Contacts of the helix formed by residues 524 - 539 (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 GLU 524 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496X ILE* 6.0 0.5 - - - +
519X LEU* 3.4 25.3 + - + +
522X VAL* 3.3 24.1 + - + +
523X ASN* 1.3 73.6 - - - +
525X TYR* 1.3 63.3 + - - +
526X GLN* 3.3 5.1 + - + +
527X GLU* 2.9 45.5 + - + +
528X ALA* 3.4 18.2 + - - +
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Residues in contact with TYR 525 (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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520X VAL* 4.2 34.2 + - + +
523X ASN* 3.2 54.1 + - - -
524X GLU* 1.3 71.7 - - - +
526X GLN* 1.3 55.9 + - - +
527X GLU 3.4 0.2 - - - -
528X ALA* 3.5 5.6 - - + +
529X MET* 2.7 55.8 + - + +
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Residues in contact with GLN 526 (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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524X GLU* 3.3 2.2 - - + -
525X TYR* 1.3 77.2 - - - +
527X GLU* 1.3 73.4 + - + +
529X MET* 3.6 6.3 + - - +
530X ASP* 3.3 25.2 + - - +
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Residues in contact with GLU 527 (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* 3.2 29.5 + - - +
519X LEU* 3.6 12.7 - - + +
524X GLU* 2.9 46.0 + - + +
525X TYR 3.4 0.2 - - - -
526X GLN* 1.3 90.5 - - + +
528X ALA* 1.3 64.5 + - - +
530X ASP* 3.3 8.7 + - - +
531X GLN* 3.1 26.2 + - - +
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Residues in contact with ALA 528 (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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516X GLY* 4.0 4.5 - - - +
519X LEU* 3.6 19.0 - - + +
520X VAL* 3.8 29.6 - - + +
524X GLU 3.4 12.9 + - - +
525X TYR* 3.2 14.5 + - + +
527X GLU* 1.3 76.0 - - - +
529X MET* 1.3 63.6 + - - +
531X GLN* 3.4 2.9 + - - +
532X TYR* 3.1 32.3 + - + -
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Residues in contact with MET 529 (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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525X TYR* 2.7 40.3 + - + +
526X GLN* 3.8 7.2 - - - +
527X GLU 3.4 0.2 - - - -
528X ALA* 1.3 73.0 - - - +
530X ASP* 1.3 61.4 + - - +
532X TYR* 3.6 8.4 + - - +
533X SER* 3.2 22.9 + - - -
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Residues in contact with ASP 530 (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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526X GLN* 3.3 18.9 + - - +
527X GLU* 3.3 13.1 + - - +
529X MET* 1.3 79.0 - - - +
531X GLN* 1.3 68.9 + - - +
533X SER* 3.4 8.8 + - - -
534X ILE* 3.2 36.5 + - - +
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Residues in contact with GLN 531 (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* 4.6 8.5 + - - -
503X LEU* 3.7 16.8 - - - +
512X HIS* 3.2 54.6 + - - +
515X LEU* 4.0 15.2 - - + +
516X GLY* 3.8 8.5 - - - +
519X LEU* 3.7 17.9 - - + -
527X GLU 3.1 17.6 + - - +
528X ALA 3.4 7.6 + - - +
530X ASP* 1.3 83.4 - - - +
532X TYR* 1.3 64.4 + - - +
534X ILE* 3.4 8.5 + - - +
535X ALA* 3.2 20.6 + - - +
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Residues in contact with TYR 532 (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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512X HIS 5.4 0.4 - - - -
513X ARG* 4.5 25.8 - - + +
516X GLY* 3.8 24.5 - - - -
517X ASP* 2.7 32.2 + - - -
520X VAL* 4.5 14.2 - - + +
528X ALA* 3.1 26.1 + - + +
529X MET* 3.9 9.2 - - - +
531X GLN* 1.3 77.6 - - - +
533X SER* 1.3 52.0 + - - +
535X ALA* 3.3 8.2 + - + +
536X LEU* 2.8 46.3 + - + +
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Residues in contact with SER 533 (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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529X MET 3.2 14.8 + - - -
530X ASP* 3.5 14.1 - - - -
531X GLN 3.3 0.2 - - - -
532X TYR* 1.3 76.9 - - - +
534X ILE* 1.3 59.5 + - - +
536X LEU* 3.1 13.9 + - - +
537X SER* 2.9 28.1 + - - -
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Residues in contact with ILE 534 (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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508X ASP* 5.5 0.4 - - - +
512X HIS* 3.5 39.0 - - + +
530X ASP* 3.2 28.6 + - - +
531X GLN* 3.8 9.4 - - - +
532X TYR 3.4 0.2 - - - -
533X SER* 1.3 73.9 - - - +
535X ALA* 1.3 63.7 + - - +
537X SER* 2.7 25.9 + - - +
538X LEU* 3.1 16.5 + - + +
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Residues in contact with ALA 535 (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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509X CYS 4.4 6.7 - - - +
512X HIS* 4.0 18.1 - - + +
513X ARG* 4.1 20.2 - - + +
531X GLN 3.2 13.2 + - - +
532X TYR* 3.4 12.8 - - + +
534X ILE* 1.3 76.8 - - - +
536X LEU* 1.3 57.1 + - + +
538X LEU* 3.5 2.6 + - - -
539X ASP* 2.9 44.7 + - - +
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Residues in contact with LEU 536 (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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532X TYR* 2.8 30.1 + - + +
533X SER* 3.1 12.5 + - - +
535X ALA* 1.3 78.0 - - + +
537X SER* 1.3 57.0 + - - +
539X ASP 4.0 8.5 - - - +
540X PRO* 3.1 39.5 - - + +
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Residues in contact with SER 537 (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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533X SER 2.9 10.6 + - - -
534X ILE* 2.7 29.5 + - - +
536X LEU* 1.3 77.1 - - - +
538X LEU* 1.3 66.3 + - - +
540X PRO* 3.9 7.4 - - - +
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Residues in contact with LEU 538 (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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319X GLY 5.5 2.6 - - - +
508X ASP* 3.7 37.2 - - + +
509X CYS* 3.9 10.3 - - + +
512X HIS* 3.8 15.5 - - + -
534X ILE* 3.1 22.2 + - + +
535X ALA* 4.8 1.1 - - - -
537X SER* 1.3 85.1 + - - +
539X ASP* 1.3 68.9 + - - +
540X PRO* 3.7 4.4 - - - +
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Residues in contact with ASP 539 (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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509X CYS* 4.1 28.5 - - - +
535X ALA* 2.9 23.3 + - - +
536X LEU* 3.4 10.1 - - - +
538X LEU* 1.3 87.3 - - - +
540X PRO* 1.4 65.9 - - - +
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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