Contacts of the strand formed by residues 470 - 477 (chain A) in PDB entry 3DF0
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 GLU 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLU* 2.4 41.7 - - - +
212A ALA* 4.5 3.5 - - - +
410A GLY* 4.0 6.4 - - - -
411A LEU 3.1 13.7 - - - +
412A ILE* 3.8 20.7 - - + +
468A LEU* 3.6 21.8 - - - +
469A ARG* 1.3 82.9 - - + +
471A VAL* 1.3 71.7 + - - +
472A LEU* 3.1 20.4 + - + +
500A ARG* 2.7 27.8 + - - -
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Residues in contact with VAL 471 (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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410A GLY* 3.6 0.7 - - - -
411A LEU* 2.9 29.0 + - + +
429A ILE* 3.3 48.5 - - + +
430A GLY* 4.1 2.2 - - - +
431A PHE* 3.7 9.0 - - + -
462A SER* 3.8 29.2 - - - +
463A ASP* 5.3 0.9 - - + +
464A THR 4.5 6.5 - - - +
466A ILE* 4.3 16.8 - - + -
468A LEU* 5.4 1.6 - - + -
470A GLU* 1.3 72.6 - - - +
472A LEU* 1.3 60.4 + - - +
473A ASN* 4.1 8.1 - - - +
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Residues in contact with LEU 472 (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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211A ILE* 3.9 32.3 - - + -
212A ALA* 4.2 23.6 - - + +
213A GLU* 6.2 2.0 - - + -
408A LEU* 4.2 17.9 - - + -
409A VAL 3.0 17.5 - - - +
410A GLY* 3.3 10.1 - - - -
431A PHE* 4.9 0.4 - - - -
470A GLU* 3.1 30.8 + - - +
471A VAL* 1.3 75.3 - - - +
473A ASN* 1.3 72.4 + - - +
474A ARG* 5.8 0.4 - - - +
500A ARG* 3.8 12.3 - - + +
502A PHE* 5.7 3.1 - - + -
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Residues in contact with ASN 473 (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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408A LEU* 3.5 3.6 - - - +
409A VAL 3.2 17.4 + - - +
431A PHE* 4.4 2.5 - - - -
461A ARG 5.4 0.2 - - - -
462A SER* 3.6 13.2 - - - -
463A ASP* 3.1 51.1 + - - +
471A VAL* 4.1 6.9 - - - +
472A LEU* 1.3 85.8 + - - +
474A ARG* 1.3 62.0 + - - +
475A PHE* 3.3 34.0 - - + -
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Residues in contact with ARG 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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211A ILE* 4.7 4.0 - - - +
213A GLU* 3.2 33.5 + - - +
342A ASN* 5.8 0.2 - - - +
345A PRO 2.7 29.7 + - - -
346A ASP 4.2 3.2 + - - -
347A THR* 4.0 22.3 - - - +
356A TRP* 4.6 6.3 - - - -
406A THR* 4.9 8.2 - - + +
407A PHE 3.6 4.3 - - - +
408A LEU* 3.4 33.3 - - + +
472A LEU* 5.8 0.4 - - - +
473A ASN* 1.3 74.6 - - - +
475A PHE* 1.3 72.0 + - - +
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Residues in contact with PHE 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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406A THR* 3.3 8.3 - - - +
407A PHE* 2.8 72.0 + + + -
409A VAL* 3.9 11.4 - - + -
431A PHE* 3.6 33.0 - + - -
433A ILE* 4.2 5.8 - - + -
460A GLU* 3.3 35.9 - - + -
461A ARG 3.6 16.8 - - - -
473A ASN* 3.3 38.1 - - + -
474A ARG* 1.3 78.2 - - - +
476A LYS* 1.3 62.7 + - - +
477A LEU* 5.0 3.1 - - + -
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Residues in contact with LYS 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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397A ASP* 2.6 39.2 + - - -
399A GLU* 2.9 12.1 + - - +
400A ASP* 5.2 2.7 - - + +
402A GLU* 2.7 66.5 + - + +
404A GLY* 3.8 15.5 - - - +
405A CYS 3.4 8.3 - - - +
406A THR* 3.4 33.7 - - - +
459A ARG* 5.0 2.1 + - - -
460A GLU* 5.7 1.4 - - - +
475A PHE* 1.3 76.2 - - - +
477A LEU* 1.3 69.4 + - - +
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Residues in contact with LEU 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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391A LEU* 4.4 4.6 - - + +
402A GLU* 5.1 0.2 - - - -
403A ARG 5.2 0.2 - - - -
404A GLY* 4.2 4.3 - - - -
405A CYS* 2.8 32.4 + - - +
407A PHE* 3.6 32.2 - - + -
433A ILE* 4.4 5.8 - - + -
459A ARG* 3.6 39.0 - - + +
460A GLU* 3.8 33.0 - - + -
476A LYS* 1.3 83.3 - - - +
478A PRO* 1.4 72.6 - - + +
482A TYR* 3.7 30.5 - - + +
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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