Contacts of the strand formed by residues 450 - 453 (chain H) in PDB entry 1NZX
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 450 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490G THR* 3.3 17.2 - - + +
492G THR* 5.1 2.0 - - - +
427H LEU 3.3 9.5 + - - -
428H ALA* 3.2 7.6 - - - +
429H ALA 2.9 26.9 + - - +
448H ALA* 3.9 0.6 - - - +
449H GLY* 1.3 82.6 + - - +
451H VAL* 1.3 66.2 + - - +
452H TRP* 3.5 42.2 - - + +
458H VAL 5.5 0.4 - - - +
464H PRO 3.9 11.6 + - - -
465H PHE* 3.7 23.5 - - + -
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Residues in contact with VAL 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489G LYS* 3.9 18.6 - - + -
490G THR 2.8 11.4 + - - +
491G VAL* 3.3 9.6 - - + +
492G THR 3.1 22.1 + - - -
429H ALA* 3.3 6.5 - - + +
431H VAL* 4.5 5.4 - - + -
443H SER* 3.7 46.9 - - - +
446H LEU* 4.2 27.4 - - + -
448H ALA* 4.2 8.3 - - + +
450H THR* 1.3 76.8 - - - +
452H TRP* 1.3 70.5 + - - +
453H VAL* 4.8 1.8 - - + -
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Residues in contact with TRP 452 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492G THR* 3.5 23.1 - - - -
303H CYS* 3.9 14.4 - - + -
428H ALA* 3.5 26.2 - - + -
429H ALA 2.9 21.6 + - - +
430H ALA* 3.2 2.2 - - + -
431H VAL 2.9 24.9 + - - -
450H THR* 3.5 22.3 - - + +
451H VAL* 1.3 75.2 - - - +
453H VAL* 1.3 63.6 + - - +
454H ASN 4.1 0.2 - - - -
455H CYS* 3.1 27.4 - - - +
456H TYR* 3.6 29.6 - + - -
457H ASP* 3.7 22.0 - - - -
458H VAL* 3.1 51.1 + - + +
459H PHE* 4.2 12.8 - + - -
465H PHE* 4.6 2.5 - + - -
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Residues in contact with VAL 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436E LEU* 3.9 28.5 - - + -
491G VAL* 4.3 13.9 - - + -
492G THR 2.9 8.7 + - - -
493G VAL* 3.9 28.5 - - + -
494G LYS 3.1 21.8 + - - -
431H VAL* 3.3 13.5 - - + +
433H THR* 5.2 1.6 - - + +
439H ALA* 4.0 20.0 - - + +
443H SER* 4.7 12.6 - - - -
451H VAL* 4.5 2.9 - - + +
452H TRP* 1.3 77.2 - - - +
454H ASN* 1.3 73.5 - - - +
455H CYS* 3.1 3.4 + - - -
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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