Contacts of the helix formed by residues 572 - 581 (chain L) in PDB entry 6PSR
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562L ARG* 4.2 2.5 - - - +
570L ASP 4.1 0.2 + - - -
571L TYR* 1.3 74.5 - - - +
573L LEU* 1.3 66.5 + - - +
574L GLU* 3.4 7.5 + - - +
575L GLU* 3.6 7.5 + - - +
576L VAL* 3.0 28.2 + - - +
55P T 3.5 41.2 + - - +
56P G 3.0 27.1 - - - +
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Residues in contact with LEU 573 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562L ARG* 3.5 33.0 - - - +
572L THR* 1.3 73.4 - - - +
574L GLU* 1.3 58.8 + - - +
576L VAL* 3.2 5.9 + - - +
577L GLY* 2.9 25.5 + - - -
584L ARG* 3.8 27.7 - - + +
587L ILE* 3.9 22.5 - - + +
588L ARG* 4.5 13.2 - - + +
591L GLU* 5.8 0.7 - - + -
55P T 5.6 0.7 - - + -
56P G 2.5 66.1 + - + +
57P T 4.5 10.8 - - + +
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Residues in contact with GLU 574 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572L THR* 3.4 6.5 - - - +
573L LEU* 1.3 77.8 - - - +
575L GLU* 1.3 58.8 + - - +
577L GLY* 3.2 2.9 + - - +
578L LYS* 2.9 53.3 + - - +
582L VAL 5.7 0.5 - - - +
583L THR* 5.3 6.1 - - - +
584L ARG* 4.1 41.5 + - - +
55P T 5.2 11.0 - - - +
56P G 4.6 0.2 + - - -
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Residues in contact with GLU 575 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571L TYR* 3.4 47.9 - - + -
572L THR* 3.6 9.1 + - - +
573L LEU 3.3 0.6 - - - -
574L GLU* 1.3 75.2 - - - +
576L VAL* 1.3 63.9 + - - +
578L LYS* 3.0 29.6 + - - +
579L GLN* 2.9 38.8 + - - +
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Residues in contact with VAL 576 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558L VAL* 3.8 18.2 - - + -
561L MET* 4.2 23.8 - - + -
562L ARG* 4.0 26.5 - - + +
571L TYR* 4.4 12.8 - - + +
572L THR 3.0 18.6 - - - +
573L LEU 3.2 6.7 + - - +
575L GLU* 1.3 75.6 - - - +
577L GLY* 1.3 57.7 + - - +
579L GLN* 3.3 8.5 + - - +
580L PHE* 2.9 27.6 + - + +
587L ILE* 3.6 27.6 - - + -
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Residues in contact with GLY 577 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573L LEU 2.9 14.7 + - - -
574L GLU* 3.2 5.1 + - - -
575L GLU 3.2 0.2 - - - -
576L VAL* 1.3 77.2 - - - +
578L LYS* 1.3 51.0 + - - +
580L PHE 2.9 0.4 + - - -
581L ASP* 2.3 36.8 + - - -
582L VAL 2.9 30.2 + - - -
583L THR 5.2 0.7 - - - -
587L ILE* 4.0 11.6 - - - +
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Residues in contact with LYS 578 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574L GLU* 2.9 38.4 + - - +
575L GLU* 3.0 34.3 + - - +
577L GLY* 1.3 74.2 - - - +
579L GLN* 1.3 62.2 + - + +
581L ASP* 3.4 18.5 - - - +
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Residues in contact with GLN 579 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557L LYS* 5.7 1.9 - - - -
561L MET* 3.8 20.2 - - - +
571L TYR* 3.5 37.4 + - - -
575L GLU* 2.9 31.5 + - + +
576L VAL* 3.6 9.2 - - - +
578L LYS* 1.3 77.2 - - + +
580L PHE* 1.3 70.5 + - + +
581L ASP* 3.5 5.4 - - - +
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Residues in contact with PHE 580 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553L ALA 4.6 0.4 - - - -
554L ARG* 3.3 44.4 - - + -
557L LYS* 4.1 19.1 - - + -
558L VAL* 3.3 28.3 - - + -
561L MET* 3.8 19.3 - - + -
576L VAL* 2.9 17.6 + - + +
577L GLY 3.1 1.8 - - - +
579L GLN* 1.3 85.8 - - + +
581L ASP* 1.3 71.8 + - - +
582L VAL* 3.0 25.0 - - + +
587L ILE* 4.3 12.1 - - + -
590L ILE* 5.1 0.7 - - + -
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Residues in contact with ASP 581 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577L GLY 2.3 18.3 + - - -
578L LYS* 3.4 16.1 + - - +
579L GLN 3.5 4.9 - - - +
580L PHE* 1.3 78.3 - - - +
582L VAL* 1.3 58.5 + - - +
25O A 5.3 0.2 - - - +
26O T 4.3 4.2 + - - -
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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