Contacts of the strand formed by residues 468 - 476 (chain H) in PDB entry 1PQB
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 ARG 468 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14H SER* 3.7 35.3 + - - +
461H THR 3.8 0.3 - - - +
462H TYR* 4.0 2.9 - - - -
463H ASN* 2.9 29.8 + - - +
466H ASN* 3.2 24.2 + - - +
467H GLY* 1.3 83.2 - - - +
469H VAL* 1.3 68.1 + - - +
470H ARG* 3.8 3.9 + - + +
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Residues in contact with VAL 469 (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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243H ILE* 3.7 28.3 - - - +
244H ASP* 3.9 19.1 - - + +
460H ALA* 3.8 26.9 - - + +
461H THR 3.3 9.9 - - - +
462H TYR* 4.1 20.2 - - + +
468H ARG* 1.3 75.8 - - - +
470H ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 470 (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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460H ALA* 3.7 5.6 - - - -
461H THR* 2.9 31.7 + - - +
463H ASN* 6.0 3.1 - - + -
468H ARG* 3.8 5.8 + - + +
469H VAL* 1.3 77.7 - - - +
471H VAL* 1.3 104.5 + - - +
472H ASP* 3.1 1.6 + - - +
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Residues in contact with VAL 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375H TYR* 3.8 39.7 - - + -
376H ASN* 4.6 10.3 - - + +
458H ASN* 3.9 30.5 - - + +
459H ILE 4.5 0.2 - - - +
460H ALA* 3.7 9.6 - - + +
470H ARG* 1.3 104.9 + - - +
472H ASP* 1.3 62.0 + - - +
473H THR* 3.9 8.9 + - + +
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Residues in contact with ASP 472 (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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458H ASN* 3.2 8.7 - - - +
459H ILE 3.0 12.6 + - - +
461H THR* 3.1 24.7 + - - +
470H ARG* 3.1 2.4 + - - +
471H VAL* 1.3 70.7 - - - +
473H THR* 1.3 64.6 + - - +
474H GLY* 3.0 20.6 + - - -
475H SER* 2.6 44.7 + - - +
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Residues in contact with THR 473 (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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376H ASN* 5.8 1.8 - - - +
458H ASN* 3.5 25.5 + - - +
471H VAL* 3.9 8.8 + - + +
472H ASP* 1.3 74.0 + - - +
474H GLY* 1.3 59.0 + - - +
475H SER 3.4 0.4 - - - -
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Residues in contact with GLY 474 (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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472H ASP* 3.0 14.1 + - - -
473H THR* 1.3 80.5 + - - +
475H SER* 1.3 60.9 + - - +
476H ASN* 5.5 0.7 - - - -
479H GLU* 3.9 14.0 - - - +
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Residues in contact with SER 475 (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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232H PRO* 5.7 1.3 - - - +
458H ASN* 2.9 29.6 + - - -
459H ILE* 3.1 25.6 + - - -
461H THR* 3.7 14.3 - - - +
472H ASP* 2.6 30.4 + - - +
474H GLY* 1.3 78.1 - - - +
476H ASN* 1.3 60.9 + - - +
479H GLU* 4.6 1.8 - - - -
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Residues in contact with ASN 476 (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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456H TYR 4.3 5.2 + - - +
457H GLY* 3.5 15.5 + - - +
458H ASN* 3.7 17.3 - - - +
459H ILE* 3.8 4.4 - - - +
474H GLY 5.5 0.7 - - - -
475H SER* 1.3 74.1 - - - +
477H TRP* 1.3 64.7 + - - +
478H SER* 2.9 38.3 + - - -
479H GLU* 3.0 46.1 + - - +
480H VAL* 3.6 7.1 + - - +
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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