Contacts of the strand formed by residues 455 - 461 (chain A) in PDB entry 4DN5
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 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A LEU* 3.8 22.2 - - + -
382A LEU* 3.6 17.2 - - + +
441A LEU* 3.8 17.3 - - + +
444A CYS* 4.0 32.3 + - - +
445A ALA* 3.7 32.1 - - + +
446A GLY 5.4 1.7 + - - +
447A LEU 5.9 0.2 + - - -
453A VAL 3.5 2.2 + - - -
454A PRO* 1.3 71.4 - - - +
456A TYR* 1.3 65.4 + - - +
457A GLY 3.8 7.4 - - - +
467A ILE* 3.6 25.6 - - + -
468A PHE 3.4 15.9 - - - +
469A MET* 4.5 4.0 - - + -
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Residues in contact with TYR 456 (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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381A LEU* 3.7 6.1 - - - +
382A LEU* 2.7 30.7 + - - +
383A THR* 3.7 28.0 + - + +
385A LYS* 4.4 15.2 + - - -
386A LEU* 4.2 6.4 - - + +
424A PHE* 3.6 34.7 - + - -
426A CYS* 3.7 14.6 - - + -
454A PRO* 3.9 19.9 - - + +
455A LEU* 1.3 79.0 - - - +
457A GLY* 1.3 53.1 + - - +
468A PHE* 2.8 21.2 + - + +
469A MET 3.5 15.5 - - - -
470A GLU* 3.3 46.5 + - - +
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Residues in contact with GLY 457 (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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353A LEU* 3.9 15.0 - - - -
380A VAL 3.4 13.2 - - - -
381A LEU* 4.5 1.1 - - - -
382A LEU* 4.3 3.8 - - - -
455A LEU* 3.4 8.9 + - - +
456A TYR* 1.3 81.5 - - - +
458A ALA* 1.3 62.7 + - - +
467A ILE* 3.8 0.9 - - - -
468A PHE* 2.8 33.0 + - - +
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Residues in contact with ALA 458 (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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353A LEU* 3.5 8.3 - - + +
360A TRP* 3.5 12.2 - - + -
379A GLY* 3.2 20.1 - - - -
380A VAL 3.3 13.0 + - - -
381A LEU* 4.4 0.2 - - - +
441A LEU* 3.8 31.2 - - + -
457A GLY* 1.3 74.9 - - - +
459A VAL* 1.3 63.4 + - - +
465A VAL* 5.1 0.2 - - + -
466A ASN 3.1 14.1 - - - +
467A ILE* 4.3 8.5 - - + -
468A PHE* 4.1 2.7 - - - -
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Residues in contact with VAL 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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345A VAL* 3.7 22.9 - - + -
360A TRP* 4.1 4.5 - - - -
377A ASN* 4.8 2.2 - - - +
378A GLU 3.3 8.1 - - - +
379A GLY* 4.0 4.7 - - - -
381A LEU* 3.6 25.4 - - + -
393A TYR* 3.7 26.9 - - + +
399A TRP* 4.9 2.0 - - - +
458A ALA* 1.3 78.8 - - - +
460A ARG* 1.3 59.8 + - - +
461A GLU* 5.5 1.6 - - + -
465A VAL* 4.8 0.4 - - - -
466A ASN* 2.9 42.1 + - - +
468A PHE* 3.6 22.6 - - + -
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Residues in contact with ARG 460 (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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360A TRP* 3.6 32.2 - - + +
363A ARG* 3.3 40.1 - - - +
376A ASP* 3.5 31.6 + - - +
377A ASN* 3.0 22.3 + - - -
378A GLU* 2.6 63.4 + - + +
433A LEU* 4.1 11.7 - - + +
459A VAL* 1.3 73.6 - - - +
461A GLU* 1.3 61.7 + - - +
462A GLY* 2.6 37.6 + - - +
464A TRP 3.5 3.4 - - - +
465A VAL* 3.9 21.1 - - + +
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Residues in contact with GLU 461 (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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375A GLU* 3.9 13.4 - - - +
376A ASP 3.4 5.4 - - - -
377A ASN* 3.7 19.3 - - - +
393A TYR 4.4 2.9 - - - +
394A ARG* 3.5 28.4 + - + +
395A GLU* 2.8 37.8 + - - +
399A TRP* 4.5 1.4 - - - -
459A VAL* 5.5 0.9 - - + -
460A ARG* 1.3 69.9 - - - +
462A GLY* 1.3 62.7 + - - +
463A PRO* 3.5 0.2 - - - +
464A TRP* 2.8 38.5 + - + +
466A ASN* 4.1 14.2 - - - +
408B ARG* 3.4 26.5 + - - +
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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