Contacts of the strand formed by residues 483 - 489 (chain D) in PDB entry 3DLX
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 GLY 483 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406D LYS* 3.3 27.1 - - - -
407D TYR* 4.0 9.9 - - - -
477D ASP 4.5 0.2 - - - -
478D VAL* 3.4 2.1 - - - -
479D ASP* 2.5 43.0 + - - +
481D LYS 3.5 1.4 - - - -
482D LYS* 1.3 77.5 - - - +
484D LEU* 1.3 60.4 + - - -
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Residues in contact with LEU 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405D SER 5.0 1.1 - - - +
406D LYS* 3.6 22.8 + - + +
452D ILE* 5.3 6.1 - - + -
469D ILE* 4.5 8.1 - - + -
476D PHE* 3.7 35.0 - - + -
477D ASP 3.4 4.3 - - - +
478D VAL* 3.3 31.6 - - + -
482D LYS 4.4 2.8 + - - +
483D GLY* 1.3 74.8 - - - -
485D THR* 1.3 64.0 + - - +
502D THR* 4.7 10.1 - - + -
504D CYS* 4.4 16.4 - - - -
505D ASP 4.8 1.9 + - - +
506D PHE* 3.5 27.9 - - + +
507D ALA* 3.5 18.2 + - - +
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Residues in contact with THR 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D PHE* 4.5 1.3 - - - -
477D ASP* 2.9 39.9 + - - -
484D LEU* 1.3 76.0 - - - +
486D LEU* 1.3 66.5 + - - +
487D ILE* 3.3 9.7 + - - +
507D ALA* 3.0 18.4 - - - +
509D SER* 5.1 5.4 - - - -
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Residues in contact with LEU 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D ALA* 3.2 24.9 - - + -
475D VAL 3.4 9.2 - - - +
476D PHE* 3.9 24.7 - - + -
484D LEU 4.3 0.2 - - - -
485D THR* 1.3 69.2 - - - +
487D ILE* 1.3 59.3 + - - +
488D GLU 3.0 25.6 - - - +
489D LEU* 4.6 8.3 - - + -
498D VAL* 4.2 15.5 - - + -
506D PHE* 4.1 25.1 - - + -
507D ALA 3.3 6.3 + - - -
508D VAL* 4.2 11.9 - - + -
509D SER* 3.0 26.2 + - - -
512D LEU* 3.5 24.1 - - + +
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Residues in contact with ILE 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D ARG* 3.1 40.6 - - - +
475D VAL* 3.1 22.1 + - + +
476D PHE 4.7 0.2 - - - +
477D ASP* 3.4 22.7 - - + +
485D THR* 3.3 17.3 - - - +
486D LEU* 1.3 73.0 - - - +
488D GLU* 1.3 74.4 + - + +
509D SER* 4.2 17.9 - - - +
511D LYS 3.8 5.5 - - - +
512D LEU* 3.2 12.1 - - - +
513D MET* 3.1 23.4 + - - +
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Residues in contact with GLU 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D ARG* 2.9 30.0 + - - -
468D ARG* 5.3 0.2 + - - -
475D VAL* 3.1 24.9 + - + +
486D LEU* 3.0 24.0 - - - +
487D ILE* 1.3 95.2 - - + +
489D LEU* 1.3 62.9 + - - +
512D LEU* 4.4 0.7 - - - -
513D MET* 3.5 11.9 - - + -
514D PRO 3.9 6.5 - - - +
515D MET* 3.3 8.2 - - - +
516D GLN* 2.7 58.9 + - - +
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Residues in contact with LEU 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D LYS* 3.5 11.7 - - + +
474D ALA* 4.1 1.6 - - + +
486D LEU* 4.6 9.2 - - + -
488D GLU* 1.3 79.9 - - - +
490D TRP* 1.3 72.6 + - - +
497D ASP* 5.6 6.3 - - + -
498D VAL* 3.2 36.3 - - + +
512D LEU* 4.4 20.0 - - + -
513D MET 3.6 10.2 + - - +
514D PRO* 3.3 8.5 - - + +
515D MET* 2.8 25.2 + - - +
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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