4 - - + +
471A ILE* 3.8 18.2 - - + -
472A LEU* 4.0 18.4 - - + +
497A PHE* 2.9 38.0 + - + +
498A HIS* 3.7 4.3 - - - +
499A ARG 3.3 0.2 - - - -
500A SER* 1.3 74.5 - - - +
502A MET* 1.3 60.5 + - - +
504A CYS* 3.3 1.7 + - - +
505A CYS* 2.9 40.5 + - - -
536A VAL* 3.8 13.4 - - + +
539A VAL* 6.1 1.3 - - + -
540A VAL* 3.7 26.9 - - + -
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Residues in contact with MET 502 (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 LEU* 3.6 31.4 - - + +
434A ILE* 3.7 31.6 - - + -
461A LEU* 3.6 31.2 - - + -
464A ALA* 3.6 26.2 - - + +
465A GLU* 3.8 14.4 - - + +
468A TYR* 3.8 21.5 - - + -
498A HIS 2.9 17.5 + - - +
501A LEU* 1.3 77.5 - - - +
503A ALA* 1.3 56.3 + - - +
505A CYS* 3.3 3.9 + - - +
506A LEU* 2.9 36.8 + - + +
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Residues in contact with ALA 503 (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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499A ARG 2.9 8.4 + - - +
500A SER 3.7 3.6 - - - +
502A MET* 1.3 74.2 - - - +
504A CYS* 1.3 62.0 + - - +
506A LEU* 3.2 6.3 + - - +
507A GLU* 2.8 29.4 + - - +
522A ILE* 3.9 9.7 - - + +
523A ILE* 4.5 3.6 - - + -
526A LEU* 3.8 18.1 - - + +
528A LEU* 3.4 32.8 - - + -
533A PHE* 3.9 10.1 - - + -
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Residues in contact with CYS 504 (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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500A SER 2.8 18.2 + - - +
501A LEU 3.7 4.9 - - - +
503A ALA* 1.3 76.3 - - - +
505A CYS* 1.3 57.9 + - - +
507A GLU* 3.2 5.6 + - - +
508A ILE* 2.9 33.5 + - - +
533A PHE* 3.8 10.9 - - + -
536A VAL* 4.0 17.3 - - + -
537A ILE* 4.4 11.2 - - - -
540A VAL* 3.8 28.3 - - + -
555A LEU* 3.7 28.3 - - - -
558A ILE* 5.5 0.2 - - - -
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Residues in contact with CYS 505 (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 ALA* 3.5 22.0 - - + +
467A LEU* 3.8 13.1 - - + +
468A TYR* 3.6 33.2 - - - -
471A ILE* 4.0 16.8 - - - -
501A LEU* 2.9 28.6 + - - +
502A MET* 3.5 7.4 - - - +
504A CYS* 1.3 77.4 - - - +
506A LEU* 1.3 62.9 + - - +
508A ILE* 3.2 9.7 + - - +
509A VAL* 3.1 27.7 + - - +
540A VAL* 5.8 0.7 - - - -
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Residues in contact with LEU 506 (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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434A ILE* 3.9 26.9 - - + -
438A PHE* 4.3 27.1 - - + -
460A ARG* 4.4 4.5 - - + +
461A LEU* 4.2 22.7 - - + -
464A ALA* 3.6 21.1 - - + -
502A MET* 2.9 23.0 + - + +
503A ALA 3.2 7.4 + - - +
505A CYS* 1.3 74.8 - - - +
507A GLU* 1.3 59.7 + - - +
509A VAL* 3.3 3.7 + - + +
510A LEU* 2.9 36.9 + - + +
522A ILE* 3.7 28.3 - - + -
526A LEU* 4.2 3.4 - - + -
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Residues in contact with GLU 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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503A ALA 2.8 16.5 + - - +
504A CYS* 3.5 9.9 - - - +
506A LEU* 1.3 74.7 - - - +
508A ILE* 1.3 59.9 + - - +
510A LEU* 4.4 10.0 - - - +
511A PHE* 2.9 30.7 + - - +
517A ARG 4.9 3.2 - - - +
519A PHE* 3.8 27.8 + - + +
522A ILE* 3.5 24.7 + - + +
