Contacts of the strand formed by residues 458 - 463 (chain A) in PDB entry 1NRV
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 LEU 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ILE* 3.6 30.1 - - + +
452A GLN* 3.7 33.7 - - + +
455A VAL* 3.0 30.5 + - + +
456A ASP 3.3 1.2 + - - -
457A GLY* 1.3 76.7 - - - +
459A PHE* 1.3 58.1 + - - +
475A LEU* 3.2 4.5 - - - +
476A CYS* 3.1 28.9 + - - -
529A HIS* 3.2 24.9 - - + +
530A HIS 3.8 12.3 - - - +
531A CYS* 3.4 23.8 - - - -
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Residues in contact with PHE 459 (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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435A TRP* 3.5 39.9 - + + -
449A ILE* 4.9 0.4 - - - -
457A GLY 3.4 9.6 - - - -
458A LEU* 1.3 78.1 - - - +
460A LEU* 1.3 64.9 + - - +
461A LEU* 3.9 18.6 - - + -
473A LEU* 4.0 6.5 - - + -
474A THR 3.2 13.0 - - - +
475A LEU* 3.6 13.5 - - + -
513A VAL* 4.0 14.1 - - + -
517A GLN* 4.2 8.1 - - - -
527A LEU* 3.7 33.7 - - + -
528A LYS 4.0 2.7 - - - -
529A HIS* 3.0 47.3 + - - -
530A HIS* 3.3 7.2 - - + +
531A CYS* 2.8 28.2 + - - -
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TRP 3.5 5.8 - - - -
437A HIS* 3.7 38.6 - - + +
440A ILE* 4.2 12.8 - - + -
445A SER* 3.8 34.8 - - - +
448A ILE* 4.3 4.7 - - + -
449A ILE* 5.8 1.1 - - + -
459A PHE* 1.3 81.0 - - - +
461A LEU* 1.3 79.7 + - - +
462A ARG* 4.2 7.9 - - + -
473A LEU* 3.5 4.9 - - - +
474A THR* 2.9 48.8 + - + +
531A CYS* 4.2 15.0 - - + -
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TRP* 2.9 26.4 + - + +
436A PHE* 3.6 14.1 - - + -
437A HIS* 2.9 26.5 + - - -
459A PHE* 3.9 11.0 - - + -
460A LEU* 1.3 83.2 - - - +
462A ARG* 1.3 62.2 + - - +
471A PHE* 5.4 1.1 - - + -
472A VAL 3.3 8.3 - - - +
473A LEU* 3.8 20.9 - - + -
486A ILE* 3.8 24.7 - - + -
509A LEU* 4.1 18.4 - - + -
512A LEU* 4.9 2.5 - - + -
513A VAL* 3.7 33.7 - - + -
527A LEU* 5.1 0.2 - - + -
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Residues in contact with ARG 462 (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 PHE* 4.2 9.2 - - - -
438A GLY 3.3 14.8 - - - +
440A ILE* 3.9 22.0 + - + +
441A SER* 4.0 1.4 - - - +
442A ARG* 3.7 39.1 - - - +
445A SER* 2.9 27.8 + - - -
460A LEU* 4.2 4.0 - - + -
461A LEU* 1.3 77.3 - - - +
463A ASP* 1.3 66.1 + - - +
464A SER* 5.7 1.4 - - - +
465A GLN* 5.9 3.4 - - - +
471A PHE* 3.2 6.5 - - - +
472A VAL* 2.8 65.9 + - + +
474A THR* 3.4 9.7 + - - -
483A ASN* 3.0 27.5 + - - +
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Residues in contact with ASP 463 (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 HIS* 4.8 0.7 + - - -
436A PHE* 3.4 12.1 - - - -
438A GLY* 2.8 34.1 + - - +
439A ARG* 3.4 30.1 + - - +
440A ILE 4.1 9.4 - - - +
462A ARG* 1.3 85.1 + - - +
464A SER* 1.3 66.1 + - - +
465A GLN* 3.6 1.9 + - - +
468A PRO 5.7 0.7 - - - +
470A ALA 4.0 5.0 - - - +
471A PHE* 3.2 25.0 - - - -
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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