Contacts of the helix formed by residues 482 - 499 (chain K) in PDB entry 7JOA
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 ASP 482 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478K GLN 4.0 6.8 + - - -
480K LEU 4.3 0.6 - - - -
481K ILE* 1.3 75.5 - - - +
483K ARG* 1.3 84.2 + - - +
484K LYS* 3.1 42.1 + - - +
485K SER* 3.1 26.1 + - - +
486K LYS* 3.4 9.7 + - - -
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Residues in contact with ARG 483 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463K GLU* 3.1 34.5 + - - +
478K GLN* 3.5 26.2 - - + +
481K ILE 3.4 2.8 + - - -
482K ASP* 1.3 79.6 + - - +
484K LYS* 1.3 56.9 + - - +
486K LYS* 3.2 17.3 + - - +
487K GLU* 2.9 37.2 + - + +
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Residues in contact with LYS 484 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482K ASP* 3.1 29.8 + - - +
483K ARG* 1.3 75.8 - - - +
485K SER* 1.3 66.5 + - - +
487K GLU* 3.7 8.1 - - - +
488K PHE* 2.9 28.8 + - - +
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Residues in contact with SER 485 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414K GLU* 4.0 19.7 + - - +
415K LEU* 3.9 5.4 - - - +
417K ALA* 6.0 3.2 - - - +
418K PHE* 4.1 18.2 - - - -
481K ILE* 4.3 6.1 - - - -
482K ASP* 3.1 21.3 + - - +
484K LYS* 1.3 82.4 - - - +
486K LYS* 1.3 58.4 + - - +
488K PHE* 3.3 7.8 + - - +
489K LEU* 2.9 27.7 + - - +
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Residues in contact with LYS 486 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K PHE* 3.7 15.7 - - + -
460K LEU* 4.1 25.8 - - + +
463K GLU* 2.9 37.8 + - + -
476K PHE* 3.4 34.8 + - + -
477K SER 4.0 3.0 + - - -
478K GLN* 4.5 0.4 - - - +
481K ILE* 2.7 47.4 + - + +
482K ASP 3.4 7.4 + - - -
483K ARG* 3.2 8.4 + - - +
485K SER* 1.3 76.2 - - - +
487K GLU* 1.3 60.7 + - - +
489K LEU* 3.3 3.9 + - - +
490K SER* 2.8 33.9 + - - -
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Residues in contact with GLU 487 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483K ARG* 2.9 27.4 + - + +
484K LYS* 3.7 9.2 - - - +
486K LYS* 1.3 77.5 - - - +
488K PHE* 1.3 61.4 + - - +
490K SER* 3.3 12.2 + - - -
491K LYS* 3.0 24.1 + - - +
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Residues in contact with PHE 488 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412K PHE* 3.5 41.1 - + + -
414K GLU* 4.4 25.4 - - + -
415K LEU* 3.7 20.0 - - + -
484K LYS 2.9 15.2 + - - +
485K SER* 3.3 11.2 - - - +
487K GLU* 1.3 76.2 - - - +
489K LEU* 1.3 62.3 + - - +
491K LYS* 3.2 12.1 + - + +
492K LYS* 3.0 57.7 + - + +
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Residues in contact with LEU 489 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405K LEU* 4.7 14.1 - - + -
408K LEU* 3.8 19.5 - - + -
415K LEU* 3.8 23.8 - - + -
418K PHE* 4.1 27.6 - - + -
456K PHE* 3.6 31.9 - - + -
460K LEU* 4.3 2.9 - - + -
485K SER 2.9 17.4 + - - +
486K LYS* 3.7 5.4 - - - +
488K PHE* 1.3 77.4 - - - +
490K SER* 1.3 58.2 + - - +
492K LYS* 3.2 3.2 + - - -
493K ILE* 2.8 49.3 + - + +
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Residues in contact with SER 490 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457K LEU* 4.1 14.7 - - - +
460K LEU* 3.1 31.2 - - - +
486K LYS 2.8 26.1 + - - -
487K GLU* 3.4 13.7 + - - -
489K LEU* 1.3 72.8 - - - +
491K LYS* 1.3 58.6 + - - +
493K ILE* 3.4 2.0 + - - +
494K GLU* 2.9 32.1 + - - +
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Residues in contact with LYS 491 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487K GLU 3.0 13.6 + - - +
