Contacts of the helix formed by residues 483 - 500 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482P GLU* 1.3 72.7 - - - +
484P GLU* 1.3 66.4 + - - +
485P GLN 3.6 0.2 - - - -
486P ALA* 3.8 0.7 + - - +
487P ALA* 3.2 27.9 + - - +
522P LYS* 3.3 48.1 + - - +
523P CYS* 4.4 2.6 + - - -
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Residues in contact with GLU 484 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482P GLU* 4.1 6.3 - - + +
483P SER* 1.3 81.1 - - - +
485P GLN* 1.3 86.0 + - - +
487P ALA* 3.7 3.8 - - - +
488P GLN* 3.1 36.0 + - - +
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Residues in contact with GLN 485 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477P HIS* 4.0 21.1 - - + +
482P GLU* 3.3 30.7 + - - +
484P GLU* 1.3 95.3 + - - +
486P ALA* 1.3 63.6 + - - +
488P GLN* 3.4 19.8 + - - +
489P CYS* 3.1 29.0 + - - -
492P LYS* 5.9 0.5 + - - -
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Residues in contact with ALA 486 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474P ALA* 4.0 8.0 - - - +
477P HIS* 3.3 36.8 - - + +
478P GLU* 4.2 11.7 - - + +
482P GLU* 3.6 20.9 - - - +
483P SER 3.8 1.3 + - - +
484P GLU 3.4 0.4 - - - -
485P GLN* 1.3 76.3 - - - +
487P ALA* 1.3 63.7 + - - +
489P CYS* 3.2 7.4 + - - +
490P TYR* 3.1 29.9 + - + -
522P LYS* 5.3 2.2 - - + +
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Residues in contact with ALA 487 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483P SER* 3.2 19.3 + - - +
484P GLU* 3.7 4.7 - - - +
486P ALA* 1.3 79.1 - - - +
488P GLN* 1.3 60.7 + - - +
490P TYR* 3.4 11.7 + - - +
491P ILE* 3.1 27.8 + - - +
519P TYR* 2.8 43.3 - - + +
522P LYS* 6.2 1.3 - - + -
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Residues in contact with GLN 488 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484P GLU* 3.1 30.2 + - - +
485P GLN* 3.6 24.0 - - - +
486P ALA 3.3 0.2 - - - -
487P ALA* 1.3 72.3 - - - +
489P CYS* 1.3 65.5 + - - +
491P ILE* 3.1 41.1 - - - +
492P LYS* 3.1 39.6 + - + +
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Residues in contact with CYS 489 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457P TRP* 5.7 3.6 - - - -
470P LEU* 4.2 15.3 - - + +
473P LEU* 3.8 33.4 - - - -
474P ALA* 3.7 17.9 - - + +
477P HIS* 3.9 13.7 - - - -
485P GLN* 3.1 21.9 + - - -
486P ALA 3.2 8.7 + - - +
488P GLN* 1.3 77.8 - - - +
490P TYR* 1.3 62.0 + - - +
492P LYS* 3.3 11.5 + - - +
493P TYR* 3.1 20.8 + - - +
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Residues in contact with TYR 490 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471P VAL* 4.5 13.3 + - + -
474P ALA* 3.6 23.6 - - + -
475P LYS* 3.8 13.2 + - - +
478P GLU* 3.2 33.1 + - + +
486P ALA 3.1 24.6 + - - -
487P ALA* 3.6 10.3 - - - +
488P GLN 3.3 0.2 - - - -
489P CYS* 1.3 79.5 - - - +
491P ILE* 1.3 57.9 + - + +
493P TYR* 3.1 9.8 + + + +
494P ILE* 2.8 43.5 + - + +
515P TYR* 3.3 55.2 - + + +
516P LEU* 5.6 0.2 - - - -
518P GLN* 3.0 24.8 + - - -
519P TYR* 4.9 6.7 - - + -
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Residues in contact with ILE 491 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487P ALA 3.1 17.0 + - - +
488P GLN* 3.1 47.3 - - - +
490P TYR* 1.3 74.0 - - + +
492P LYS* 1.3 59.8 + - + +
494P ILE* 3.3 6.0 + - + +
495P GLN* 2.8 31.1 + - - +
516P LEU* 4.0 25.8 - - + -
519P TYR* 4.6 17.0 - - + +
