Contacts of the helix formed by residues 574 - 582 (chain A) in PDB entry 1AUQ
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 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A ILE 4.7 0.2 - - - +
500A SER* 4.5 6.1 - - - +
501A GLU* 3.5 36.3 - - + +
544A LEU 5.9 1.6 - - - +
546A ILE* 3.7 43.2 - - + +
572A LYS 3.7 2.2 - - - +
573A ARG* 1.4 83.8 - - + +
575A SER* 1.3 54.9 + - - +
577A LEU* 3.3 12.5 + - + +
578A ARG* 2.9 50.3 + - - +
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Residues in contact with SER 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A GLU* 2.6 34.9 + - - -
573A ARG* 3.7 12.5 - - - +
574A PRO* 1.3 70.8 - - - +
576A GLU* 1.3 66.6 + - - +
578A ARG* 3.4 23.7 + - - +
579A ARG* 3.1 31.5 + - - +
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Residues in contact with GLU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ILE* 6.0 1.2 - - - +
572A LYS* 3.5 37.5 + - + +
573A ARG* 3.0 22.7 + - + +
575A SER* 1.3 79.0 + - - +
577A LEU* 1.3 68.2 + - - +
579A ARG* 2.9 35.1 + - - +
580A ILE* 3.0 34.7 + - + +
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Residues in contact with LEU 577 (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 MET* 3.9 16.6 - - + +
546A ILE* 3.8 28.9 - - + -
553A VAL* 4.2 11.0 - - + -
566A ILE* 3.6 37.6 - - + +
570A ASP* 4.5 13.7 - - + +
572A LYS* 3.8 39.7 - - + +
573A ARG 3.1 10.0 + - - +
574A PRO* 3.6 7.0 - - + +
576A GLU* 1.3 77.7 - - - +
578A ARG* 1.3 61.6 + - - +
580A ILE* 3.1 5.4 + - - +
581A ALA* 3.0 21.8 + - - +
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Residues in contact with ARG 578 (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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501A GLU* 4.4 2.8 + - - +
504A LEU* 3.8 27.3 - - - +
538A VAL* 3.5 21.7 - - + +
541A MET* 3.9 27.1 + - + -
542A GLU* 3.5 45.2 + - - +
546A ILE* 5.1 2.0 - - + +
574A PRO* 2.9 41.1 + - - +
575A SER* 3.6 28.3 - - - +
576A GLU 3.2 0.2 - - - -
577A LEU* 1.3 74.8 - - - +
579A ARG* 1.3 63.0 + - - +
581A ALA* 3.3 4.0 + - - +
582A SER* 3.1 18.7 + - - -
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Residues in contact with ARG 579 (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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573A ARG* 6.2 0.4 - - - +
575A SER* 3.1 20.3 + - - +
576A GLU* 2.9 42.5 + - - +
578A ARG* 1.3 75.2 - - - +
580A ILE* 1.3 67.6 + - + +
582A SER* 3.0 21.6 + - - +
583A GLN* 3.1 36.0 + - + +
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Residues in contact with ILE 580 (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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565A TYR* 3.8 29.4 - - + +
566A ILE* 3.5 30.7 - - + -
572A LYS* 4.1 22.0 - - + +
576A GLU* 3.0 40.9 + - + +
577A LEU* 3.5 6.5 - - - +
579A ARG* 1.3 76.3 - - + +
581A ALA* 1.3 63.9 + - - +
583A GLN* 3.1 22.6 + - - +
584A VAL* 3.2 12.3 + - - +
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Residues in contact with ALA 581 (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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519A LEU* 5.6 0.3 - - - +
534A LYS* 3.8 11.0 - - - +
537A VAL* 4.3 12.9 - - + +
538A VAL* 4.2 8.3 - - + -
541A MET* 3.9 22.2 - - - -
555A VAL* 4.5 12.8 - - + -
566A ILE* 5.2 0.6 - - + +
577A LEU 3.0 11.1 + - - +
578A ARG 3.5 8.3 - - - +
579A ARG 3.2 0.4 - - - -
580A ILE* 1.3 79.5 - - - +
582A SER* 1.3 60.2 + - - +
584A VAL* 3.0 29.7 + - + +
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Residues in contact with SER 582 (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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531A GLU* 4.3 2.4 - - - +
534A LYS* 2.9 30.2 + - - +
535A ALA* 6.3 0.7 - - - -
538A VAL* 3.9 15.2 - - - +
578A ARG 3.1 13.0 + - - -
579A ARG* 3.0 16.3 + - - +
581A ALA* 1.3 76.3 - - - +
583A GLN* 1.3 61.2 + - - +
584A VAL 3.3 1.3 - - - -
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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