Contacts of the helix formed by residues 483 - 500 (chain C) in PDB entry 5G04
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 SER 483 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482C GLU* 1.3 72.9 - - - +
484C GLU* 1.3 65.5 - - - +
485C GLN 3.6 0.2 - - - -
486C ALA 4.3 0.2 - - - -
487C ALA* 3.2 12.2 + - - +
515C TYR* 2.4 28.6 + - - -
519C TYR* 3.6 31.6 + - - +
522C LYS* 4.2 28.2 + - - +
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Residues in contact with GLU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C GLU* 4.1 5.9 - - + +
483C SER* 1.3 81.1 - - - +
485C GLN* 1.3 79.5 + - - +
487C ALA* 3.7 2.4 - - - +
488C GLN* 3.0 44.7 + - - +
519C TYR* 4.5 24.5 + - + +
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Residues in contact with GLN 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C HIS* 4.1 19.4 + - + +
482C GLU* 3.3 32.0 - - - +
484C GLU* 1.3 91.3 + - - +
486C ALA* 1.3 64.1 + - - +
488C GLN* 3.4 24.7 + - - +
489C CYS* 3.1 22.7 + - - +
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Residues in contact with ALA 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C ALA* 4.0 8.2 - - - +
477C HIS* 3.3 37.3 - - + +
478C GLU* 4.2 4.3 - - + -
482C GLU* 3.6 13.6 - - - +
483C SER 3.8 0.4 + - - -
484C GLU 3.4 0.2 - - - -
485C GLN* 1.3 75.7 - - - +
487C ALA* 1.3 60.7 + - - +
489C CYS* 3.2 7.8 + - - +
490C TYR* 3.1 28.7 + - - -
515C TYR* 2.9 24.0 - - + +
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Residues in contact with ALA 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C SER 3.2 16.1 + - - +
484C GLU 3.7 4.0 - - - +
486C ALA* 1.3 74.9 - - - +
488C GLN* 1.3 60.9 + - - +
490C TYR 3.4 1.7 + - - -
491C ILE* 3.1 23.9 + - - +
515C TYR* 2.9 25.8 + - + +
516C LEU* 3.6 16.0 - - + +
519C TYR* 3.8 32.3 - - + -
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Residues in contact with GLN 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C GLU* 3.0 36.0 + - - +
485C GLN* 3.6 24.8 + - - +
486C ALA 3.3 0.2 - - - -
487C ALA* 1.3 71.8 - - - +
489C CYS* 1.3 66.1 + - - +
491C ILE* 3.1 33.3 - - + +
492C LYS* 3.1 34.3 + - - +
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Residues in contact with CYS 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C TRP* 6.1 0.2 - - - -
470C LEU* 3.2 50.4 - - - +
473C LEU* 3.8 21.5 - - + -
474C ALA* 3.7 12.8 - - + -
477C HIS* 5.0 2.7 - - + +
485C GLN 3.1 13.1 + - - +
486C ALA* 3.2 9.6 + - - +
488C GLN* 1.3 76.5 - - - +
490C TYR* 1.3 61.7 + - - +
492C LYS* 3.3 10.8 + - - +
493C TYR* 3.1 21.0 + - - +
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Residues in contact with TYR 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C VAL* 4.5 15.5 - - + -
474C ALA* 3.6 23.2 - - + -
475C LYS* 2.9 44.4 + - + +
478C GLU* 3.3 25.3 + - + -
486C ALA 3.1 21.3 + - - -
487C ALA 3.6 6.1 - - - +
488C GLN 3.3 0.2 - - - -
489C CYS* 1.3 79.1 - - - +
491C ILE* 1.3 56.6 + - - +
493C TYR* 3.1 17.0 + + + +
494C ILE* 2.8 39.7 + - + +
511C THR* 5.7 1.2 + - - -
512C ALA* 3.6 26.9 - - + -
515C TYR* 3.7 20.6 - + - -
516C LEU* 3.8 11.2 - - + -
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Residues in contact with ILE 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C ALA 3.1 17.2 + - - +
488C GLN* 3.1 39.0 - - + +
490C TYR* 1.3 72.4 - - - +
492C LYS* 1.3 65.5 + - + +
494C ILE* 3.7 7.3 - - + +
495C GLN* 2.8 52.0 + - - +
