Contacts of the strand formed by residues 482 - 489 (chain B) in PDB entry 3DDN
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 ILE 482 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472B GLY* 4.8 12.6 - - - +
475B LEU* 4.5 17.3 - - + -
476B GLY 6.0 0.4 - - - +
480B VAL 4.5 5.6 - - - +
481B ASN* 1.3 76.1 - - - +
483B GLN* 1.3 63.3 + - - +
484B ALA* 3.6 26.0 - - - +
485B ALA* 4.0 12.8 - - + +
500B LEU* 4.2 18.8 - - + -
501B ARG 3.6 4.9 - - - +
502B LEU* 4.1 14.8 - - + -
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Residues in contact with GLN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B GLN* 5.8 0.3 + - - -
454B GLY* 5.9 0.5 - - - -
481B ASN* 3.8 1.1 + - + -
482B ILE* 1.3 75.2 - - - +
484B ALA* 1.3 60.3 + - - +
501B ARG* 2.7 53.2 + - - +
502B LEU 4.1 12.0 + - - +
503B ASP* 3.8 26.0 - - + +
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Residues in contact with ALA 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B LEU* 3.8 21.7 - - + +
482B ILE* 3.6 4.9 - - - +
483B GLN* 1.3 80.2 - - - +
485B ALA* 1.3 62.6 + - - +
486B GLN* 5.8 0.9 - - - +
499B LEU 4.1 0.2 - - - +
501B ARG* 2.9 50.6 + - - +
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Residues in contact with ALA 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B LEU* 4.9 1.1 - - - -
482B ILE* 4.0 11.2 - - + -
484B ALA* 1.3 78.7 - - - +
486B GLN* 1.3 72.8 + - - +
498B ILE* 4.6 6.1 - - + -
499B LEU 3.2 12.6 - - - +
500B LEU* 4.0 22.0 - - + -
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Residues in contact with GLN 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PHE* 3.4 27.1 - - + +
449B ASP* 2.9 46.6 + - - +
450B LEU* 3.6 23.2 - - + +
484B ALA* 5.8 0.6 - - - +
485B ALA* 1.3 82.7 - - - +
487B LEU* 1.3 61.7 + - - +
498B ILE* 3.4 3.9 - - - +
499B LEU 3.0 31.1 + - - -
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B PHE* 4.8 0.2 - - - -
461B TYR* 3.7 27.1 - - - +
463B ASP* 6.2 0.4 - - - +
468B LEU* 4.2 24.5 - - + -
486B GLN* 1.3 76.2 - - - +
488B SER* 1.3 68.1 + - - +
496B ALA* 3.8 9.4 - - + -
497B THR 3.3 34.5 - - - +
498B ILE* 3.9 17.3 - - + -
530B TLA 4.9 2.8 + - - -
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Residues in contact with SER 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ARG* 3.9 5.6 - - - +
447B HIS 3.5 18.3 + - - -
448B PHE* 3.7 16.1 - - - -
487B LEU* 1.3 78.8 - - - +
489B GLU* 1.3 63.4 - - - +
496B ALA* 3.6 1.6 - - - -
497B THR* 3.0 35.6 + - - +
530B TLA 3.3 41.0 + - - -
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Residues in contact with GLU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B ARG* 2.9 22.4 + - - +
463B ASP* 6.6 0.2 - - + -
487B LEU* 5.1 0.4 - - - +
488B SER* 1.3 73.8 - - - +
490B ASP* 1.3 75.2 + - - +
495B GLY 4.2 6.3 - - - +
496B ALA* 4.5 5.2 - - + +
530B TLA 3.4 15.4 + - - +
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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