Contacts of the helix formed by residues 506 - 515 (chain A) in PDB entry 1ASZ
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 PRO 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ALA* 4.2 16.4 - - + -
504A GLU 3.4 4.7 - - - +
505A ASP* 1.3 98.8 - - - +
507A GLY* 1.3 53.8 + - - +
508A LEU 3.3 0.3 + - - -
509A LYS* 3.5 13.5 + - + +
510A ASP* 4.2 0.3 - - - +
556B ARG* 2.5 32.4 + - - +
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Residues in contact with GLY 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ALA* 4.2 8.6 - - - +
279A PRO 3.9 13.7 - - - -
280A SER* 4.1 14.0 - - - -
304A PHE* 4.7 2.6 - - - -
505A ASP* 2.7 17.0 + - - -
506A PRO* 1.3 75.6 - - - +
508A LEU* 1.3 61.3 + - - +
510A ASP* 5.0 0.2 - - - +
511A TYR* 4.4 9.0 + - - +
556B ARG* 3.5 19.9 + - - -
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A SER 3.9 19.1 - - - +
281A GLU* 5.0 2.7 - - + -
304A PHE* 3.8 28.3 - - + -
455A PHE* 4.3 10.5 - - + -
496A MET* 4.2 19.1 - - + -
501A LEU* 3.6 31.9 - - + -
502A SER 3.4 24.5 - - - +
503A PRO* 4.3 1.8 - - + -
505A ASP* 3.3 18.9 + - + +
506A PRO 3.3 0.4 - - - -
507A GLY* 1.3 77.6 - - - +
509A LYS* 1.3 66.9 + - - +
511A TYR* 2.9 16.9 + - + +
512A CYS* 2.9 14.7 + - - +
676R A 4.4 3.1 - - - +
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Residues in contact with LYS 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A PRO* 3.5 19.2 + - - +
504A GLU 4.8 2.0 - - - +
505A ASP 2.9 14.8 + - - +
506A PRO* 3.5 8.4 + - + +
508A LEU* 1.3 74.9 - - - +
510A ASP* 1.3 95.4 + - - +
512A CYS* 3.1 4.5 + - - +
513A ASP* 3.0 67.3 + - - +
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLN* 3.9 5.9 + - - +
507A GLY 5.0 0.4 - - - +
508A LEU 3.4 0.4 - - - -
509A LYS* 1.3 106.9 + - - +
511A TYR* 1.3 63.1 + - - +
513A ASP* 3.8 1.4 - - - +
514A GLY* 3.4 17.7 + - - -
233B ASP 5.6 1.9 - - - +
236B VAL* 5.5 2.4 - - - +
556B ARG* 3.2 39.1 + - - +
557B PRO* 3.6 34.0 - - + +
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Residues in contact with TYR 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A PHE* 3.3 50.5 - + + -
307A GLN* 2.6 48.5 + - + -
308A GLN* 2.8 44.6 + - - +
455A PHE* 3.5 30.3 - + - -
456A TYR* 3.5 15.4 - - - +
492A LEU* 4.4 11.1 - - + +
496A MET* 4.2 9.4 - - + -
507A GLY 4.4 3.3 + - - +
508A LEU* 2.9 11.7 + - + +
510A ASP* 1.3 78.5 - - - +
512A CYS* 1.3 66.7 + - - +
514A GLY 3.7 0.2 + - - -
515A PHE* 3.7 16.7 - + - -
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Residues in contact with CYS 512 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A HIS* 2.9 38.6 - - - -
492A LEU* 4.6 3.6 - - - -
493A GLN* 3.6 26.0 - - - -
496A MET* 4.1 15.5 - - + -
503A PRO* 4.1 13.2 - - + -
508A LEU 2.9 12.2 + - - +
509A LYS* 3.1 8.2 + - - +
511A TYR* 1.3 76.9 - - - +
513A ASP* 1.3 59.2 + - - +
514A GLY 3.0 4.3 - - - -
515A PHE* 2.8 36.8 + - - +
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Residues in contact with ASP 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A HIS* 3.7 8.7 - - + +
509A LYS* 3.0 55.9 + - - +
510A ASP* 3.8 3.1 - - - +
512A CYS* 1.3 72.8 - - - +
514A GLY* 1.3 64.7 + - - +
515A PHE 2.8 6.9 + - - -
516A SER* 2.9 29.4 + - - +
517A TYR* 3.2 28.3 + - + +
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Residues in contact with GLY 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLN* 3.9 11.4 - - - -
311A VAL* 3.3 24.6 - - - +
510A ASP 3.4 14.0 + - - -
512A CYS 2.9 3.4 + - - -
513A ASP* 1.3 83.1 + - - +
515A PHE* 1.3 60.5 + - - +
517A TYR* 3.6 25.2 + - - +
518A GLY 4.7 0.2 + - - -
236B VAL* 4.6 9.2 - - - -
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Residues in contact with PHE 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLN* 3.8 24.0 - - + -
308A GLN* 4.8 0.9 - - - -
311A VAL* 3.8 15.9 - - + -
486A ILE 4.1 8.5 - - - -
487A HIS* 4.0 15.6 - - - +
489A HIS* 3.9 20.4 - - + +
492A LEU* 3.3 35.4 - - + -
511A TYR* 3.7 25.8 - + - -
512A CYS 2.8 19.1 + - - +
513A ASP 2.8 0.2 - - - -
514A GLY* 1.3 76.0 - - - +
516A SER* 1.3 50.6 + - - +
517A TYR 2.9 4.7 - - - -
518A GLY* 2.7 32.4 + - - -
519A CYS* 3.5 41.4 + - + +
522A HIS* 4.3 4.0 - + - -
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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