Contacts of the helix formed by residues 503 - 508 (chain F) in PDB entry 6T8O
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 GLU 503 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473F SER* 3.3 36.5 - - - +
477F ASN* 4.3 16.1 + - - +
498F ASP* 3.5 3.0 + - - -
500F LYS* 6.4 0.9 - - + -
502F LEU* 1.3 105.8 - - + +
504F LEU* 1.3 65.3 + - + +
505F SER 3.2 8.0 + - - -
506F ILE* 3.6 19.2 + - - +
595F ASP* 3.9 15.3 - - - +
698F ASP* 5.7 1.0 - - - +
801F ADP 4.2 11.0 + - - +
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Residues in contact with LEU 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476F VAL* 4.2 12.8 - - + -
477F ASN* 3.9 10.8 - - - +
480F LEU* 3.9 12.3 - - + -
496F MET* 4.5 5.1 - - + +
497F ILE 4.8 2.0 - - - +
498F ASP* 2.7 31.7 + - + +
503F GLU* 1.3 73.8 - - + +
505F SER* 1.3 60.4 + - - -
506F ILE 3.2 3.2 + - - -
507F TYR* 3.6 43.2 + - + +
517F VAL* 3.8 19.7 - - + +
593F VAL* 4.2 22.0 - - + -
594F VAL 5.3 0.2 - - - -
595F ASP* 3.8 37.2 - - + +
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Residues in contact with SER 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548E ARG* 5.2 8.7 + - - -
498F ASP* 3.7 2.5 + - - +
500F LYS 4.6 0.2 + - - -
501F MET* 2.7 54.5 + - - -
502F LEU 4.8 2.5 - - - -
503F GLU 3.2 2.2 - - - -
504F LEU* 1.3 76.5 - - - +
506F ILE* 1.3 62.5 + - - +
507F TYR 3.2 1.1 + - - -
508F GLU* 3.6 21.8 - - - +
517F VAL* 4.8 11.0 - - - +
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Residues in contact with ILE 506 (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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548E ARG* 3.9 36.4 + - - +
477F ASN* 5.3 2.5 - - - +
503F GLU 3.6 17.8 + - - +
505F SER* 1.3 78.7 - - - +
507F TYR* 1.3 69.9 + - + +
508F GLU* 3.1 7.5 + - - +
698F ASP* 4.5 17.7 - - + +
701F VAL* 3.7 34.1 - - + -
702F HIS* 4.2 28.5 - - + +
705F VAL* 3.6 15.8 - - + +
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Residues in contact with TYR 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477F ASN* 2.9 38.3 + - - -
480F LEU* 3.6 25.1 - - + +
481F LEU* 3.3 25.8 - - + +
484F LEU* 4.7 9.9 - - + -
496F MET* 3.6 40.4 - - + -
504F LEU* 3.6 19.3 - - + +
505F SER 3.2 1.6 - - - -
506F ILE* 1.3 80.1 - - + +
508F GLU* 1.3 63.9 + - - +
510F ILE* 3.4 21.9 - - + +
513F LEU* 3.4 8.4 - - - +
517F VAL* 5.0 1.3 - - - -
701F VAL* 3.6 22.9 - - + +
705F VAL* 3.5 23.3 - - + -
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Residues in contact with GLU 508 (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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505F SER* 3.6 18.1 - - - +
506F ILE 3.1 4.7 + - - +
507F TYR* 1.3 79.1 - - - +
509F GLY* 1.3 57.5 + - - +
510F ILE 3.6 1.6 + - - -
513F LEU* 4.5 2.2 - - - -
516F PRO* 3.6 8.1 - - - +
517F VAL* 3.0 40.1 + - + +
705F VAL* 3.7 7.6 - - - +
709F LYS* 3.4 20.3 + - - +
716F TYR* 3.0 25.9 + - - -
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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