533A PHE* 5.5 1.3 - - + -
554A HIS* 2.6 34.5 + - + +
555A LEU* 5.0 3.8 - - + -
558A ILE* 3.9 22.0 - - + -
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Residues in contact with ILE 508 (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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397A LEU* 3.9 14.4 - - + -
467A LEU* 3.9 22.2 - - + -
471A ILE* 6.3 1.8 - - + -
504A CYS* 2.9 22.1 + - - +
505A CYS* 3.4 10.1 - - - +
507A GLU* 1.3 77.7 - - - +
509A VAL* 1.3 58.8 + - - +
511A PHE* 3.4 7.0 + - + +
512A ALA* 3.0 27.5 + - - +
540A VAL* 5.1 5.6 - - + -
547A LEU* 4.6 17.9 - - + -
551A MET* 4.6 18.8 - - + +
554A HIS* 5.6 4.0 - - + -
555A LEU* 3.5 43.7 - - + -
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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
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397A LEU* 4.0 19.5 - - + -
460A ARG* 3.7 40.6 - - + +
463A LEU* 4.1 8.3 - - + -
464A ALA* 3.9 25.6 - - - +
467A LEU* 4.3 8.5 - - + -
505A CYS 3.1 14.3 + - - +
506A LEU* 3.6 8.3 - - + +
508A ILE* 1.3 73.8 - - - +
510A LEU* 1.3 66.7 + - - +
512A ALA* 3.1 10.2 + - - +
513A TYR* 3.2 33.1 - - + -
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Residues in contact with LEU 510 (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 PHE* 4.5 17.0 - - + -
442A TYR* 4.7 8.3 - - + -
460A ARG* 4.5 24.9 - - + +
506A LEU* 2.9 25.1 + - + +
507A GLU* 3.8 11.0 - - - +
509A VAL* 1.3 76.8 - - + +
511A PHE* 1.3 62.5 + - - +
513A TYR* 3.3 7.8 + - - -
515A SER* 2.9 50.4 + - - +
517A ARG* 4.5 13.9 - - + +
521A TRP* 4.2 29.4 - - + -
522A ILE* 4.6 11.0 - - + -
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Residues in contact with PHE 511 (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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393A SER* 4.7 9.0 - - - -
507A GLU* 2.9 20.2 + - - +
508A ILE* 3.7 6.5 - - + +
510A LEU* 1.3 75.6 - - - +
512A ALA* 1.3 62.1 + - - +
514A SER* 2.9 23.4 + - - +
515A SER 4.8 1.1 - - - +
550A ASP* 3.7 27.1 - - + -
551A MET* 4.0 20.2 - - + -
554A HIS* 3.4 54.7 - + + +
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Residues in contact with ALA 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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391A THR* 4.0 4.2 + - - -
393A SER* 3.7 37.6 - - - +
394A VAL* 3.3 18.4 - - + +
397A LEU* 3.8 22.4 - - + -
508A ILE 3.0 13.9 + - - +
509A VAL 3.1 9.4 + - - +
511A PHE* 1.3 78.6 - - + +
513A TYR* 1.3 58.0 + - + +
514A SER* 3.3 2.9 + - - -
551A MET* 4.7 6.5 - - + -
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Residues in contact with TYR 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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390A PHE* 5.7 2.2 - + - -
394A VAL* 3.7 36.6 - - + +
397A LEU* 4.4 4.5 - - + -
398A GLN* 5.2 3.1 + - - +
459A ASN* 4.0 9.4 + - - -
460A ARG* 3.6 50.0 + - - +
463A LEU* 3.9 21.4 - - + +
509A VAL* 3.2 37.9 + - + +
510A LEU 3.3 4.5 + - - +
511A PHE 3.1 1.0 - - - -
512A ALA* 1.3 80.5 - - + +
514A SER* 1.3 69.8 + - - +
515A SER* 3.3 4.1 + - - +
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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