Contacts of the strand formed by residues 405 - 410 (chain D) in PDB entry 4PE5
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 HIS 405 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D ARG* 5.7 10.0 - - + +
394D MET 5.2 3.8 - - - +
395D THR* 5.4 10.5 - - - -
396D GLN* 3.5 21.0 + - + +
404D ASP* 1.3 79.0 - - - +
406D LEU* 1.3 62.4 + - - +
475D THR* 2.4 48.3 + - - +
476D TYR* 3.9 1.1 - - - -
477D ASP* 2.8 46.2 + - - +
772D TRP* 5.8 0.2 - - - -
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Residues in contact with LEU 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D ASP 4.2 1.0 - - - -
405D HIS* 1.3 79.8 + - - +
407D SER* 1.3 61.5 + - - +
408D ILE* 4.0 9.2 - - + -
474D PHE* 4.4 19.7 - - + -
475D THR 3.0 7.1 + - - -
476D TYR* 3.4 6.8 - - - +
477D ASP 3.3 21.3 + - - -
507D TYR* 4.1 28.3 - - + -
508D MET* 5.0 3.1 - - - -
772D TRP* 6.0 6.3 - - + +
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Residues in contact with SER 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D LEU* 1.3 71.7 - - - +
408D ILE* 1.3 61.9 + - - +
477D ASP* 4.2 10.2 + - - +
479D TYR* 3.7 21.1 - - - -
505D ARG 3.9 8.0 + - - -
506D ALA* 3.3 5.0 - - - -
507D TYR* 2.5 40.1 + - - +
508D MET 3.2 3.1 + - - -
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Residues in contact with ILE 408 (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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406D LEU* 4.0 4.9 + - + +
407D SER* 1.3 79.4 + - - +
409D VAL* 1.3 70.9 + - - +
465D LEU* 3.6 26.7 - - + -
474D PHE* 3.8 14.8 - - + -
476D TYR* 3.7 25.4 - - + -
477D ASP 3.8 5.5 + - - -
478D LEU* 3.3 14.1 - - + +
479D TYR* 3.1 28.2 + - - -
508D MET* 3.2 39.0 - - + +
510D VAL* 3.9 23.3 - - + -
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Residues in contact with VAL 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D ILE* 1.3 76.2 - - - +
410D THR* 1.3 64.7 + - - +
478D LEU* 4.3 0.7 - - - -
479D TYR* 3.3 45.1 - - + +
481D VAL* 3.7 26.9 - - + +
497D MET* 3.7 12.3 - - + +
500D GLU* 4.3 12.1 - - + -
501D VAL* 4.7 0.2 - - + -
506D ALA* 3.9 8.7 - - + +
508D MET 2.9 10.7 + - - +
509D ALA* 3.2 21.4 - - + -
510D VAL 2.9 25.3 + - - +
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Residues in contact with THR 410 (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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409D VAL* 1.3 75.7 - - - +
411D LEU* 1.3 67.3 + - - +
417D VAL* 3.3 27.8 - - + +
457D CYS* 5.0 1.1 - - - -
462D ILE* 5.2 0.6 - - + +
478D LEU* 3.8 29.8 - - + -
479D TYR 3.1 6.1 + - - +
480D LEU* 3.5 23.8 - - + -
481D VAL* 3.0 26.5 + - - +
497D MET* 3.8 6.1 - - - -
510D VAL* 3.0 29.3 + - - +
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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
------------------------------------------------------------
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