Contacts of the helix formed by residues 474 - 482 (chain D) in PDB entry 2NPP
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 474 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470D VAL* 2.9 21.5 + - - -
471D GLU 4.6 0.6 + - - -
472D LYS 3.7 1.6 - - - -
473D PHE* 1.3 72.7 - - - +
475D LYS* 1.3 68.0 + - - -
476D GLU* 3.2 10.3 - - - -
477D TRP* 2.9 18.2 + - - +
478D ALA* 3.1 10.4 + - - +
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Residues in contact with LYS 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470D VAL* 4.2 13.7 + - - +
474D GLY* 1.3 71.2 - - - -
476D GLU* 1.3 93.7 + - - +
478D ALA* 3.0 5.6 + - - +
479D HIS* 2.9 22.7 + - - +
511D VAL 4.1 16.5 + - - +
512D CYS* 3.9 21.1 + - - +
513D GLY* 4.6 9.9 - - - +
516D ILE* 3.7 19.5 - - + +
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Residues in contact with GLU 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D PHE 5.8 0.4 - - - +
474D GLY* 4.2 6.5 - - - -
475D LYS* 1.3 106.0 + - - +
477D TRP* 1.3 62.7 + - + +
479D HIS* 3.3 11.8 + - + +
480D ALA* 3.1 25.3 + - - +
516D ILE* 4.9 2.2 - - - +
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Residues in contact with TRP 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D VAL* 3.6 17.2 - - + +
439D PHE* 3.7 24.9 - + - -
440D ASP* 3.0 29.0 + - - -
469D LEU* 3.9 24.0 - - + -
470D VAL* 4.0 11.9 - - + -
473D PHE* 3.6 48.5 - + + +
474D GLY 2.9 13.4 + - - +
476D GLU* 1.3 80.2 - - - +
478D ALA* 1.3 71.3 + - - +
480D ALA* 3.2 4.1 + - - -
481D THR* 2.9 45.0 + - + -
482D ILE* 3.2 32.5 - - + -
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Residues in contact with ALA 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470D VAL* 4.0 36.3 - - + -
474D GLY 3.1 4.6 + - - +
475D LYS 3.0 9.9 + - - +
477D TRP* 1.3 84.3 - - + +
479D HIS* 1.3 56.8 + - - +
480D ALA 3.0 1.4 + - - -
482D ILE* 2.9 19.6 + - + +
483D ILE* 2.8 31.4 + - + -
508D LEU* 5.3 1.3 - - + -
512D CYS* 4.0 13.2 - - - -
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Residues in contact with HIS 479 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475D LYS 2.9 14.8 + - - +
476D GLU* 3.8 8.1 - - - +
478D ALA* 1.3 75.1 - - - +
480D ALA* 1.3 59.9 + - + +
483D ILE* 3.6 13.0 - - - +
484D PRO* 4.2 12.9 - - - +
516D ILE* 3.9 29.5 - - + +
520D HIS* 3.2 49.0 + + - +
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Residues in contact with ALA 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D GLU 3.1 16.0 + - - +
477D TRP* 4.0 4.7 - - - +
478D ALA 3.0 0.8 - - - -
479D HIS* 1.3 83.5 - - + +
481D THR* 1.3 62.4 + - - +
484D PRO* 4.7 8.3 - - - +
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Residues in contact with THR 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D ASP* 3.8 20.6 + - - +
444D ASN* 3.8 28.2 + - - +
448D MET* 5.1 0.5 - - - +
477D TRP* 2.9 32.3 + - + +
480D ALA* 1.3 83.8 + - - +
482D ILE* 1.3 67.3 + - + +
484D PRO* 4.1 7.2 - - - +
485D LYS* 4.1 19.2 - - - +
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Residues in contact with ILE 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ASN* 4.4 6.7 - - - +
448D MET* 4.3 12.3 - - + -
466D LEU* 3.9 33.9 - - + -
469D LEU* 4.9 2.0 - - + -
470D VAL* 4.9 8.1 - - + -
477D TRP* 3.2 39.5 - - + -
478D ALA* 2.9 14.0 + - + +
481D THR* 1.3 91.0 - - + +
483D ILE* 1.3 69.2 + - - +
484D PRO* 2.7 4.9 - - - -
485D LYS* 3.0 14.4 + - - +
486D VAL* 3.1 31.2 + - + +
508D LEU* 5.1 8.3 - - + -
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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