Contacts of the helix formed by residues 553 - 559 (chain A) in PDB entry 3RGZ
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 553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A ILE* 3.2 50.3 - - + +
529A PRO 4.4 2.2 - - - +
530A LYS* 4.6 10.8 - - + -
532A ILE* 4.8 0.7 - - + -
551A ASN* 3.5 7.8 - - + +
552A ILE* 1.3 91.4 - - + +
554A ALA* 1.3 63.3 + - - +
555A GLU* 3.2 22.3 + - + +
556A LEU* 3.3 27.5 + - + +
577A PRO* 4.4 2.1 - - - +
580A MET* 4.6 1.0 - - - +
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Residues in contact with ALA 554 (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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552A ILE 3.5 3.6 + - - -
553A PRO* 1.3 71.8 - - - +
555A GLU* 1.3 64.4 + - - +
556A LEU 3.0 0.7 - - - -
557A GLY* 2.8 24.4 + - - -
577A PRO* 4.1 20.8 - - + +
579A ALA* 4.0 21.9 - - + -
580A MET* 4.0 6.3 + - - +
582A LYS* 4.0 7.9 + - - -
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Residues in contact with GLU 555 (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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530A LYS* 3.2 57.0 + - + +
532A ILE* 4.5 1.1 - - + -
533A GLY* 3.1 24.3 - - - +
553A PRO* 3.1 12.8 - - + +
554A ALA* 1.3 87.8 + - - +
556A LEU* 1.3 57.7 + - - +
557A GLY 3.0 0.4 - - - -
558A ASP* 2.9 32.4 + - - +
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Residues in contact with LEU 556 (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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528A ILE* 4.7 10.5 - - + -
532A ILE* 3.9 24.3 - - + +
538A LEU* 5.9 0.2 - - + -
541A LEU* 3.9 26.9 - - + -
552A ILE* 3.6 31.6 - - + -
553A PRO* 3.3 18.3 + - + +
554A ALA 3.0 1.0 + - - -
555A GLU* 1.3 78.3 - - - +
557A GLY* 1.3 58.6 + - - +
558A ASP 3.0 4.2 + - - -
559A CYS* 3.1 26.3 + - - +
562A LEU* 4.2 25.7 - - + +
565A LEU* 4.2 17.0 - - + -
567A LEU* 5.0 0.2 - - + -
580A MET* 4.4 14.0 - - + +
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Residues in contact with GLY 557 (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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554A ALA 2.8 10.4 + - - -
556A LEU* 1.3 77.1 - - - +
558A ASP* 1.3 57.3 + - - +
559A CYS 3.4 0.2 - - - -
579A ALA 3.4 22.7 - - - -
580A MET* 3.5 15.4 - - - +
582A LYS* 3.2 21.4 + - - +
583A GLN* 2.8 26.0 - - - +
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Residues in contact with ASP 558 (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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533A GLY* 3.6 17.0 - - - +
536A GLU* 2.9 20.8 - - - +
555A GLU* 2.9 31.6 + - - +
557A GLY* 1.3 78.4 - - - +
559A CYS* 1.3 62.2 + - - +
560A ARG* 3.2 6.6 + - - +
582A LYS* 2.7 32.8 + - - -
583A GLN* 4.1 7.7 - - - +
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Residues in contact with CYS 559 (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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532A ILE* 3.3 37.5 - - - -
533A GLY* 3.8 8.1 - - - -
535A LEU 4.2 12.1 - - - +
536A GLU* 3.8 4.3 - - - -
538A LEU* 4.8 9.0 - - - +
556A LEU* 3.1 28.5 + - - +
558A ASP* 1.3 75.2 - - - +
560A ARG* 1.3 63.8 + - - +
561A SER 3.2 2.3 + - - +
562A LEU* 3.6 25.7 + - + +
583A GLN* 3.6 11.6 - - - +
587A ILE* 4.0 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