Contacts of the strand formed by residues 345 - 348 (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 GLN 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B LYS* 5.9 0.2 - - - -
340B ALA 5.0 0.2 - - - +
341B ILE* 3.6 24.6 - - + +
342B ASN* 3.1 52.8 + - - +
343B LYS 3.4 1.6 + - - +
344B ASP* 1.3 83.4 - - - +
346B GLU* 1.3 65.0 + - - +
356B LEU* 3.7 26.6 - - + +
357B LEU 3.2 14.3 - - - +
358B GLN* 4.6 3.4 - - - -
359B LYS* 3.8 10.4 - - - +
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ILE* 4.3 6.5 - - - -
345B GLN* 1.3 78.0 - - - +
347B VAL* 1.3 64.3 + - - +
348B VAL* 4.0 15.8 - - + +
356B LEU* 3.4 6.7 - - - +
357B LEU* 2.9 58.2 + - + +
359B LYS* 3.4 12.2 - - + +
360B GLY* 2.6 35.7 + - - -
362B TRP* 5.7 2.8 - - - +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 4.1 19.5 - - + -
327B LYS* 3.6 18.6 - - + +
328B GLY* 3.4 36.4 + - - +
339B LEU* 4.5 5.2 - - + -
341B ILE* 4.5 6.7 - - + +
346B GLU* 1.3 79.7 - - - +
348B VAL* 1.3 71.5 + - - +
349B GLU 4.4 0.2 + - - -
354B PHE* 4.6 1.3 - - + -
355B TYR 3.2 9.6 - - - +
356B LEU* 3.9 18.2 - - + -
379B TYR* 4.1 17.9 - - + -
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLU* 4.0 19.7 - - + +
347B VAL* 1.3 79.5 - - - +
349B GLU* 1.3 64.0 + - - +
350B HIS 3.7 4.9 - - - +
354B PHE* 3.6 2.6 - - - -
355B TYR* 3.0 33.9 + - - +
357B LEU* 4.1 10.8 - - + -
362B TRP* 3.6 58.3 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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