488K PHE* 3.2 15.0 + - + +
490K SER* 1.3 75.6 - - - +
492K LYS* 1.3 71.8 + - + +
494K GLU* 3.8 4.7 - - - +
495K TYR* 3.0 30.2 + - + +
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Residues in contact with LYS 492 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408K LEU* 3.6 27.4 - - + -
412K PHE* 3.4 38.4 - - + -
415K LEU* 5.2 1.3 - - + -
488K PHE* 3.0 53.8 + - + +
489K LEU* 3.2 5.8 + - + +
491K LYS* 1.3 88.5 - - + +
493K ILE* 1.3 57.1 + - - +
495K TYR* 3.3 13.3 + - + +
496K GLU* 2.9 36.1 + - - +
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Residues in contact with ILE 493 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401K MET* 5.0 8.1 - - + -
404K LEU* 4.7 11.2 - - + +
408K LEU* 4.2 10.1 - - + -
453K LEU* 4.0 25.6 - - + +
456K PHE* 3.7 27.8 - - + -
457K LEU* 4.4 19.3 - - + -
460K LEU* 4.3 4.7 - - + -
489K LEU* 2.8 50.8 + - + +
490K SER* 3.9 3.6 - - - +
492K LYS* 1.3 71.0 - - - +
494K GLU* 1.3 59.8 + - - +
496K GLU* 3.3 6.2 + - - +
497K ARG* 2.9 31.5 + - + +
501K PHE* 5.6 0.2 - - - -
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Residues in contact with GLU 494 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457K LEU* 4.1 21.7 - - + +
490K SER 2.9 18.9 + - - +
491K LYS* 3.8 4.9 - - - +
493K ILE* 1.3 77.4 - - - +
495K TYR* 1.3 63.9 + - - +
497K ARG* 4.1 19.6 + - - +
498K ASN* 2.2 63.3 + - - +
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Residues in contact with TYR 495 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491K LYS* 3.0 19.6 + - + +
492K LYS* 3.5 14.8 - - + +
493K ILE 3.2 0.2 - - - -
494K GLU* 1.3 77.9 - - - +
496K GLU* 1.3 83.8 + - + +
498K ASN* 4.8 0.7 - - - -
499K ASN* 2.7 59.6 + - + +
502K PRO* 4.1 17.6 - - + +
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Residues in contact with GLU 496 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404K LEU* 4.2 13.2 - - + -
408K LEU* 4.5 9.5 - - + +
412K PHE* 6.1 0.3 - - - -
492K LYS* 2.9 23.4 + - + +
493K ILE* 3.8 4.5 - - - +
495K TYR* 1.3 91.6 - - + +
497K ARG* 1.3 62.8 + - - +
499K ASN 3.2 0.3 + - - -
500K GLY 3.2 5.0 + - - -
501K PHE* 2.7 45.0 + - + -
502K PRO* 3.1 18.8 - - - +
503K ILE* 3.0 54.8 + - + +
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Residues in contact with ARG 497 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450K ASP* 2.5 49.8 + - - +
453K LEU* 3.7 27.9 - - + +
454K ALA* 5.0 13.7 - - - +
457K LEU* 4.5 19.1 - - - +
493K ILE* 2.9 19.3 + - + +
494K GLU* 3.9 21.6 + - - +
496K GLU* 1.3 77.1 - - - +
498K ASN* 1.3 61.2 + - - +
499K ASN 3.6 0.2 + - - -
500K GLY* 4.1 5.0 + - - -
501K PHE* 4.0 16.6 - - + -
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Residues in contact with ASN 498 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494K GLU* 2.2 57.8 + - - +
495K TYR* 4.0 2.2 - - - +
497K ARG* 1.3 79.0 - - - +
499K ASN* 1.3 68.5 + - - +
500K GLY 3.6 1.1 - - - -
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Residues in contact with ASN 499 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K LYS* 4.9 0.9 + - - -
495K TYR* 2.7 62.9 + - + +
496K GLU 3.2 0.6 + - - -
498K ASN* 1.3 85.7 - - - +
500K GLY* 1.3 62.5 + - - +
501K PHE 3.3 2.2 - - - -
502K PRO* 3.2 25.9 - - + +
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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
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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