Contacts of the strand formed by residues 608 - 612 (chain F) in PDB entry 3GUT
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 ALA 608 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215E LEU* 4.1 22.9 - - + -
248E VAL* 6.1 0.7 - - + -
249E ALA* 5.5 1.3 - - + -
567F TYR* 6.3 0.4 - - + -
568F LEU 2.9 12.8 - - - +
569F LEU* 3.5 20.2 - - + -
570F CYS* 3.8 1.5 - - - -
603F VAL* 3.3 3.6 - - - +
604F HIS* 2.9 33.2 + - + +
607F PHE* 1.3 79.7 - - + +
609F ILE* 1.3 73.3 + - - +
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Residues in contact with ILE 609 (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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566F ILE 3.6 1.0 - - - +
567F TYR* 6.1 0.2 - - - -
568F LEU* 2.6 51.3 + - + +
570F CYS* 4.7 7.2 - - - -
573F VAL* 4.8 1.6 - - + -
578F ILE* 3.8 31.2 - - + -
580F ILE* 4.2 18.6 - - + -
598F PHE* 4.0 27.8 - - + -
602F ASP 3.7 4.5 - - - +
603F VAL* 3.6 22.4 - - + -
608F ALA* 1.3 87.4 - - - +
610F VAL* 1.3 69.4 + - - +
611F PHE* 3.5 11.5 + - + -
631F LEU* 5.0 1.1 - - + -
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Residues in contact with VAL 610 (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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198E ARG* 3.3 41.1 - - - +
215E LEU* 4.4 13.7 - - + -
565F GLU* 3.1 34.5 - - + +
566F ILE 3.6 3.1 - - - -
567F TYR* 3.8 29.6 - - + +
598F PHE* 3.9 0.3 - - - +
602F ASP* 3.0 38.0 + - - +
604F HIS* 5.7 0.4 - - + -
609F ILE* 1.3 74.5 - - - +
611F PHE* 1.3 59.4 + - - +
612F LYS* 4.6 1.9 + - - -
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Residues in contact with PHE 611 (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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553F MET* 4.8 9.2 - - + -
565F GLU* 3.1 10.6 - - - +
566F ILE* 2.9 71.9 + - + +
568F LEU* 4.0 18.6 - - + -
580F ILE* 3.7 31.6 - - + -
582F PHE* 3.8 21.3 - + - -
596F GLY* 3.9 17.5 - - - -
597F ASP 4.1 6.5 - - - +
598F PHE* 3.9 24.7 - - + -
609F ILE* 3.9 13.9 - - + -
610F VAL* 1.3 74.9 - - - +
612F LYS* 1.3 80.1 + - - +
613F THR* 4.7 2.5 - - - -
629F VAL* 5.4 0.2 - - + -
645F PHE* 6.2 0.2 - + - -
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Residues in contact with LYS 612 (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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563F GLY* 3.7 23.8 - - - +
564F GLU 3.0 6.3 - - - +
565F GLU* 4.1 15.0 - - + -
596F GLY* 3.6 3.5 - - - -
597F ASP* 2.6 71.7 + - + +
598F PHE* 4.6 0.8 - - - +
602F ASP* 4.4 13.6 + - - -
610F VAL 4.6 0.4 + - - -
611F PHE* 1.3 88.6 - - - +
613F THR* 1.3 67.7 + - - +
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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