Contacts of the helix formed by residues 492 - 506 (chain X) 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 TYR 492 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487X SER* 4.0 28.4 + - - -
490X GLN* 3.3 41.2 + - + +
491X LYS* 1.3 74.1 - - - +
493X GLU* 1.3 78.1 + - - +
494X ASP 3.5 0.2 - - - -
495X GLY 3.2 9.8 + - - -
496X ILE* 3.4 9.4 + - - +
517X ASP 5.7 1.1 - - - -
518X PHE* 3.4 41.4 - + + +
521X ALA* 3.6 36.6 - - + -
522X VAL* 5.1 1.8 - - + -
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Residues in contact with GLU 493 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491X LYS* 3.5 3.4 - - + +
492X TYR* 1.3 86.2 - - - +
494X ASP* 1.3 63.8 + - - +
495X GLY 3.4 0.3 + - - -
496X ILE* 3.6 14.6 + - - +
497X ALA* 3.6 12.3 + - - +
521X ALA 5.2 1.4 - - - +
522X VAL* 3.5 34.9 - - - +
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Residues in contact with ASP 494 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486X LEU* 3.5 19.3 - - + +
491X LYS* 2.3 71.5 - - - +
493X GLU* 1.3 72.9 - - - +
495X GLY* 1.3 61.9 + - - -
497X ALA* 3.6 8.0 + - - +
498X LEU* 3.2 23.7 + - - +
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Residues in contact with GLY 495 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483X ALA* 6.0 1.8 - - - +
486X LEU* 3.5 19.7 - - - -
492X TYR 3.2 3.0 + - - -
494X ASP* 1.3 83.0 + - - +
496X ILE* 1.3 58.9 + - - +
498X LEU* 3.4 5.2 + - - +
499X LEU* 2.8 33.1 + - - +
518X PHE* 3.5 24.0 - - - -
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Residues in contact with ILE 496 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492X TYR 3.4 12.3 + - - +
493X GLU* 3.6 8.3 + - - +
494X ASP 3.5 0.4 - - - -
495X GLY* 1.3 72.1 - - - +
497X ALA* 1.3 66.0 + - - +
499X LEU* 4.0 4.4 - - - +
500X ARG* 3.0 53.9 + - + +
515X LEU* 4.3 8.7 - - + -
518X PHE* 3.7 30.0 - - + +
519X LEU* 3.8 24.7 - - + -
522X VAL* 3.5 31.6 - - + -
524X GLU* 6.0 0.2 - - - +
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Residues in contact with ALA 497 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493X GLU 3.6 10.1 + - - +
494X ASP* 3.7 11.4 - - - +
495X GLY 3.4 0.2 - - - -
496X ILE* 1.3 80.8 - - - +
498X LEU* 1.3 61.1 + - - +
500X ARG* 3.7 5.2 + - - +
501X ASN* 3.5 17.5 + - - +
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Residues in contact with LEU 498 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469X LEU* 4.3 13.7 - - + -
479X VAL* 4.6 12.3 - - + -
482X LYS* 3.7 50.9 - - + +
483X ALA* 4.9 9.6 - - + +
486X LEU* 4.1 21.3 - - + -
494X ASP 3.2 13.3 + - - +
495X GLY* 3.7 3.1 - - - +
497X ALA* 1.3 76.7 - - - +
499X LEU* 1.3 65.6 + - + +
501X ASN* 3.3 18.5 + - + +
502X ALA* 3.4 10.2 + - - +
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Residues in contact with LEU 499 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479X VAL* 3.7 24.0 - - + -
483X ALA* 4.2 18.4 - - + -
495X GLY 2.8 22.0 + - - +
496X ILE* 4.0 2.2 - - - +
498X LEU* 1.3 72.5 - - + +
500X ARG* 1.3 59.0 + - - +
502X ALA* 3.3 6.6 + - - +
503X LEU* 2.8 31.2 + - + +
511X LEU* 3.9 21.3 - - + +
514X ILE* 3.7 17.7 - - + +
515X LEU* 3.5 50.0 - - + +
518X PHE* 4.5 12.1 - - + -
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Residues in contact with ARG 500 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496X ILE* 3.0 35.8 + - + +
497X ALA* 3.9 6.5 - - - +
498X LEU 3.3 0.2 - - - -
499X LEU* 1.3 73.7 - - - +
501X ASN* 1.3 54.8 + - - +
503X LEU* 3.2 11.4 + - - +
504X ALA* 2.8 32.9 + - - +
515X LEU* 3.6 35.8 - - + +
519X LEU* 4.0 8.5 - - - +
527X GLU* 3.2 27.9 + - - +
531X GLN* 4.6 10.0 + - - -
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Residues in contact with ASN 501 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474X ASP* 3.1 19.3 + - - +
497X ALA 3.5 9.1 + - - +
498X LEU* 3.3 14.7 + - + +
500X ARG* 1.3 75.4 - - - +
502X ALA* 1.3 64.1 + - - +
504X ALA* 3.3 22.0 + - - +
505X ASN 3.9 0.2 + - - -
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Residues in contact with ALA 502 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474X ASP* 3.1 16.8 + - + +
479X VAL* 3.6 41.3 - - + -
498X LEU 3.4 3.7 + - - +
499X LEU 3.3 10.9 + - - +
501X ASN* 1.3 76.0 - - - +
503X LEU* 1.3 61.2 - - - +
505X ASN* 3.2 20.8 + - - +
506X GLN 3.7 2.9 + - - -
507X SER* 4.3 6.2 + - - -
511X LEU* 4.2 16.1 - - + +
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Residues in contact with LEU 503 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499X LEU* 2.8 20.5 + - + +
500X ARG* 3.2 15.4 + - - +
502X ALA* 1.3 70.4 - - - +
504X ALA* 1.3 52.8 + - - +
506X GLN* 2.3 49.8 + - - +
508X ASP* 4.6 7.2 - - - +
511X LEU* 3.7 35.9 - - + -
512X HIS* 3.8 27.4 - - + +
515X LEU* 3.7 24.7 - - + -
531X GLN* 3.7 22.9 - - - +
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Residues in contact with ALA 504 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500X ARG 2.8 15.6 + - - +
501X ASN* 3.3 19.5 - - - +
502X ALA 3.2 0.8 - - - -
503X LEU* 1.3 73.0 - - - +
505X ASN* 1.3 63.2 + - - +
506X GLN* 3.6 9.3 + - - +
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Residues in contact with ASN 505 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288X LYS* 5.2 3.5 + - - -
473X PRO* 4.2 8.3 + - - +
474X ASP* 3.1 38.3 + - + +
501X ASN 3.9 1.1 + - - +
502X ALA 3.2 11.5 + - - +
503X LEU 3.2 0.8 - - - -
504X ALA* 1.3 80.9 - - - +
506X GLN* 1.3 65.2 + - - +
507X SER* 3.5 6.8 + - - +
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Residues in contact with GLN 506 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288X LYS* 4.1 9.4 + - - -
502X ALA 3.7 0.8 + - - -
503X LEU* 2.3 47.5 + - - +
504X ALA* 3.6 11.5 + - - +
505X ASN* 1.3 77.4 - - - +
507X SER* 1.3 65.3 + - - +
508X ASP* 3.0 37.9 - - - +
512X HIS* 4.1 15.0 - - - +
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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