Contacts of the helix formed by residues 456 - 464 (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 GLY 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ARG* 3.7 13.6 - - - +
454A SER 3.0 2.0 + - - -
455A ILE* 1.3 78.2 - - - +
457A GLU* 1.3 55.9 + - - +
458A PHE 3.0 6.5 - - - -
459A ASP* 2.9 31.7 + - - +
511A PHE* 3.9 17.6 - - - -
452B GLY* 4.4 13.2 + - - -
455B ILE* 4.2 8.8 - - - +
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Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.4 7.6 - - - +
48A ARG* 3.0 32.5 + - - +
49A HIS* 3.4 7.3 + - - +
52A ALA* 3.4 32.4 - - + +
425A PHE* 3.7 22.9 - - + -
426A GLY 5.2 1.3 - - - +
429A LEU* 4.2 8.3 - - + +
454A SER* 2.9 25.5 + - - +
456A GLY* 1.3 72.4 - - - +
458A PHE* 1.3 64.6 + - - +
459A ASP 3.1 0.4 - - - -
460A THR* 2.6 42.7 + - - +
461A LEU* 3.0 16.5 + - - +
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Residues in contact with PHE 458 (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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425A PHE* 3.7 18.2 - + - -
451A VAL* 4.6 5.2 - - + -
455A ILE* 3.3 40.0 + - + +
456A GLY 3.0 0.4 - - - -
457A GLU* 1.3 78.7 - - - +
459A ASP* 1.3 61.0 + - - +
461A LEU* 3.4 15.4 + - + +
462A VAL* 3.2 26.3 + - - +
470A VAL* 3.8 28.9 - - + -
472A ILE* 5.3 0.4 - - + -
504A TYR 5.0 1.1 - - - -
508A ALA* 4.0 23.1 - - + -
511A PHE* 3.8 20.4 - + + -
513A ALA* 4.1 11.4 - - + -
538A ALA 3.9 13.9 - - - -
539A CYS* 3.6 36.1 - - + -
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Residues in contact with ASP 459 (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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48A ARG* 3.1 32.3 + - + +
456A GLY 2.9 14.7 + - - +
458A PHE* 1.3 78.1 - - - +
460A THR* 1.3 56.2 + - - +
462A VAL* 3.3 2.4 + - - +
463A ARG* 2.6 55.2 + - - +
511A PHE* 3.7 23.9 - - + -
499B LEU* 4.0 0.7 - - - +
501B ASN* 2.8 46.3 + - - +
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Residues in contact with THR 460 (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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45A ILE* 4.7 4.7 - - + -
46A ASP 3.5 21.1 - - - +
47A THR* 4.1 6.7 - - + -
48A ARG* 3.4 10.2 + - - +
429A LEU* 3.8 17.3 - - + -
457A GLU* 2.6 33.2 + - - +
459A ASP* 1.3 75.4 - - - +
461A LEU* 1.3 60.4 + - - +
463A ARG* 3.1 19.9 + - - +
464A LYS* 2.8 47.8 + - + +
466A LEU* 5.4 0.2 - - - -
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Residues in contact with LEU 461 (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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425A PHE* 3.6 31.4 - - + -
429A LEU* 3.5 31.9 - - + -
457A GLU 3.0 8.1 + - - +
458A PHE* 3.4 23.1 - - + +
460A THR* 1.3 76.9 - - - +
462A VAL* 1.3 56.5 + - - +
465A GLN* 2.9 8.7 + - - -
466A LEU* 2.9 56.7 + - + +
468A LEU* 4.1 26.5 - - + +
470A VAL* 4.5 1.1 - - + -
537A PRO* 3.9 16.1 - - + +
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Residues in contact with VAL 462 (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 3.2 11.2 + - - +
459A ASP 3.3 4.7 + - - +
461A LEU* 1.3 76.1 - - - +
463A ARG* 1.3 66.2 + - - +
465A GLN* 3.3 17.9 + - - +
511A PHE 3.4 13.2 - - - +
512A GLY* 3.4 35.7 - - - +
513A ALA* 3.5 11.9 - - + +
537A PRO* 4.2 9.9 - - + -
501B ASN* 3.5 24.9 - - - +
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Residues in contact with ARG 463 (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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46A ASP* 2.9 40.4 + - - -
47A THR 4.0 4.0 + - - -
48A ARG* 3.6 11.3 - - - +
459A ASP* 2.6 42.7 + - - +
460A THR* 3.1 29.0 + - - +
462A VAL* 1.3 75.0 - - - +
464A LYS* 1.3 81.7 + - + +
465A GLN* 3.6 4.3 + - - +
498B ARG 4.3 5.6 + - - -
499B LEU* 3.6 32.0 - - - +
500B GLU 4.7 3.4 - - - +
501B ASN* 4.0 20.0 - - + -
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Residues in contact with LYS 464 (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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44A ILE 4.3 6.9 + - - -
45A ILE* 4.4 21.8 - - + -
46A ASP* 2.7 36.4 + - - +
460A THR* 2.8 34.6 + - + +
463A ARG* 1.3 97.8 - - + +
465A GLN* 1.3 70.9 + - - +
466A LEU* 3.3 24.2 + - + +
496B GLY* 5.6 1.0 - - - -
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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