Contacts of the helix formed by residues 509 - 523 (chain X) in PDB entry 5A31
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 CYS 509 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317X ARG 5.2 10.1 - - - +
476X ILE* 6.0 4.9 - - + -
507X SER 4.3 5.4 - - - +
508X ASP* 1.3 78.4 - - - +
510X VAL* 1.3 82.3 + - + +
511X LEU 3.5 0.3 + - - -
512X HIS* 3.5 15.6 + - - +
513X ARG* 3.8 3.5 + - - +
535X ALA* 4.4 6.6 - - - +
538X LEU* 3.9 10.5 - - - +
539X ASP* 4.2 26.0 - - - +
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Residues in contact with VAL 510 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476X ILE* 4.1 16.8 - - + -
480X VAL* 3.8 26.0 - - + -
509X CYS* 1.3 88.1 - - - +
511X LEU* 1.3 64.2 + - - +
513X ARG* 3.1 34.0 + - + +
514X ILE* 2.9 29.8 + - + +
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Residues in contact with LEU 511 (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 5.7 0.4 - - - +
476X ILE* 4.3 16.4 - - + +
479X VAL* 4.4 8.7 - - + -
480X VAL* 3.5 29.8 - - + -
499X LEU* 4.1 22.6 - - + +
502X ALA* 3.4 29.4 - - + -
503X LEU* 3.6 20.1 - - + +
507X SER* 3.3 24.5 - - - +
508X ASP 3.0 14.5 + - - +
510X VAL* 1.3 82.3 - - - +
512X HIS* 1.3 57.7 + - - +
514X ILE* 3.2 5.2 + - + +
515X LEU* 2.9 29.8 + - - +
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Residues in contact with HIS 512 (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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503X LEU* 3.8 20.6 - - + +
506X GLN* 4.2 12.4 + - - +
508X ASP* 3.0 51.1 + - + -
509X CYS 3.5 7.7 + - - +
510X VAL 3.3 0.8 - - - -
511X LEU* 1.3 76.3 - - - +
513X ARG* 1.3 63.1 - - - +
515X LEU* 3.3 2.0 + - - +
516X GLY* 3.0 18.9 + - - -
531X GLN* 3.4 45.8 + - - +
534X ILE* 3.3 33.3 - - + +
535X ALA 4.4 4.5 - - - +
538X LEU* 3.9 4.7 - - + -
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Residues in contact with ARG 513 (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 3.8 1.4 + - - -
510X VAL* 3.1 30.2 + - + +
512X HIS* 1.3 77.7 - - - +
514X ILE* 1.3 82.8 + - - +
516X GLY* 3.3 3.7 + - - -
517X ASP* 3.1 43.6 + - - +
531X GLN 5.3 1.3 - - - -
532X TYR* 4.6 20.9 - - + -
535X ALA* 4.2 19.6 - - + +
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Residues in contact with ILE 514 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480X VAL* 4.4 23.8 - - + +
483X ALA* 4.1 21.8 - - + -
499X LEU* 3.5 19.1 - - + -
510X VAL* 2.9 26.1 + - + +
511X LEU* 3.2 7.2 + - - +
513X ARG* 1.3 103.5 - - - +
515X LEU* 1.3 63.4 + - - +
517X ASP* 3.2 12.0 + - + +
518X PHE* 3.1 31.8 + - + -
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Residues in contact with LEU 515 (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* 4.2 10.3 - - + +
499X LEU* 3.3 27.7 - - + +
500X ARG* 3.5 35.2 - - + +
503X LEU* 3.2 31.2 - - + -
511X LEU 2.9 14.1 + - - +
512X HIS 3.3 3.6 + - - +
514X ILE* 1.3 75.2 - - - +
516X GLY* 1.3 63.2 + - - +
518X PHE* 3.2 3.5 + - - -
519X LEU* 3.0 53.6 + - + +
531X GLN* 4.1 11.9 - - + +
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Residues in contact with GLY 516 (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 3.0 11.8 + - - -
