Contacts of the helix formed by residues 482 - 492 (chain A) in PDB entry 2C0O
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 THR 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A GLU* 3.4 19.5 - - - +
416A LYS* 4.0 12.6 - - - +
419A VAL* 4.8 0.7 - - - -
481A PRO* 1.3 77.4 - - - +
483A PHE* 1.3 62.9 + - - +
484A GLU* 3.5 11.5 + - - +
485A TYR* 2.9 31.7 + - + +
486A ILE* 3.0 14.2 + - - +
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Residues in contact with PHE 483 (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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345A ALA* 4.2 7.6 - - - +
348A MET* 3.4 57.0 - - + -
349A ALA* 3.6 22.4 - - - +
352A GLU* 2.7 27.4 + - - +
361A LEU* 4.7 0.2 - - + -
415A ILE* 3.8 17.5 - - + -
418A ASP* 3.7 6.1 - - + -
419A VAL* 3.6 36.5 - - + +
422A PHE* 3.7 31.4 - + + -
481A PRO 4.1 0.4 + - - -
482A THR* 1.3 71.0 - - - +
484A GLU* 1.3 56.6 + - - +
486A ILE* 3.2 10.3 + - + +
487A GLN* 2.7 36.9 + - - +
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Residues in contact with GLU 484 (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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349A ALA* 4.1 13.6 - - + +
352A GLU* 3.2 11.2 + - - +
482A THR* 3.7 11.9 + - - +
483A PHE* 1.3 78.9 - - - +
485A TYR* 1.3 57.9 + - - +
487A GLN* 4.0 4.8 - - - +
488A SER* 3.3 21.8 + - - -
471B ARG* 5.2 8.7 + - - -
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Residues in contact with TYR 485 (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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468A ILE* 5.7 5.6 - - + -
471A ARG* 3.3 34.1 + - - -
481A PRO* 4.0 16.6 - - + -
482A THR* 2.9 25.2 + - - +
484A GLU* 1.3 74.9 + - - +
486A ILE* 1.3 73.9 + - + +
487A GLN 3.1 1.1 - - - -
488A SER* 2.8 26.3 + - - -
489A VAL* 3.0 31.4 + - + +
485B TYR* 4.1 31.6 - + - -
488B SER* 4.5 17.8 + - - -
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Residues in contact with ILE 486 (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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345A ALA* 4.0 4.0 - - + -
419A VAL* 4.3 15.0 - - + -
422A PHE* 3.5 35.0 - - + -
468A ILE* 4.4 14.8 - - + -
472A CYS* 3.6 31.0 - - - -
481A PRO* 3.9 22.4 - - + -
482A THR 3.0 14.0 + - - +
483A PHE* 3.8 11.7 - - + +
485A TYR* 1.3 79.8 - - + +
487A GLN* 1.3 64.9 + - - +
489A VAL* 3.1 4.6 + - - +
490A LEU* 3.0 36.2 + - + +
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Residues in contact with GLN 487 (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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342A ALA* 4.1 5.6 - - - +
345A ALA* 3.7 18.5 - - + +
346A GLU* 3.6 45.9 - - + +
349A ALA* 3.6 12.3 - - - +
483A PHE 2.7 23.7 + - - +
484A GLU* 4.0 6.0 - - - +
486A ILE* 1.3 72.2 - - - +
488A SER* 1.3 57.0 + - - +
490A LEU* 3.3 2.3 + - - +
491A ASP* 2.8 59.2 + - - +
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Residues in contact with SER 488 (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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484A GLU 3.3 14.3 + - - -
485A TYR* 2.8 29.4 + - - -
487A GLN* 1.3 78.4 - - - +
489A VAL* 1.3 63.5 + - - +
491A ASP* 3.9 5.4 + - - +
492A ASP* 3.5 28.4 + - - +
485B TYR* 4.5 15.7 + - - -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ILE* 3.8 26.9 - - + -
485A TYR* 3.0 49.3 + - + +
486A ILE* 3.7 5.8 - - - +
488A SER* 1.3 83.0 + - - +
490A LEU* 1.3 59.6 + - - +
492A ASP* 3.3 3.3 + - - -
493A PHE* 3.0 30.7 + - + -
497B THR* 3.7 31.0 + - + +
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Residues in contact with LEU 490 (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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131A LYS* 5.1 0.3 + - - -
338A ILE* 3.9 22.1 - - + +
341A SER* 3.7 29.2 - - - +
342A ALA* 3.9 17.8 - - + +
345A ALA* 4.4 1.1 - - + -
422A PHE* 3.9 13.7 - - + -
426A LEU* 4.7 3.1 - - + -
465A LEU* 3.7 28.3 - - + -
468A ILE* 5.0 8.5 - - + -
486A ILE* 3.0 38.1 + - + +
487A GLN 3.9 1.8 - - - +
489A VAL* 1.3 75.7 - - + +
491A ASP* 1.3 67.3 + - - +
492A ASP 3.0 0.7 + - - -
493A PHE* 3.2 25.2 + - + +
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Residues in contact with ASP 491 (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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130A ARG* 5.9 0.7 - - - +
131A LYS* 2.7 53.6 + - + +
135A ARG* 3.8 11.1 + - - -
342A ALA* 3.2 26.7 - - - +
346A GLU* 5.5 2.7 - - - +
487A GLN* 2.8 44.3 + - - +
488A SER* 4.0 6.2 - - - +
490A LEU* 1.3 79.0 - - - +
492A ASP* 1.3 65.4 + - - +
493A PHE 3.8 0.2 + - - -
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Residues in contact with ASP 492 (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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130A ARG* 2.8 45.4 + - - -
131A LYS* 5.3 0.9 - - - +
488A SER* 3.5 16.3 + - - +
489A VAL* 3.3 6.0 + - - +
490A LEU 3.0 0.6 - - - -
491A ASP* 1.3 85.5 - - - +
493A PHE* 1.3 64.0 + - - +
494A TYR 3.0 5.1 + - - -
495A THR* 3.1 36.1 + - - +
500A GLN* 3.6 18.5 + - - +
497B THR* 4.7 4.9 + - - -
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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