Contacts of the helix formed by residues 503 - 518 (chain A) in PDB entry 5JZU
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 LYS 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A LYS* 4.8 7.2 - - - +
498A LEU* 2.9 27.9 + - + +
501A GLN* 3.9 30.3 - - + +
502A ASN* 1.3 75.3 - - - +
504A ILE* 1.3 64.7 + - - +
506A GLU* 3.2 38.5 - - + +
507A SER* 3.0 22.5 + - - -
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Residues in contact with ILE 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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499A LYS* 3.9 25.8 - - + +
502A ASN* 3.1 37.1 + - - +
503A LYS* 1.3 74.4 - - - +
505A ALA* 1.3 64.4 + - - +
506A GLU* 3.7 0.4 + - - -
507A SER* 2.7 23.5 + - - -
508A ILE* 3.4 8.5 - - - +
534A ALA* 3.4 34.3 - - - +
537A ARG* 4.2 30.7 - - + +
538A VAL* 3.7 13.5 - - + -
618A ASN* 4.5 0.4 - - - +
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Residues in contact with ALA 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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504A ILE* 1.3 79.5 - - - +
506A GLU* 1.3 69.9 + - + +
507A SER 3.2 0.7 + - - -
508A ILE* 3.5 15.5 + - + +
509A PRO* 3.3 16.8 - - - +
538A VAL* 4.6 9.4 - - + +
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Residues in contact with GLU 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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498A LEU* 4.0 12.3 - - + -
503A LYS* 3.2 47.2 - - + +
504A ILE 3.7 0.3 + - - -
505A ALA* 1.3 83.3 + - - +
507A SER* 1.3 60.9 + - - +
509A PRO* 3.3 13.6 - - - +
510A TYR* 3.4 19.7 - - + -
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Residues in contact with SER 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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495A GLY* 3.3 24.0 - - - -
498A LEU* 3.8 10.1 - - - -
499A LYS* 3.6 21.4 - - - +
503A LYS 3.0 13.7 + - - -
504A ILE* 2.7 19.2 + - - -
505A ALA 3.1 0.2 - - - -
506A GLU* 1.3 77.4 - - - +
508A ILE* 1.3 65.6 + - - +
509A PRO 3.5 0.2 - - - -
510A TYR* 3.2 4.4 + - - +
511A LEU* 3.0 27.7 + - - +
534A ALA* 3.9 9.7 - - - +
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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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504A ILE 3.4 16.6 - - - +
505A ALA* 3.8 11.4 - - + +
506A GLU 3.4 0.2 - - - -
507A SER* 1.3 78.2 - - - +
509A PRO* 1.3 73.0 - - + +
510A TYR 3.2 0.2 + - - -
511A LEU* 3.3 1.5 + - - -
512A LYS* 2.9 27.5 + - + +
531A LEU* 3.8 20.6 - - + +
534A ALA* 3.9 24.0 - - + +
535A MET* 4.2 18.8 - - + +
538A VAL* 3.7 31.2 - - + -
540A ASN* 5.4 4.5 - - - +
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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
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505A ALA 3.3 12.1 - - - +
506A GLU* 3.3 18.8 - - - +
508A ILE* 1.3 96.0 - - + +
510A TYR* 1.3 63.0 + - + +
512A LYS* 4.5 4.9 - - + -
513A GLU* 2.8 54.9 + - + +
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Residues in contact with TYR 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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481A LEU* 4.1 13.8 - - + +
491A LYS* 3.4 49.1 - - + +
494A TYR* 3.6 35.8 - + - -
495A GLY* 3.7 8.1 - - - -
498A LEU* 4.0 9.4 - - + -
506A GLU* 3.4 24.7 - - + -
507A SER 3.2 6.2 + - - +
508A ILE 3.2 0.6 - - - -
509A PRO* 1.3 83.0 - - + +
511A LEU* 1.3 60.8 + - - +
513A GLU* 4.9 3.4 - - - -
514A GLY* 3.0 26.5 + - - -