516C LEU* 4.0 23.6 - - + -
519C TYR* 6.6 0.2 - - + -
520C TYR* 5.0 13.7 - - + +
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Residues in contact with LYS 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C TRP* 4.6 22.5 - - + -
460C TYR* 4.6 18.7 + - + +
470C LEU* 4.1 18.4 - - + +
488C GLN* 3.1 46.2 + - + +
489C CYS* 3.7 10.1 - - - +
491C ILE* 1.3 81.6 - - + +
493C TYR* 1.3 58.0 + - - +
495C GLN* 3.4 12.3 + - - +
496C ASP* 3.0 27.5 + - - +
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Residues in contact with TYR 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C GLU 4.9 1.1 + - - -
467C LYS* 3.9 35.7 - - + -
468C MET* 4.4 13.5 - - + +
470C LEU* 3.6 24.8 - - + +
471C VAL* 3.5 34.4 - - + +
489C CYS 3.1 11.1 + - - +
490C TYR* 3.5 18.2 - + + +
492C LYS* 1.3 73.6 - - - +
494C ILE* 1.3 71.5 + - + +
496C ASP* 3.3 4.6 + - - +
497C ILE* 3.1 53.2 + - + +
509C GLU* 4.5 22.8 + - + +
512C ALA* 6.4 0.9 - - + -
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Residues in contact with ILE 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C TYR* 2.8 31.3 + - + +
491C ILE* 3.9 7.6 - - + +
493C TYR* 1.3 82.6 - - + +
495C GLN* 1.3 62.0 + - - +
497C ILE* 3.5 12.8 + - + +
498C TYR* 3.3 47.5 + - + -
512C ALA* 5.1 6.5 - - + -
513C PHE* 3.7 41.1 - - + -
516C LEU* 3.7 22.2 - - + -
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Residues in contact with GLN 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C ILE* 2.8 44.9 + - - +
492C LYS* 3.5 12.2 - - - +
494C ILE* 1.3 76.3 - - - +
496C ASP* 1.3 52.2 + - - +
498C TYR* 3.4 2.8 + - - +
499C SER* 2.8 38.9 + - - -
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Residues in contact with ASP 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C TYR* 5.4 7.0 - - + +
464C ASP* 6.1 0.4 - - - +
467C LYS* 4.3 25.5 + - + +
470C LEU* 5.1 5.8 - - + -
492C LYS 3.0 14.8 + - - +
493C TYR* 3.3 12.3 + - - +
495C GLN* 1.3 71.4 - - - +
497C ILE* 1.3 63.4 + - - +
499C SER* 3.5 7.6 + - - -
500C CYS* 3.4 22.5 + - - +
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Residues in contact with ILE 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C LYS* 5.3 10.8 - - + -
493C TYR* 3.1 59.6 + - + +
494C ILE* 3.8 16.2 - - + +
495C GLN 3.5 0.2 - - - -
496C ASP* 1.3 73.5 - - - +
498C TYR* 1.3 81.2 + - + +
500C CYS* 3.5 21.2 + - - +
509C GLU 5.9 3.6 - - - +
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Residues in contact with TYR 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494C ILE* 3.3 37.5 + - + +
495C GLN* 3.7 2.2 - - - +
496C ASP 3.3 0.2 - - - -
497C ILE* 1.3 96.3 - - + +
499C SER* 1.3 63.5 + - - +
500C CYS 3.1 9.0 + - - +
513C PHE* 5.4 5.9 - + - -
539C PHE* 5.0 11.4 - - - -
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Residues in contact with SER 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C GLN 2.8 20.5 + - - -
496C ASP* 3.8 9.0 - - - -
497C ILE 3.5 0.2 - - - -
498C TYR* 1.3 75.8 - - - +
500C CYS* 1.3 57.5 + - - +
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Residues in contact with CYS 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C LYS* 5.3 10.5 - - + +
496C ASP 3.4 13.3 + - - +
497C ILE* 3.5 16.1 + - - +
498C TYR* 3.1 7.9 - - - +
499C SER* 1.3 81.0 - - - +
73R LYS* 5.0 14.6 - - - +
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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