Contacts of the strand formed by residues 473 - 478 (chain A) in PDB entry 4N41
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 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ALA* 3.2 4.1 - - - +
472A GLU* 1.3 80.9 - - - +
474A ALA* 1.3 60.6 + - - +
475A VAL* 4.1 11.2 - - + -
493A ALA* 4.0 14.8 - - + -
494A VAL 3.2 18.4 - - - +
495A GLY* 3.6 13.5 - - - -
502A LEU* 5.4 4.9 - - + -
526A THR* 3.9 22.2 - - + -
527A LEU* 4.3 10.1 - - + -
530A PHE* 4.2 20.4 - - + -
538A PRO* 4.2 17.9 - - + -
540A ARG 3.6 2.4 + - - -
541A VAL* 3.2 28.1 - - + +
542A LEU 2.8 23.4 + - - -
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Residues in contact with ALA 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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473A LEU* 1.3 74.2 - - - +
475A VAL* 1.3 63.0 + - - +
493A ALA* 3.1 3.2 - - - -
494A VAL* 2.9 37.1 + - + +
542A LEU* 3.3 20.0 - - + +
544A LEU* 5.1 1.3 - - + -
634A GLN* 4.3 8.3 - - - +
638A LEU* 3.7 33.0 - - + -
655A PRO* 3.7 10.6 - - + +
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Residues in contact with VAL 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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473A LEU* 4.1 25.8 - - + +
474A ALA* 1.3 78.1 - - - +
476A GLY* 1.3 60.0 + - - +
477A PHE* 3.4 32.2 - - + -
491A ALA* 4.1 12.1 - - + -
492A CYS 3.2 11.2 - - - +
493A ALA* 3.8 6.7 - - + -
523A LEU* 4.2 9.6 - - + -
526A THR* 4.2 10.5 - - + +
541A VAL* 5.1 1.6 - - + -
542A LEU 2.9 8.4 + - - +
543A LEU* 3.6 21.5 - - + -
544A LEU* 2.9 27.5 + - - +
655A PRO* 4.1 2.0 - - - -
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Residues in contact with GLY 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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475A VAL* 1.3 73.6 - - - +
477A PHE* 1.3 61.7 + - - -
491A ALA* 3.1 7.0 - - - +
492A CYS 2.9 32.4 + - - -
544A LEU* 3.3 9.4 - - - -
655A PRO* 3.4 15.7 - - - +
656A LEU* 3.6 15.3 - - - -
659A ALA* 3.7 6.1 - - - +
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Residues in contact with PHE 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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475A VAL* 3.4 33.2 - - + -
476A GLY* 1.3 74.8 - - - -
478A ASP* 1.3 62.4 + - - +
485A PHE* 3.7 18.2 - + + -
490A ALA 3.5 2.9 - - - -
491A ALA* 4.0 10.5 - - + -
519A VAL* 3.9 26.7 - - + -
522A LEU* 4.2 14.1 - - + -
523A LEU* 4.1 22.2 - - + -
543A LEU* 3.8 26.2 - - + -
544A LEU 2.9 19.8 + - - +
545A ARG* 4.1 4.0 - - + -
546A ASP* 3.9 13.0 + - - +
554A PHE* 3.7 30.1 - + + -
557A ALA* 5.9 0.2 - - + -
656A LEU* 3.8 13.8 - - - +
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Residues in contact with ASP 478 (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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477A PHE* 1.3 76.2 - - - +
479A ALA* 1.3 58.4 + - - +
480A GLY* 2.8 29.2 + - - -
481A GLY 4.9 3.4 + - - -
485A PHE* 3.5 5.1 - - - -
489A GLY* 3.2 4.0 - - - -
490A ALA 2.9 37.9 + - - +
546A ASP* 4.6 8.1 - - - +
656A LEU* 4.9 3.1 - - + +
659A ALA* 3.7 24.9 - - + +
660A ASP* 3.9 31.7 + - - +
663A VAL* 3.5 16.4 - - + +
6D T 5.1 3.1 + - - -
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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