Contacts of the helix formed by residues 494 - 508 (chain Z) in PDB entry 5GJQ
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 ARG 494 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489Z TYR* 4.2 8.7 - - + +
492Z SER 4.0 6.3 - - - +
493Z ASN* 1.3 75.7 - - - +
495Z GLU* 1.3 63.5 + - - +
496Z ASP* 3.5 16.7 + - + +
497Z VAL* 3.9 14.1 + - + +
498Z LEU* 4.0 7.1 + - - +
525Z ILE* 4.9 8.3 - - - +
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Residues in contact with GLU 495 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494Z ARG* 1.3 71.5 - - - +
496Z ASP* 1.3 53.0 + - - +
498Z LEU* 3.0 12.4 + - + +
499Z THR* 2.4 38.7 + - - -
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Residues in contact with ASP 496 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494Z ARG* 3.2 10.6 - - + +
495Z GLU* 1.3 75.3 - - - +
497Z VAL* 1.3 50.7 - - - +
499Z THR* 2.7 11.8 + - - -
500Z LEU* 2.2 41.6 + - - +
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Residues in contact with VAL 497 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485Z LEU* 4.7 22.2 - - + +
489Z TYR* 5.5 6.1 - - + -
494Z ARG* 3.9 14.0 + - + +
495Z GLU 3.4 0.4 - - - -
496Z ASP* 1.3 75.9 - - - +
498Z LEU* 1.3 51.4 + - - +
500Z LEU* 3.2 9.1 - - - +
501Z LEU* 2.3 41.6 + - + +
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Residues in contact with LEU 498 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494Z ARG 4.0 3.6 + - - +
495Z GLU* 3.0 19.5 + - + +
497Z VAL* 1.3 76.3 - - - +
499Z THR* 1.3 56.1 + - - +
501Z LEU* 2.5 11.4 + - - -
502Z LEU* 2.2 44.6 + - + +
522Z CYS* 5.7 11.8 - - + +
534Z VAL* 6.5 0.9 - - + -
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Residues in contact with THR 499 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495Z GLU* 2.4 24.3 + - - -
496Z ASP* 2.7 14.5 + - - -
498Z LEU* 1.3 71.4 - - - +
500Z LEU* 1.3 58.4 + - - +
502Z LEU* 4.2 8.2 - - - +
503Z PRO* 4.5 11.3 - - - +
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Residues in contact with LEU 500 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470Z VAL* 6.5 1.3 - - + -
471Z LEU* 6.3 2.9 - - - -
496Z ASP 2.2 26.6 + - - +
497Z VAL* 3.2 14.6 - - - +
498Z LEU 2.8 2.2 + - - -
499Z THR* 1.3 70.4 - - - +
501Z LEU* 1.3 59.7 + - + +
503Z PRO* 4.0 2.6 - - - +
504Z VAL* 3.5 17.9 + - - +
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Residues in contact with LEU 501 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497Z VAL 2.3 32.4 + - - +
498Z LEU* 2.5 4.1 + - - +
500Z LEU* 1.3 68.0 - - + +
502Z LEU* 1.3 51.4 + - - +
504Z VAL* 2.9 10.0 + - + -
505Z MET* 2.1 42.9 + - + +
518Z THR* 4.1 26.0 - - - -
522Z CYS* 5.8 5.2 - - + -
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Residues in contact with LEU 502 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498Z LEU* 2.2 42.9 + - + +
499Z THR* 4.2 5.6 - - - +
501Z LEU* 1.3 65.2 - - - +
503Z PRO* 1.3 51.2 - - - +
505Z MET* 3.0 10.5 - - - +
506Z GLY* 2.4 32.4 + - - -
537Z THR* 5.3 14.4 - - - -
541Z THR* 5.6 1.2 - - - -
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Residues in contact with PRO 503 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498Z LEU 4.3 0.4 - - - -
499Z THR 4.5 8.8 - - - +
500Z LEU 4.0 6.3 - - - +
501Z LEU 3.3 0.2 - - - -
502Z LEU* 1.3 74.8 - - - +
504Z VAL* 1.3 57.2 + - - +
506Z GLY* 3.0 4.4 + - - +
507Z ASP* 2.3 36.1 + - - +
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Residues in contact with VAL 504 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473Z ASN* 5.0 13.7 - - + -
500Z LEU 3.5 14.6 + - - +
501Z LEU* 2.9 12.9 + - + +
503Z PRO* 1.3 77.1 - - - +
505Z MET* 1.3 51.7 + - - +
507Z ASP* 3.0 12.5 + - - +
508Z SER 2.6 29.6 + - - -
513Z GLU* 3.9 16.1 - - + +
515Z ALA* 3.1 17.4 - - + +
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Residues in contact with MET 505 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501Z LEU* 2.1 28.7 + - + +
502Z LEU* 3.0 18.8 - - - +
504Z VAL* 1.3 65.7 - - - +
506Z GLY* 1.3 58.3 + - - +
508Z SER* 2.8 26.9 + - - -
515Z ALA* 3.4 17.2 - - + +
518Z THR* 6.2 0.2 - - - -
519Z ALA* 6.0 5.6 - - + +
541Z THR* 5.2 12.3 - - - -
546Z SER* 3.9 3.7 - - - -
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Residues in contact with GLY 506 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502Z LEU 2.4 23.3 + - - -
503Z PRO* 3.1 6.7 - - - -
505Z MET* 1.3 67.0 - - - +
507Z ASP* 1.3 60.7 + - - +
541Z THR* 5.1 4.3 - - - -
546Z SER* 3.3 26.4 - - - -
547Z GLU* 3.5 8.8 + - - +
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Residues in contact with ASP 507 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473Z ASN* 6.2 2.7 - - + -
503Z PRO 2.3 26.5 + - - +
504Z VAL* 3.1 18.6 - - - +
506Z GLY* 1.3 71.1 - - - +
508Z SER* 1.3 65.8 + - - +
509Z LYS* 3.6 4.7 - - + +
513Z GLU* 4.3 9.6 - - + -
547Z GLU* 3.0 12.9 - - - +
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Residues in contact with SER 508 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504Z VAL 2.6 16.2 + - - -
505Z MET* 2.8 18.7 + - - +
506Z GLY 3.9 0.2 - - - -
507Z ASP* 1.3 77.0 - - - +
509Z LYS* 1.3 58.1 + - - +
510Z SER 4.3 0.4 - - - -
515Z ALA* 4.7 2.5 - - - -
516Z GLY 5.9 1.1 - - - +
546Z SER* 3.2 28.9 - - - -
547Z GLU* 3.5 4.0 - - - -
548Z THR* 3.5 24.0 + - - -
549Z GLU 5.0 1.6 - - - -
554Z TYR* 5.6 8.7 - - - -
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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