Contacts of the helix formed by residues 479 - 487 (chain L) in PDB entry 6PST
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 479 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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937I ASP* 5.0 8.8 + - - -
474L MET* 4.8 4.3 - - + -
476L ARG* 4.2 23.9 - - - +
477L GLU 3.4 4.4 + - - -
478L PRO* 1.3 71.9 - - - +
480L PRO* 1.3 68.4 - - - +
481L GLU* 3.8 11.9 + - + +
482L GLU* 2.5 46.8 + - + +
483L LEU* 3.0 8.1 - - - +
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Residues in contact with PRO 480 (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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937I ASP* 4.9 5.8 - - - +
478L PRO 4.3 2.0 - - - +
479L THR* 1.3 89.2 - - - +
481L GLU* 1.3 59.4 + - - +
483L LEU* 3.3 13.7 + - + +
484L ALA* 2.9 25.3 + - - +
491L GLU* 3.8 5.5 - - - +
494L ILE* 4.1 9.8 - - + +
495L ARG* 3.5 36.6 - - + +
498L LEU* 4.1 24.9 - - + -
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Residues in contact with GLU 481 (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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937I ASP* 4.9 20.0 - - - +
479L THR* 3.2 10.7 + - + +
480L PRO* 1.3 78.4 - - - +
482L GLU* 1.3 59.6 + - - +
484L ALA* 3.4 2.1 + - - +
485L GLU* 2.9 29.2 + - - +
491L GLU* 3.6 27.2 + - + +
495L ARG* 4.7 4.3 + - - +
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Residues in contact with GLU 482 (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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470L MET* 3.4 26.0 - - - +
474L MET* 4.2 17.3 - - + -
479L THR* 2.5 39.0 + - + +
481L GLU* 1.3 74.9 - - - +
483L LEU* 1.3 54.9 + - - +
485L GLU* 3.3 28.6 + - - +
486L ARG* 2.9 30.3 + - - +
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Residues in contact with LEU 483 (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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463L LEU* 3.3 30.5 - - + +
466L ILE* 5.3 5.6 - - + -
467L SER* 4.5 15.5 - - - -
470L MET* 4.8 2.9 - - - -
478L PRO* 3.0 37.9 - - + +
479L THR 3.0 35.7 + - - +
480L PRO* 3.6 9.9 - - + +
481L GLU 3.3 0.2 - - - -
482L GLU* 1.3 74.8 - - - +
484L ALA* 1.3 56.7 + - - +
486L ARG* 4.4 4.3 - - - +
487L MET* 2.5 42.5 + - + +
494L ILE* 3.6 11.7 - - + -
498L LEU* 4.9 12.1 - - + -
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Residues in contact with ALA 484 (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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480L PRO 2.9 8.4 + - - +
481L GLU 3.9 1.8 - - - +
483L LEU* 1.3 75.8 - - - +
485L GLU* 1.3 54.6 + - - +
487L MET* 2.7 24.6 - - - +
488L LEU 4.3 0.5 - - - -
489L MET 3.6 14.2 - - - +
491L GLU* 3.3 53.4 - - + +
494L ILE* 3.2 14.7 - - + +
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Residues in contact with GLU 485 (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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481L GLU 2.9 17.4 + - - +
482L GLU* 3.3 28.2 - - - +
484L ALA* 1.3 74.4 - - - +
486L ARG* 1.3 59.7 + - - +
487L MET 2.7 14.2 - - - +
488L LEU* 5.4 1.4 - - - +
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Residues in contact with ARG 486 (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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466L ILE* 4.0 20.8 - - + +
469L GLN* 3.2 27.8 + - - +
470L MET* 3.1 51.0 - - + +
473L GLU* 2.2 46.6 + - - -
482L GLU* 2.9 14.2 + - - +
483L LEU 3.8 1.6 - - - +
485L GLU* 1.3 73.7 - - - +
487L MET* 1.3 65.8 + - - +
488L LEU* 5.2 2.9 - - - +
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Residues in contact with MET 487 (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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459L THR* 4.9 4.0 - - + +
462L LYS* 3.9 29.4 - - + -
463L LEU* 3.4 41.7 - - + +
466L ILE* 3.3 28.0 - - + -
483L LEU* 2.5 21.4 + - - +
484L ALA 2.7 20.7 - - - +
485L GLU 2.7 12.5 - - - +
486L ARG* 1.3 73.2 - - - +
488L LEU* 1.3 65.7 + - - +
489L MET* 4.0 34.3 - - + +
494L ILE* 3.7 13.9 - - + -
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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