Contacts of the helix formed by residues 338 - 345 (chain C) in PDB entry 5U0A
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 LEU 338 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C ARG* 3.3 51.0 + - + +
335C TRP* 3.2 57.4 + - + +
336C ARG 3.4 2.8 - - - -
337C ASP* 1.3 75.8 - - - +
339C ASP* 1.3 65.7 + - - +
341C LEU* 3.2 26.0 + - + +
342C LEU 4.5 0.2 + - - -
393C ALA* 5.0 0.2 - - - +
423C ARG* 5.1 4.9 + - + -
426C ALA* 5.6 0.9 - - + -
427C GLU* 4.4 14.1 - - + +
474C TRP* 3.5 31.0 - - + -
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Residues in contact with ASP 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C VAL* 4.5 5.9 - - - +
221C TYR* 3.7 33.8 + - + +
326C ARG* 5.4 1.7 + - - -
332C ARG* 2.9 44.3 + - - +
337C ASP* 3.5 0.8 - - - +
338C LEU* 1.3 72.3 - - - +
340C ALA* 1.3 57.9 + - - +
341C LEU 2.9 5.6 - - - -
342C LEU* 2.9 31.0 + - - +
376C ALA* 4.5 9.2 - - + -
391C PHE* 3.6 30.7 - - + -
393C ALA* 5.0 2.8 - - + +
423C ARG* 4.7 1.7 + - - +
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ASP 3.9 6.0 + - - +
338C LEU 3.3 1.4 - - - -
339C ASP* 1.3 73.4 - - - +
341C LEU* 1.3 58.6 + - - +
342C LEU 2.9 10.2 + - - -
343C HIS* 3.7 9.7 + - - +
344C TYR* 5.2 0.2 - - - -
374C LEU* 3.4 28.6 - - - +
376C ALA* 5.1 2.0 - - - +
393C ALA* 3.3 23.0 + - - +
394C THR 3.6 2.0 - - - +
395C THR* 3.2 41.3 + - - +
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Residues in contact with LEU 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TRP* 4.2 21.5 - - + +
337C ASP* 3.9 11.2 - - - +
338C LEU* 3.3 16.2 - - + +
339C ASP 2.9 1.4 - - - -
340C ALA* 1.3 74.6 - - - +
342C LEU* 1.3 57.9 + - - +
343C HIS 3.1 3.4 - - - -
344C TYR* 3.2 19.7 + - + +
395C THR* 3.3 23.1 - - - +
396C PRO* 3.7 17.0 - - + -
399C LEU* 3.9 16.6 - - + -
419C ILE* 5.9 0.4 - - + -
423C ARG* 2.3 45.4 + - + +
481C PHE* 4.1 28.5 - - + -
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C TYR* 4.4 7.9 - - + +
314C ILE* 3.6 30.3 - - + -
326C ARG* 5.3 2.9 - - - +
339C ASP* 2.9 17.7 + - - +
340C ALA 2.9 0.6 - - - -
341C LEU* 1.3 77.1 - - - +
343C HIS* 1.3 61.8 + - - +
345C GLY* 3.2 13.5 + - - -
350C TYR 5.6 2.9 - - - +
351C ARG* 4.8 12.0 + - + -
352C PRO* 4.3 6.3 - - + -
355C LEU* 3.9 33.9 - - + -
374C LEU* 3.5 14.8 - - + -
423C ARG* 2.8 27.3 + - - +
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Residues in contact with HIS 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PRO* 5.5 2.2 - - - +
340C ALA 3.7 9.0 + - - +
341C LEU 3.1 0.2 - - - -
342C LEU* 1.3 82.4 - - - +
344C TYR* 1.3 68.8 + - + +
345C GLY* 3.1 7.8 + - - -
351C ARG* 5.7 1.2 + - - -
355C LEU* 5.3 12.2 - - + +
359C THR* 2.7 36.8 - - - -
372C LEU* 2.5 43.8 - - + +
373C ARG* 4.9 0.2 - - - -
374C LEU* 4.1 25.4 - - + +
395C THR* 6.5 0.2 - - - -
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Residues in contact with TYR 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C LEU* 3.2 28.8 + - + +
343C HIS* 1.3 83.0 - - + +
345C GLY* 1.3 62.5 + - - +
395C THR* 4.3 19.1 + - + +
396C PRO 5.5 0.9 + - - -
399C LEU* 4.2 19.1 - - + +
400C ARG* 3.6 32.4 + - + +
416C VAL* 4.9 25.1 - - + -
419C ILE* 4.6 19.1 - - + +
420C THR* 3.4 34.9 - - - +
423C ARG* 4.2 10.4 - - - -
424C LYS* 5.3 0.5 + - - +
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Residues in contact with GLY 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C LEU 4.3 1.0 + - - -
342C LEU 3.2 11.6 + - - -
343C HIS 3.1 9.1 + - - -
344C TYR* 1.3 81.8 - - - +
351C ARG* 2.3 43.8 + - - -
423C ARG* 4.2 13.8 - - - +
424C LYS* 3.1 28.7 + - - -
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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