Contacts of the strand formed by residues 500 - 505 (chain B) in PDB entry 3TNF
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 LYS 500 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495B LEU 3.8 0.2 - - - +
496B GLU* 3.2 7.3 - - - +
497B LYS 2.9 36.1 + - - +
498B ASP* 4.0 8.3 - - + +
499B GLY* 1.3 82.6 - - - +
501B PHE* 1.3 66.6 + - - +
502B TYR* 3.4 23.3 - - - +
524B GLU* 3.0 34.3 + - - +
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Residues in contact with PHE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B LEU* 3.9 32.8 - - + -
494B ILE* 4.3 6.7 - - + -
495B LEU 3.5 1.3 - - - +
496B GLU* 3.5 38.1 - - + -
499B GLY* 4.0 16.4 - - - -
500B LYS* 1.3 75.8 - - - +
502B TYR* 1.3 62.9 + - - +
523B ALA 3.8 0.3 - - - +
524B GLU* 3.5 29.7 + - - +
527B PHE* 3.5 43.1 - + + +
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Residues in contact with TYR 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B LYS 3.5 1.6 - - - +
494B ILE* 3.2 9.0 - - - +
495B LEU* 2.9 58.5 + - + +
497B LYS* 4.3 18.0 + - + +
500B LYS* 3.4 40.2 - - + +
501B PHE* 1.3 74.2 - - - +
503B LEU* 1.3 60.0 + - - +
504B LEU* 3.7 16.7 + - + +
510B TRP* 4.0 21.5 - + - -
513B ILE* 4.2 9.4 - - + -
520B GLN* 3.6 37.4 + - + +
523B ALA* 3.4 15.3 - - + -
524B GLU* 3.7 21.8 - - + -
527B PHE* 4.4 2.5 - - - -
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B ILE* 4.0 7.9 - - + -
492B GLN* 3.4 46.7 - - + +
493B LYS 3.3 17.5 - - - +
494B ILE* 3.9 14.1 - - + -
502B TYR* 1.3 71.4 - - - +
504B LEU* 1.3 59.5 + - - +
523B ALA* 2.8 27.7 + - - +
526B ASP* 3.6 40.7 - - + +
527B PHE* 3.7 8.6 - - - +
530B LEU* 4.2 23.3 - - + -
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Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B GLN* 3.2 10.4 - - - +
493B LYS* 2.9 37.9 + - + -
495B LEU* 3.9 38.1 - - + -
502B TYR* 4.0 10.5 - - + +
503B LEU* 1.3 74.2 - - - +
505B LYS* 1.3 69.6 + - - +
508B GLU* 3.9 38.1 - - + +
509B ASP* 4.6 4.5 - - - +
513B ILE* 4.2 19.1 - - + -
523B ALA* 3.5 27.6 - - + -
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Residues in contact with LYS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLU* 3.5 10.5 - - + +
492B GLN* 4.4 4.6 - - + +
493B LYS* 3.6 3.3 - - - +
504B LEU* 1.3 80.4 - - - +
506B GLN* 1.3 63.3 + - - +
507B GLY* 3.0 8.6 + - - +
508B GLU* 3.1 50.7 + - + +
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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