Contacts of the helix formed by residues 572 - 580 (chain F) in PDB entry 1DE4
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 572 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ASN* 4.0 2.7 - - - -
414F PRO* 3.3 32.1 - - + -
416F ALA* 3.4 8.8 - - - +
563F TYR* 4.7 0.7 + - - -
569F THR 3.6 11.0 - - - +
570F MET* 2.8 13.3 + - - -
571F ASP* 1.3 73.4 - - - +
573F TYR* 1.3 64.7 + - - +
574F LYS* 3.7 13.2 + - - +
575F GLU* 3.3 17.2 + - - +
576F LEU* 2.9 22.3 + - - +
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Residues in contact with TYR 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F THR* 3.0 30.6 + - - +
144F ILE* 3.7 24.7 - - + -
145F LYS* 3.9 45.4 - - + +
148F ASN* 2.9 28.6 + - + +
416F ALA* 4.2 1.6 - - - -
572F THR* 1.3 72.4 - - - +
574F LYS* 1.3 77.1 + - + +
576F LEU* 2.9 16.2 + - + -
577F ILE* 2.9 50.3 + - + +
583F LEU* 3.7 21.3 - - + +
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Residues in contact with LYS 574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F LYS* 6.0 3.4 - - - +
572F THR* 3.8 12.1 - - - +
573F TYR* 1.3 88.9 - - + +
575F GLU* 1.3 62.0 + - + +
577F ILE* 3.6 4.9 - - - +
578F GLU* 3.0 35.3 + - - +
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Residues in contact with GLU 575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563F TYR* 3.9 3.1 - - - +
565F TYR* 3.1 38.7 + - + -
570F MET* 3.3 37.4 - - + +
572F THR* 3.3 8.8 + - - +
573F TYR 3.1 0.6 - - - -
574F LYS* 1.3 81.4 - - + +
576F LEU* 1.3 63.0 + - - +
578F GLU* 3.4 20.3 + - - +
579F ARG* 2.9 38.5 + - - +
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Residues in contact with LEU 576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ILE* 4.1 11.0 - - + -
416F ALA* 4.5 12.3 - - + -
417F ALA* 4.3 7.0 - - + +
421F VAL* 3.6 28.7 - - + -
488F VAL* 4.3 19.3 - - + +
489F LEU* 5.5 0.2 - - - -
563F TYR* 3.3 27.3 + - + +
572F THR 2.9 14.3 + - - +
573F TYR* 2.9 10.7 + - + +
575F GLU* 1.3 76.1 - - - +
577F ILE* 1.3 57.3 + - - +
579F ARG* 3.3 1.2 + - - +
580F ILE* 2.8 46.4 + - + +
583F LEU* 3.8 25.4 - - + -
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Residues in contact with ILE 577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F THR* 4.9 5.4 - - + +
573F TYR* 2.9 63.2 + - + +
574F LYS* 3.6 7.0 - - - +
576F LEU* 1.3 72.2 - - - +
578F GLU* 1.3 66.6 + - - +
580F ILE 3.6 7.2 - - - +
581F PRO* 2.8 54.1 - - + +
583F LEU* 4.4 13.2 - - + -
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Residues in contact with GLU 578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574F LYS* 3.0 25.4 + - - +
575F GLU* 3.7 22.3 - - - +
577F ILE* 1.3 84.0 - - + +
579F ARG* 1.3 62.3 + - + +
581F PRO* 4.1 5.7 - - - +
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Residues in contact with ARG 579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F PRO* 6.1 2.6 - - - +
489F LEU 4.3 7.3 + - - -
490F GLY* 6.0 0.2 - - - -
559F GLU* 5.4 3.4 + - - -
561F THR* 6.0 2.6 - - - +
563F TYR* 3.5 34.4 - - + -
564F PRO* 3.9 25.1 - - - +
565F TYR* 3.7 28.2 + - - -
575F GLU* 2.9 32.5 + - - +
576F LEU 3.7 3.1 - - - +
578F GLU* 1.3 80.4 - - + +
580F ILE* 1.3 62.1 + - + +
581F PRO* 3.5 6.9 - - - +
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Residues in contact with ILE 580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488F VAL* 3.6 18.8 - - + -
489F LEU 5.5 2.5 - - - +
490F GLY* 3.4 33.7 - - - +
491F THR* 3.9 8.3 - - - +
563F TYR* 5.8 0.9 - - + -
576F LEU* 2.8 41.8 + - + +
577F ILE* 3.1 6.7 - - - +
579F ARG* 1.3 81.5 - - + +
581F PRO* 1.3 57.4 - - - +
582F GLU* 3.7 11.2 - - - +
583F LEU* 3.1 28.9 + - + +
586F VAL* 3.6 23.8 - - + -
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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