Contacts of the strand formed by residues 538 - 543 (chain A) in PDB entry 2AG1
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 ALA 538 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A PHE* 3.9 8.7 - - - -
468A LEU 3.0 9.4 + - - +
469A ILE* 4.5 9.9 - - + -
470A VAL* 3.0 26.6 + - - +
513A ALA* 4.8 1.8 - - - +
514A ASP* 3.3 14.4 - - + +
516A TYR* 4.0 11.7 - - + +
531A ALA* 3.9 27.8 - - + -
536A ARG 3.8 3.1 + - - +
537A PRO* 1.3 76.9 - - - +
539A CYS* 1.3 61.7 + - - +
540A ILE* 5.1 0.2 - - + -
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Residues in contact with CYS 539 (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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458A PHE* 3.6 15.7 - - + -
470A VAL 3.3 5.6 - - - -
472A ILE* 3.8 28.5 - - - -
504A TYR 4.0 4.9 - - - -
505A HIS* 3.9 22.4 - - - -
508A ALA* 3.4 22.9 - - + -
514A ASP 2.7 10.3 + - - +
515A GLY* 4.5 1.8 - - - -
516A TYR* 2.8 31.9 + - - -
538A ALA* 1.3 74.3 - - - +
540A ILE* 1.3 69.1 + - - +
541A ASN 4.4 0.7 - - - -
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Residues in contact with ILE 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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469A ILE* 3.9 25.4 - - + -
470A VAL 2.8 11.7 + - - +
471A ILE* 3.5 9.0 - - + -
472A ILE 2.9 27.1 + - - -
516A TYR* 3.8 20.4 - - + -
518A VAL* 3.9 10.8 - - + -
524A PHE* 3.8 13.2 - - + -
527A ALA* 4.1 11.9 - - + +
528A LEU* 3.7 38.1 - - + +
531A ALA* 4.4 4.5 - - + -
538A ALA* 5.1 0.2 - - + -
539A CYS* 1.3 78.2 - - - +
541A ASN* 1.3 60.3 + - - +
542A VAL* 3.4 22.6 + - + +
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Residues in contact with ASN 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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472A ILE* 4.2 7.8 - - - +
474A ASN* 3.1 32.0 + - - +
502A GLY 4.9 0.6 + - - -
503A SER* 4.4 2.2 - - - +
504A TYR* 3.5 28.7 - - - +
505A HIS* 3.1 29.8 + - + +
516A TYR 2.8 19.4 + - - +
517A HIS* 3.3 20.3 + - - +
518A VAL* 2.9 28.3 + - - +
539A CYS* 3.9 3.4 - - - -
540A ILE* 1.3 68.9 - - - +
542A VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 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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370A LEU* 4.0 18.2 - - + -
375A ALA* 4.9 0.2 - - + -
471A ILE* 3.7 20.0 - - + -
472A ILE 2.8 19.1 + - - +
473A MSE 4.5 7.0 - - - -
474A ASN* 2.7 33.1 + - - +
518A VAL* 3.6 23.8 - - + +
524A PHE* 3.7 20.2 - - + -
540A ILE* 3.6 14.8 - - + +
541A ASN* 1.3 72.2 + - - +
543A ALA* 1.3 64.4 + - - +
544A VAL* 3.2 20.2 + - + +
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Residues in contact with ALA 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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370A LEU* 3.9 15.3 + - - +
474A ASN* 3.8 9.2 - - - +
517A HIS* 4.4 16.4 - - + +
518A VAL 2.8 17.8 + - - +
519A ASP* 3.8 23.7 - - + +
541A ASN 3.7 1.6 + - - -
542A VAL* 1.3 72.3 - - - +
544A VAL* 1.3 63.6 + - - +
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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