Contacts of the helix formed by residues 470 - 477 (chain A) in PDB entry 1N54
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 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A TRP* 3.8 33.4 - - + -
431A GLU* 3.8 27.4 - - + +
468A ILE 4.4 0.4 - - - +
469A VAL* 1.3 92.9 - - + +
471A PRO* 1.3 77.4 - - + +
472A THR* 3.3 7.4 - - - +
473A PHE* 3.0 32.8 + - + +
474A SER* 3.5 7.3 + - - -
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Residues in contact with PRO 471 (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 VAL 4.4 2.0 - - - +
470A PRO* 1.3 86.0 - - + +
472A THR* 1.3 64.9 + - + +
473A PHE 3.2 1.0 + - - -
474A SER* 3.2 22.6 - - - -
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Residues in contact with THR 472 (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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434A SER* 4.9 2.6 + - - -
437A LEU* 3.1 37.6 - - + +
470A PRO* 4.4 5.9 - - - +
471A PRO* 1.3 79.7 - - + +
473A PHE* 1.3 64.2 + - - +
474A SER 3.4 0.4 + - - -
475A ALA* 4.4 7.8 + - - +
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Residues in contact with PHE 473 (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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430A TRP* 3.7 28.3 - + + -
431A GLU* 4.3 3.8 - - - -
433A TRP* 3.1 28.9 - - + -
434A SER* 3.8 8.5 - - - -
436A CYS* 3.6 23.8 - - - -
437A LEU* 3.7 25.8 - - + -
449A VAL* 4.2 19.3 - - + -
453A LEU* 5.4 4.0 - - + +
469A VAL* 4.4 9.4 - - + -
470A PRO* 3.0 37.0 + - + +
472A THR* 1.3 76.3 - - - +
474A SER* 1.3 65.7 + - - +
475A ALA* 2.9 5.8 + - - -
476A LEU* 3.0 26.7 + - + +
477A CYS* 3.5 10.9 + - - -
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Residues in contact with SER 474 (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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466A LEU* 4.6 11.4 - - - +
469A VAL* 5.0 2.0 - - - -
470A PRO 3.5 5.2 + - - -
471A PRO* 3.2 19.6 + - - -
473A PHE* 1.3 77.2 - - - +
475A ALA* 1.3 61.7 + - - +
477A CYS* 3.1 28.4 + - - +
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Residues in contact with ALA 475 (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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437A LEU* 5.7 2.5 - - + -
450A ARG* 5.6 0.2 - - - -
472A THR 4.4 9.8 + - - +
473A PHE 2.9 2.8 + - - +
474A SER* 1.3 80.9 - - - +
476A LEU* 1.3 63.6 + - + +
477A CYS 3.3 7.8 + - - +
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Residues in contact with LEU 476 (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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436A CYS* 3.8 26.0 - - - -
437A LEU* 4.6 11.2 - - + +
441A PRO* 5.8 1.3 - - + -
446A PRO* 3.8 25.6 - - + +
449A VAL* 4.1 9.9 - - + -
450A ARG* 3.5 66.0 - - + +
453A LEU* 4.1 11.0 - - + +
473A PHE* 3.0 19.4 + - + +
475A ALA* 1.3 80.5 - - + +
477A CYS* 1.3 64.7 + - - +
478A PRO* 3.9 0.7 - - - +
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Residues in contact with CYS 477 (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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450A ARG* 5.6 1.1 - - - +
453A LEU* 5.0 4.7 - - - -
465A ILE* 4.6 5.2 - - - -
466A LEU* 3.7 26.5 - - + -
469A VAL* 3.6 35.4 - - - -
473A PHE 3.5 3.3 + - - -
474A SER* 3.1 23.5 + - - +
475A ALA 3.1 8.5 - - - +
476A LEU* 1.3 81.9 - - - +
478A PRO* 1.3 77.9 - - + +
479A ALA 3.8 0.9 + - - -
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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