Contacts of the helix formed by residues 539 - 548 (chain A) in PDB entry 1RY2
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 ASN 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ASP* 5.1 5.3 + - - -
536A ILE* 3.0 25.9 + - - +
537A TRP 2.9 24.9 + - - -
538A LYS* 1.3 82.9 - - - +
540A HIS* 1.3 58.7 + - - +
541A ASP* 2.9 16.8 + - + +
542A ARG* 3.1 45.0 + - - +
543A TYR 3.8 4.5 + - - -
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Residues in contact with HIS 540 (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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121A GLN* 4.8 18.4 + - - -
534A ARG 4.0 7.2 - - - -
535A THR* 3.0 28.9 + - - +
536A ILE 4.0 0.6 + - - -
538A LYS 4.1 0.2 - - - -
539A ASN* 1.3 72.1 - - - +
541A ASP* 1.3 57.9 + - - +
543A TYR* 3.3 36.9 - + - +
544A LEU* 3.1 46.1 + - + +
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Residues in contact with ASP 541 (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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539A ASN* 2.9 7.1 - - + -
540A HIS* 1.3 75.7 - - - +
542A ARG* 1.3 72.0 + - - +
543A TYR 3.1 1.3 - - - -
544A LEU* 3.2 14.3 + - - +
545A ASP* 3.2 35.6 + - - +
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Residues in contact with ARG 542 (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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326A ALA* 5.7 10.7 - - - +
328A LYS* 5.6 6.5 - - + -
536A ILE* 4.2 13.2 - - + -
539A ASN* 3.1 30.8 + - - +
541A ASP* 1.3 83.0 - - - +
543A TYR* 1.3 61.4 + - - +
545A ASP* 3.9 5.1 - - + -
546A THR* 2.5 40.4 + - - +
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Residues in contact with TYR 543 (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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120A PHE 4.9 5.4 + - - -
121A GLN* 6.0 0.7 - - - -
123A ASN* 5.9 0.9 - - - +
330A VAL* 6.2 0.2 - - + -
532A PHE* 3.0 25.9 - + - -
533A ALA* 2.8 27.3 + - + -
534A ARG* 3.5 17.9 + - - -
535A THR* 3.5 28.0 - - - -
536A ILE* 3.9 16.9 - - + +
539A ASN 3.8 1.8 + - - -
540A HIS* 3.3 42.8 + + - +
542A ARG* 1.3 79.2 - - - +
544A LEU* 1.3 61.9 + - + +
547A TYR* 2.9 61.5 + + - +
548A LEU* 4.4 17.0 - - + +
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Residues in contact with LEU 544 (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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121A GLN* 5.2 18.2 - - + +
540A HIS* 3.1 43.3 - - + +
541A ASP* 3.2 16.5 + - - +
543A TYR* 1.3 87.0 - - + +
545A ASP* 1.3 54.9 + - - +
548A LEU* 2.9 28.4 + - + +
549A ASN* 2.6 48.7 + - - +
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Residues in contact with ASP 545 (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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541A ASP* 3.2 24.8 + - - +
542A ARG* 3.9 6.2 - - + +
544A LEU* 1.3 75.1 - - - +
546A THR* 1.3 59.5 + - - +
549A ASN* 2.9 22.0 + - - +
550A PRO* 3.0 22.3 - - - +
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Residues in contact with THR 546 (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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328A LYS* 5.0 8.1 - - + +
536A ILE* 5.0 1.6 - - - +
542A ARG* 2.5 35.0 + - - +
543A TYR 3.9 1.3 - - - -
545A ASP* 1.3 78.6 - - - +
547A TYR* 1.3 90.8 + - + +
550A PRO* 3.6 2.9 - - - +
556A PHE* 3.5 24.3 - - - -
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Residues in contact with TYR 547 (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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328A LYS* 3.0 24.1 - - + +
330A VAL* 4.8 3.3 - - + +
473A GLU* 2.6 44.3 + - + +
532A PHE* 4.8 4.5 - + + -
536A ILE* 3.9 23.0 - - + +
543A TYR* 2.9 42.4 + + + +
546A THR* 1.3 99.9 - - + +
548A LEU* 1.3 71.0 + - + +
549A ASN 3.9 0.2 - - - -
550A PRO* 4.0 3.1 - - - -
554A TYR 4.1 0.5 - - - +
555A TYR* 3.6 31.0 - + + -
556A PHE* 3.1 34.8 + - - +
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Residues in contact with LEU 548 (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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120A PHE* 4.0 52.0 - - + +
121A GLN* 4.6 5.6 - - + +
532A PHE* 4.9 2.5 - - + -
543A TYR* 4.4 21.8 - - + +
544A LEU* 2.9 27.3 + - + +
547A TYR* 1.3 88.3 - - + +
549A ASN* 1.3 68.1 + - - +
550A PRO* 3.5 2.5 - - - -
551A TYR 4.1 2.9 - - - +
552A PRO* 3.7 20.1 - - - +
553A GLY 4.5 1.7 + - - -
554A TYR 3.6 19.1 - - - +
555A TYR* 4.2 9.4 - - + -
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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