Contacts of the strand formed by residues 482 - 487 (chain D) in PDB entry 3E20
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 THR 482 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476D LYS* 4.2 22.4 - - + -
477D TYR 3.7 7.6 - - - +
478D LYS* 2.9 27.9 - - + -
481D GLY* 1.3 73.2 - - - -
483D ILE* 1.3 71.0 + - - +
484D LEU* 4.1 4.7 - - + -
533D ARG* 3.4 1.9 - - - +
534D VAL* 3.3 44.4 + - + -
538D ASP* 2.7 33.5 + - - +
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Residues in contact with ILE 483 (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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475D SER 3.8 0.3 - - - +
476D LYS* 3.4 3.6 - - - -
477D TYR* 2.8 78.8 + - + +
479D ASP* 5.6 2.0 - - + +
481D GLY 4.4 3.4 - - - +
482D THR* 1.3 83.8 - - - +
484D LEU* 1.3 68.1 - - - +
485D GLU* 4.7 0.2 - - + -
514D TYR* 5.1 1.8 - - + -
531D ARG* 4.0 17.9 - - + -
532D LEU 3.3 5.2 - - - +
533D ARG* 3.5 53.8 - - + +
480J LEU* 4.8 9.4 - - + -
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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
----------------------------------------------------------
471D MET* 5.0 1.6 - - + -
473D ILE* 4.0 28.3 - - + -
475D SER 3.5 3.4 - - - +
476D LYS* 3.4 34.3 - - + -
482D THR* 4.1 6.0 - - + -
483D ILE* 1.3 73.2 - - - +
485D GLU* 1.3 55.4 + - - +
508D LEU* 3.9 15.9 - - + -
531D ARG* 3.6 0.5 - - - -
532D LEU* 2.6 43.0 + - + +
534D VAL* 3.7 35.0 - - + -
538D ASP* 6.0 0.9 - - + -
541D VAL* 3.8 17.3 - - + -
547D LEU* 4.1 16.8 - - + -
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Residues in contact with GLU 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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471D MET* 4.0 4.5 - - - -
473D ILE 3.8 0.5 - - - -
474D ALA* 2.8 48.2 + - - +
475D SER* 2.9 39.8 + - - +
477D TYR* 5.2 4.3 - - + -
483D ILE* 4.0 3.6 + - + +
484D LEU* 1.3 75.6 - - - +
486D GLY* 1.3 65.6 + - - +
529D GLN* 4.3 12.1 + - - +
530D VAL 3.5 9.1 - - - +
531D ARG* 3.4 30.2 + - + +
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Residues in contact with GLY 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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471D MET* 3.7 20.0 - - - +
472D PRO 3.9 9.4 - - - -
474D ALA* 4.2 5.8 - - - -
485D GLU* 1.3 80.4 + - - +
487D LYS* 1.3 61.2 + - - -
488D ILE 4.2 0.2 - - - -
529D GLN* 3.4 10.9 + - - -
530D VAL* 3.0 31.2 + - - +
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Residues in contact with LYS 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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471D MET* 3.7 4.5 - - - +
472D PRO* 3.6 12.6 + - - +
474D ALA* 5.6 0.2 - - - +
486D GLY* 1.3 71.2 - - - -
488D ILE* 1.3 70.0 + - - +
489D GLU* 3.1 46.6 + - - +
527D GLY* 4.4 20.6 - - - +
528D ASP 3.4 12.6 - - - +
529D GLN* 3.3 31.6 - - - +
639D TYR* 5.9 1.4 - - - -
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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