Contacts of the helix formed by residues 352 - 359 (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 PRO 352 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C TYR* 6.3 0.2 - - + -
310C ASP 5.3 0.7 - - - +
311C PRO 3.3 16.6 - - - +
312C TYR 3.9 7.9 - - - +
313C LEU 3.4 16.8 - - - +
314C ILE* 4.4 7.4 - - + -
340C ALA 4.9 1.1 - - - +
341C LEU* 4.2 30.1 - - + -
351C ARG* 1.4 90.2 - - + +
353C THR* 1.3 64.5 + - - +
354C ILE* 3.5 1.1 - - + -
355C LEU* 3.6 20.6 + - + -
356C ASP* 3.3 18.7 + - - +
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Residues in contact with THR 353 (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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309C LEU* 4.5 12.8 + - + +
310C ASP 5.2 0.2 + - - -
311C PRO* 3.1 29.7 + - - +
351C ARG 4.1 1.9 + - - +
352C PRO* 1.3 69.4 - - - +
354C ILE* 1.3 65.7 + - - +
356C ASP* 3.1 11.2 + - - +
357C ASN* 2.8 25.8 + - - +
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Residues in contact with ILE 354 (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* 4.6 4.3 - - + +
223C PRO* 4.4 11.2 - - + -
234C LEU 3.5 17.9 - - - +
235C ASN* 3.4 28.3 - - - +
236C ILE 4.7 3.1 - - - +
237C PRO* 4.8 10.3 - - + -
238C TYR 6.2 0.2 - - - +
311C PRO* 3.0 40.9 + - + +
312C TYR* 3.4 26.7 - - + -
352C PRO* 4.9 0.9 - - + -
353C THR* 1.3 80.0 + - - +
355C LEU* 1.3 64.9 + - + +
357C ASN* 4.8 3.8 - - - -
358C CYS* 2.8 43.5 + - + +
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Residues in contact with LEU 355 (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* 6.2 1.3 - - + +
223C PRO* 5.0 17.0 - - + -
341C LEU* 3.0 43.5 - - + +
342C LEU* 4.5 6.3 - - + -
352C PRO* 3.6 23.3 + - + -
353C THR 3.2 0.8 - - - -
354C ILE* 1.3 87.2 - - + +
356C ASP* 1.3 57.2 + - - +
358C CYS* 5.2 3.1 - - + -
359C THR* 2.9 43.8 + - - -
360C PRO* 3.8 3.1 - - - +
372C LEU* 6.0 3.6 - - + -
374C LEU* 4.6 19.1 - - + -
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Residues in contact with ASP 356 (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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343C HIS* 6.2 5.2 - - + -
352C PRO 3.3 12.3 + - - +
353C THR* 3.1 14.6 + - - +
355C LEU* 1.3 79.6 - - - +
357C ASN* 1.3 59.5 + - - +
360C PRO* 2.9 30.4 - - - +
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Residues in contact with ASN 357 (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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94C TRP* 4.8 7.9 - - - +
95C GLN* 4.0 21.0 + - - +
236C ILE 5.6 1.2 + - - -
238C TYR* 3.2 39.9 - - + +
353C THR 2.8 15.3 + - - +
354C ILE* 4.1 3.8 - - - +
356C ASP* 1.3 82.4 - - - +
358C CYS* 1.3 64.9 + - - +
359C THR 3.6 0.2 + - - -
360C PRO* 3.8 5.4 - - - +
363C GLN* 3.8 15.9 + - - +
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Residues in contact with CYS 358 (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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98C ARG* 2.9 33.9 - - - +
223C PRO* 5.2 4.3 - - + -
234C LEU* 3.1 38.7 - - + +
236C ILE 4.9 3.6 - - - -
354C ILE* 2.8 30.8 + - + +
355C LEU* 4.2 5.8 - - + +
357C ASN* 1.3 79.0 - - - +
359C THR* 1.3 62.1 + - - +
363C GLN* 4.4 9.0 - - - +
365C PRO* 4.9 1.4 - - - +
369C LEU* 3.7 14.0 - - - +
372C LEU* 6.1 0.2 - - - -
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Residues in contact with THR 359 (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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355C LEU* 2.9 39.6 + - - -
358C CYS* 1.3 76.7 - - - +
360C PRO* 1.3 68.1 - - - +
361C LEU 3.8 0.2 + - - -
369C LEU* 3.3 25.0 - - - +
372C LEU* 4.8 12.8 - - - -
398C VAL 5.6 2.5 - - - -
399C LEU* 5.0 17.8 - - - +
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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