513X ARG 3.3 4.4 + - - -
515X LEU* 1.3 76.6 - - - +
517X ASP* 1.3 60.6 + - - +
519X LEU 3.4 1.0 + - - -
520X VAL* 3.3 26.0 + - - +
528X ALA* 3.7 8.3 - - - +
531X GLN* 3.7 21.6 - - - +
532X TYR* 3.6 19.2 - - - -
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Residues in contact with ASP 517 (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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513X ARG* 3.1 46.2 + - - +
514X ILE* 3.2 15.8 + - + +
516X GLY* 1.3 74.4 - - - +
518X PHE* 1.3 71.0 + - + +
520X VAL* 3.1 26.1 - - - +
521X ALA* 3.5 4.2 + - - +
532X TYR* 2.6 26.2 + - - -
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Residues in contact with PHE 518 (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* 3.4 30.5 - - + -
486X LEU* 4.0 9.4 - - + -
487X SER* 3.8 26.0 - - - -
492X TYR* 3.4 36.1 - + - +
495X GLY* 3.5 30.1 - - - -
496X ILE* 3.6 18.3 - - + +
499X LEU* 4.9 4.7 - - + -
514X ILE* 3.1 26.9 + - + +
515X LEU* 3.7 6.7 - - - +
517X ASP* 1.3 82.4 - - + +
519X LEU* 1.3 61.9 + - - +
521X ALA* 2.9 25.5 + - - +
522X VAL* 3.0 13.3 + - - +
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Residues in contact with LEU 519 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496X ILE* 3.4 25.1 - - + -
500X ARG* 3.9 10.8 - - - +
515X LEU* 3.0 29.1 + - + +
516X GLY 3.8 4.5 - - - +
517X ASP 3.3 0.2 - - - -
518X PHE* 1.3 78.6 - - - +
520X VAL* 1.3 56.6 + - - +
522X VAL* 3.0 4.7 + - + +
523X ASN 2.9 22.0 + - - -
524X GLU* 3.3 35.5 + - + +
527X GLU* 3.3 42.2 - - + +
528X ALA* 3.4 10.5 - - - +
531X GLN* 3.6 19.7 - - + +
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Residues in contact with VAL 520 (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 3.3 15.4 + - - +
517X ASP* 3.1 19.5 - - - +
518X PHE 3.2 0.8 - - - -
519X LEU* 1.3 76.0 - - - +
521X ALA* 1.3 59.0 + - - +
523X ASN* 2.9 22.3 + - - +
525X TYR* 4.0 30.0 + - + +
528X ALA* 3.6 15.7 - - + -
532X TYR* 4.7 11.0 - - + +
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Residues in contact with ALA 521 (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* 3.3 49.2 - - + -
493X GLU* 4.6 5.9 - - - +
517X ASP 3.5 4.0 + - - +
518X PHE 2.9 14.1 + - - +
520X VAL* 1.3 79.6 - - + +
522X VAL* 1.3 61.0 + - - +
523X ASN* 3.1 4.2 + - - +
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Residues in contact with VAL 522 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492X TYR* 5.5 0.9 - - + +
493X GLU* 3.3 28.0 - - - +
496X ILE* 3.1 36.8 - - + -
518X PHE 3.0 4.0 + - - +
519X LEU* 3.0 11.8 + - + +
521X ALA* 1.3 74.4 - - - +
523X ASN* 1.3 67.3 + - - +
524X GLU* 4.1 23.8 - - + +
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Residues in contact with ASN 523 (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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519X LEU 2.9 3.8 + - - -
520X VAL 2.9 16.2 + - - +
521X ALA 4.5 2.2 + - - +
522X VAL* 1.3 82.2 - - - +
524X GLU* 1.3 58.6 + - - +
525X TYR* 3.1 33.3 + - - -
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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