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Residues in contact with LYS 492 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457P TRP* 3.6 32.4 - - + -
460P TYR* 4.4 22.5 + - - +
470P LEU* 4.1 14.6 - - + +
485P GLN* 5.9 0.6 + - - -
488P GLN* 3.1 44.7 + - + +
489P CYS* 3.3 10.7 + - - +
491P ILE* 1.3 75.3 - - + +
493P TYR* 1.3 58.3 + - - +
495P GLN* 3.4 13.3 + - - +
496P ASP* 3.0 27.0 + - - +
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Residues in contact with TYR 493 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467P LYS* 3.2 33.2 - - + -
468P MET* 4.0 18.9 - - + +
470P LEU* 3.6 28.3 - - + +
471P VAL* 3.5 33.3 - - + +
489P CYS 3.1 11.5 + - - +
490P TYR* 3.5 13.2 - + + +
492P LYS* 1.3 75.2 - - - +
494P ILE* 1.3 69.6 + - + +
496P ASP* 3.3 7.4 + - + +
497P ILE* 3.1 39.3 + - + +
511P THR* 3.0 26.6 + - - -
512P ALA* 4.0 20.0 - - + -
515P TYR* 4.9 3.6 - + - -
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Residues in contact with ILE 494 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490P TYR* 2.8 33.9 + - + +
491P ILE* 3.9 5.6 - - + +
493P TYR* 1.3 76.3 - - + +
495P GLN* 1.3 61.8 + - - +
497P ILE* 3.5 2.3 + - - -
498P TYR* 3.1 53.0 + - + +
512P ALA* 3.5 42.8 - - + +
515P TYR* 5.1 0.7 - - + -
516P LEU* 3.7 42.6 - - + +
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Residues in contact with GLN 495 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491P ILE 2.8 18.3 + - - +
492P LYS* 3.5 12.9 - - - +
493P TYR 3.2 0.2 - - - -
494P ILE* 1.3 75.3 - - - +
496P ASP* 1.3 50.3 - - - +
498P TYR* 3.4 2.7 + - - +
499P SER* 2.8 41.3 + - - -
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Residues in contact with ASP 496 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460P TYR* 5.3 8.3 - - + +
467P LYS* 5.4 17.4 + - + +
470P LEU* 5.0 7.4 - - + -
492P LYS 3.0 13.4 + - - +
493P TYR* 3.5 14.8 - - + +
495P GLN* 1.3 72.2 - - - +
497P ILE* 1.3 63.9 + - + +
499P SER* 3.5 7.5 + - - -
500P CYS* 3.3 22.3 + - - +
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Residues in contact with ILE 497 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467P LYS* 6.3 4.5 - - + +
493P TYR* 3.1 45.8 + - + +
494P ILE* 3.9 8.3 - - - +
495P GLN 3.4 0.2 - - - -
496P ASP* 1.3 75.3 - - + +
498P TYR* 1.3 79.3 + - + +
500P CYS* 3.5 21.7 - - - +
511P THR* 5.8 0.2 - - - +
512P ALA* 4.7 7.2 - - + -
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Residues in contact with TYR 498 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494P ILE* 3.1 45.0 + - + +
495P GLN* 4.4 2.5 - - - +
496P ASP 3.3 0.4 - - - -
497P ILE* 1.3 93.1 - - + +
499P SER* 1.3 63.5 + - - +
500P CYS 3.1 8.9 + - - +
512P ALA* 4.7 6.6 - - + +
513P PHE* 2.8 44.1 - + - -
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Residues in contact with SER 499 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495P GLN* 2.8 24.4 + - - -
496P ASP* 3.8 9.0 - - - -
498P TYR* 1.3 75.8 - - - +
500P CYS* 1.3 58.0 + - - +
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Residues in contact with CYS 500 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467P LYS* 4.2 21.1 - - - +
496P ASP 3.3 14.8 + - - +
497P ILE* 3.5 15.9 - - - +
498P TYR* 3.1 8.4 - - - +
499P SER* 1.3 79.3 - - - +
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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