Contacts of the helix formed by residues 334 - 341 (chain C) in PDB entry 5U07
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 ILE 334 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C TYR* 4.7 13.9 - - + +
332C ARG* 3.5 11.6 + - - +
333C ALA* 1.3 73.6 - - - +
335C TRP* 1.3 72.3 + - + +
337C ASP* 2.8 19.2 + - + +
338C LEU* 3.5 6.6 + - + +
376C ALA* 4.2 14.4 - - + -
391C PHE* 5.5 10.5 - - + -
393C ALA* 3.3 34.3 - - + -
395C THR* 3.4 28.3 - - + -
478C GLU* 6.0 1.3 - - - +
482C TRP* 6.1 2.9 - - + -
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Residues in contact with TRP 335 (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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333C ALA* 3.4 25.5 - - + +
334C ILE* 1.3 83.6 - - + +
336C ARG* 1.3 104.7 + - + +
338C LEU* 3.0 26.5 + - + +
339C ASP* 3.4 5.4 + - - +
395C THR* 6.3 0.4 - - - -
423C ARG* 4.0 9.0 - - + -
426C ALA* 3.7 24.0 - - + -
474C TRP* 3.6 19.5 + + - -
477C ALA* 4.4 13.5 - - + -
478C GLU* 3.5 34.8 - - + +
481C PHE* 3.4 55.4 - + + -
482C TRP* 4.3 24.7 - - + -
504C PHE* 4.6 1.3 - + - -
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Residues in contact with ARG 336 (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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332C ARG* 3.3 34.2 - - - +
333C ALA* 3.0 50.4 + - - +
334C ILE 2.9 3.4 + - - -
335C TRP* 1.3 100.1 - - + +
337C ASP* 1.3 63.3 + - - +
339C ASP* 3.0 19.4 + - - +
340C ALA* 3.4 4.5 + - - +
423C ARG* 3.4 24.4 + - + -
427C GLU* 3.1 30.1 + - - +
474C TRP* 3.1 45.6 - - - +
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Residues in contact with ASP 337 (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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221C TYR* 3.9 22.7 - - + +
314C ILE* 5.6 4.0 - - + -
326C ARG* 5.1 10.1 - - - +
332C ARG* 3.6 25.8 - - - +
334C ILE* 2.8 12.7 + - + +
336C ARG* 1.3 79.0 - - - +
338C LEU* 1.3 65.3 + - - +
340C ALA* 2.9 20.6 + - + +
341C LEU* 3.1 15.7 + - - +
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Residues in contact with LEU 338 (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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221C TYR* 6.0 1.7 - - - -
334C ILE* 3.5 5.4 + - + +
335C TRP* 3.0 17.8 + - - +
337C ASP* 1.3 77.5 - - - +
339C ASP* 1.3 67.7 + - - +
341C LEU* 2.9 30.4 + - + +
342C LEU* 4.0 7.2 - - + +
374C LEU* 4.8 12.8 - - + -
395C THR* 3.7 35.7 - - + +
396C PRO* 5.1 0.4 - - + -
398C VAL* 4.1 36.6 - - + -
419C ILE* 5.2 11.2 - - + -
481C PHE* 5.5 6.1 - - + -
482C TRP* 4.5 19.5 - - + -
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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
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335C TRP 3.4 3.9 + - - +
336C ARG 3.0 13.4 + - - +
338C LEU* 1.3 80.6 - - - +
340C ALA* 1.3 63.6 + - - +
342C LEU* 3.0 23.3 + - - +
347C ASP* 4.9 1.4 - - - +
416C VAL* 4.9 0.9 - - - +
419C ILE* 2.9 49.8 - - + +
420C THR* 3.0 26.6 - - - +
423C ARG* 3.0 32.3 + - + +
481C PHE* 5.1 1.6 - - + -
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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
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314C ILE* 4.6 12.6 - - + -
326C ARG* 4.7 5.8 - - - +
336C ARG 3.4 3.3 + - - +
337C ASP* 2.9 17.3 + - - +
339C ASP* 1.3 73.7 - - - +
341C LEU* 1.3 53.7 + - - +
342C LEU 2.3 32.3 + - - +
347C ASP* 5.2 9.0 - - - -
349C ASN* 3.8 27.0 + - - +
351C ARG* 4.7 11.8 - - + +
352C PRO* 5.5 1.6 - - - -
423C ARG* 4.9 5.2 - - - +
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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
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221C TYR* 4.0 15.9 - - + -
314C ILE* 3.6 37.0 - - + -
337C ASP 3.1 12.9 + - - +
338C LEU* 2.9 20.9 + - + +
340C ALA* 1.3 72.4 - - - +
342C LEU* 1.3 72.1 + - + +
352C PRO* 4.2 18.1 - - + +
355C LEU* 3.0 32.9 - - + +
374C LEU* 2.6 49.6 - - + -
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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