Contacts of the helix formed by residues 346 - 352 (chain B) in PDB entry 5FW2
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 346 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B LEU* 3.3 48.1 + - + +
344B PRO 3.0 1.0 - - - -
345B GLU* 1.3 80.7 - - + +
347B TYR* 1.3 64.4 - - - +
348B LYS 3.2 3.5 + - - -
349B GLU* 3.4 26.5 + - - +
350B ILE* 3.4 34.1 + - + +
379B ILE* 4.3 21.2 - - + +
382B LYS* 4.4 17.2 - - - +
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Residues in contact with TYR 347 (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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41A A 3.8 13.9 + - - -
42A A 5.8 1.2 + - - -
43A G 4.8 0.9 + - - -
336B LYS* 3.6 40.3 - - + +
339B VAL* 3.9 19.7 - - + -
340B ARG* 3.5 56.6 + - + +
343B LEU 3.6 2.2 + - - -
344B PRO* 3.1 16.1 + - + +
346B LYS* 1.3 77.4 - - - +
348B LYS* 1.3 65.9 + - - +
350B ILE 3.4 0.3 + - - -
351B PHE* 3.2 57.3 + + + +
352B PHE* 4.4 16.8 - + - -
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Residues in contact with LYS 348 (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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39A G 4.5 20.4 + - - -
344B PRO 4.6 1.4 + - - -
345B GLU 4.7 6.0 + - - +
346B LYS 3.2 0.8 - - - -
347B TYR* 1.3 79.0 - - - +
349B GLU* 1.3 64.5 + - - +
352B PHE* 3.1 48.4 + - + +
353B ASP* 3.5 4.4 + - + +
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Residues in contact with GLU 349 (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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345B GLU 5.4 0.4 + - - -
346B LYS* 3.4 30.7 + - - +
347B TYR 3.4 0.4 - - - -
348B LYS* 1.3 80.7 - - - +
350B ILE* 1.3 63.4 + - + +
353B ASP* 3.7 26.9 + - + +
356B LYS* 3.6 44.8 - - + +
358B GLY* 4.9 1.9 - - - -
375B PHE* 4.1 21.0 - - + -
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Residues in contact with ILE 350 (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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335B LEU* 5.3 0.4 - - + -
339B VAL* 4.2 26.5 - - + -
343B LEU* 6.2 0.2 - - + -
346B LYS* 3.4 26.2 - - + +
347B TYR 3.4 0.6 + - - -
348B LYS 3.2 0.8 - - - -
349B GLU* 1.3 83.6 - - + +
351B PHE* 1.3 88.8 + - + +
358B GLY* 3.7 6.9 - - - -
359B TYR* 3.0 37.4 + - + +
360B ALA* 3.0 7.8 + - - +
375B PHE* 4.5 17.3 - - + -
376B ILE* 4.8 16.4 - - + -
379B ILE* 4.6 22.2 - - + -
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Residues in contact with PHE 351 (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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42A A 3.2 9.1 + - - +
43A G 2.8 47.8 + - - +
332B LEU* 3.9 15.9 - - + -
335B LEU* 4.1 22.0 - - + -
336B LYS* 3.5 34.5 - - + -
339B VAL* 4.3 10.8 - - + -
347B TYR* 3.2 54.9 + + + +
350B ILE* 1.3 98.8 - - + +
352B PHE* 1.3 62.3 + - + +
359B TYR* 4.1 15.0 - + + -
360B ALA* 3.6 6.3 - - - +
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Residues in contact with PHE 352 (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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40A C 4.6 20.2 - + - -
41A A 3.8 20.6 - - - -
42A A 3.6 24.9 - + - -
43A G 5.2 1.5 + - - +
340B ARG* 6.0 0.7 - - - -
347B TYR* 4.4 18.4 - + - -
348B LYS* 3.1 35.2 + - + +
350B ILE 3.5 1.0 - - - -
351B PHE* 1.3 82.7 - - + +
353B ASP* 1.3 68.1 + - - +
354B GLN* 3.2 12.8 + - - +
360B ALA* 3.3 9.3 - - - +
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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
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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