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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
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492A VAL* 3.5 27.0 - - - +
495A GLY 3.9 9.9 - - - +
496A PHE* 3.6 12.8 - - - +
499A LYS* 4.7 2.5 - - + -
507A SER* 3.0 33.8 + - - +
508A ILE* 3.9 2.9 - - - +
510A TYR* 1.3 76.2 - - - +
512A LYS* 1.3 63.8 + - - +
514A GLY* 3.8 0.3 - - - -
515A ILE* 3.0 31.2 + - - +
527A PHE* 4.1 26.2 - - + +
530A HIS* 4.0 13.5 - - + +
531A LEU* 3.7 40.2 - - + +
534A ALA* 5.0 0.9 - - + -
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Residues in contact with LYS 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 ILE* 2.9 23.1 + - + +
509A PRO* 4.0 4.3 - - + +
511A LEU* 1.3 74.1 - - - +
513A GLU* 1.3 69.9 + - + +
514A GLY 3.2 0.2 + - - -
515A ILE* 3.3 3.3 + - - +
516A GLU* 3.0 62.2 + - - +
531A LEU* 3.8 17.7 - - + +
535A MET* 4.5 14.6 - - + -
546A TRP* 3.7 23.1 - - + +
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Residues in contact with GLU 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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491A LYS* 3.0 37.3 + - + +
509A PRO* 2.8 43.8 + - + +
510A TYR* 5.0 2.1 - - - -
512A LYS* 1.3 79.4 - - + +
514A GLY* 1.3 57.5 + - - +
516A GLU* 3.8 12.4 - - - +
517A SER* 2.9 29.8 + - - -
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Residues in contact with GLY 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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488A GLY* 3.7 12.8 - - - -
491A LYS* 4.0 5.6 - - - +
492A VAL* 3.4 17.7 - - - -
510A TYR 3.0 20.4 + - - -
513A GLU* 1.3 75.9 - - - +
515A ILE* 1.3 60.7 + - - +
517A SER* 2.5 25.3 + - - -
522A THR* 3.3 10.7 - - - +
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Residues in contact with ILE 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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492A VAL* 4.1 2.2 - - + -
511A LEU 3.0 18.1 + - - +
512A LYS 3.9 2.7 - - - +
514A GLY* 1.3 75.1 - - - +
516A GLU* 1.3 64.9 + - - +
518A GLY* 3.0 16.5 + - - -
522A THR* 3.9 24.5 + - - +
523A ASP* 5.5 0.7 - - - -
527A PHE* 3.7 40.6 - - + +
528A TYR* 3.5 45.3 - - + +
531A LEU* 4.1 15.7 - - + -
546A TRP* 4.1 11.9 - - + -
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Residues in contact with GLU 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 LYS* 3.0 61.9 + - - +
513A GLU* 3.8 10.1 - - - +
515A ILE* 1.3 73.5 - - - +
517A SER* 1.3 66.7 + - - +
518A GLY* 3.1 2.3 + - - -
546A TRP* 3.8 20.4 - - + -
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Residues in contact with SER 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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486A ASN 4.9 4.5 - - - -
488A GLY* 3.3 24.8 - - - -
491A LYS* 5.9 1.3 - - - -
513A GLU 2.9 15.1 + - - -
514A GLY 2.5 22.0 + - - -
516A GLU* 1.3 77.1 - - - +
518A GLY* 1.3 60.2 + - - +
519A ASP* 3.1 24.0 + - - +
522A THR* 3.8 0.2 - - - +
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Residues in contact with GLY 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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515A ILE 3.0 15.0 + - - -
516A GLU 3.0 2.6 - - - -
517A SER* 1.3 79.6 + - - +
519A ASP* 1.3 66.9 + - - +
520A PRO* 3.7 1.7 - - - +
522A THR* 3.8 3.8 + - - -
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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
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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