Contacts of the helix formed by residues 357 - 368 (chain C) in PDB entry 3Q29
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 THR 357 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351C ALA* 4.8 0.7 - - - -
356C GLN* 1.3 78.4 - - - +
358C VAL* 1.3 59.4 + - - +
359C ASP* 3.6 7.8 + - - +
360C GLU* 2.9 43.4 + - - +
361C ALA* 2.9 27.4 + - - +
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Residues in contact with VAL 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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190C LYS* 3.8 26.7 - - + +
193C LEU* 4.2 9.9 - - + -
194C THR* 3.6 34.5 - - + +
197C VAL* 4.0 30.5 - - + -
351C ALA* 4.4 7.2 - - + -
357C THR* 1.3 71.5 - - - +
359C ASP* 1.3 70.3 + - - +
361C ALA* 4.7 0.9 - - - -
362C LEU* 3.2 33.5 + - + +
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Residues in contact with ASP 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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185C ASP* 4.6 1.0 - - - +
190C LYS* 3.0 40.8 + - - +
357C THR* 3.3 7.1 + - - +
358C VAL* 1.3 81.1 - - - +
360C GLU* 1.3 63.6 + - + +
362C LEU* 4.1 1.2 - - - +
363C LYS* 3.1 45.1 + - - +
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Residues in contact with GLU 360 (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 ARG 4.8 0.7 - - - +
356C GLN* 3.6 24.2 - - - +
357C THR* 2.9 42.5 + - - +
359C ASP* 1.3 76.0 - - + +
361C ALA* 1.3 67.0 + - - +
363C LYS* 2.9 22.2 + - + +
364C ASP* 3.1 16.3 + - - +
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Residues in contact with ALA 361 (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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193C LEU* 5.3 0.2 - - + -
347C ALA* 3.4 35.7 - - + +
351C ALA* 4.4 7.6 - - + +
356C GLN* 3.5 28.4 - - + +
357C THR 2.9 21.3 + - - +
358C VAL 4.1 2.2 - - - +
360C GLU* 1.3 73.0 - - - +
362C LEU* 1.3 58.3 + - + +
364C ASP* 3.6 3.7 + - - +
365C ALA* 3.0 25.3 + - - +
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Residues in contact with LEU 362 (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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162C ILE* 5.7 6.1 - - + -
184C VAL* 3.3 28.2 - - + +
185C ASP* 3.0 21.1 - - - +
189C ALA* 3.9 9.0 - - + -
190C LYS* 3.8 39.0 - - + +
193C LEU* 3.6 30.7 - - + -
344C VAL* 5.9 4.5 - - + -
347C ALA* 4.1 13.0 - - + -
348C VAL* 6.3 0.2 - - + -
358C VAL* 3.2 19.7 + - + +
359C ASP* 4.3 0.9 - - - +
361C ALA* 1.3 74.9 - - - +
363C LYS* 1.3 66.2 + - - +
365C ALA* 3.4 6.8 - - + +
366C GLN* 3.1 17.2 + - - +
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Residues in contact with LYS 363 (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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185C ASP* 2.9 17.6 + - - +
190C LYS* 5.0 9.9 - - - +
359C ASP* 3.1 38.7 + - - +
360C GLU* 2.9 14.2 + - + +
362C LEU* 1.3 75.4 - - - +
364C ASP* 1.3 66.4 + - - +
366C GLN* 3.0 5.7 + - - +
367C THR* 3.0 27.0 + - - +
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Residues in contact with ASP 364 (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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356C GLN* 3.1 24.8 + - - +
360C GLU* 3.1 11.4 + - - +
361C ALA* 3.9 7.4 - - - +
363C LYS* 1.3 78.3 - - - +
365C ALA* 1.3 56.2 + - - +
367C THR* 3.8 8.3 + - - -
368C ASN* 3.0 43.3 + - - +
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Residues in contact with ALA 365 (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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184C VAL* 4.1 12.5 - - + +
343C ALA* 3.5 23.4 - - + +
344C VAL* 4.8 4.2 - - + +
347C ALA* 3.8 16.6 - - + -
361C ALA 3.0 18.2 + - - +
362C LEU* 3.4 15.0 - - + +
363C LYS 3.0 0.8 - - - -
364C ASP* 1.3 78.3 - - - +
366C GLN* 1.3 53.0 + - - +
368C ASN 3.5 0.3 + - - -
369C SER* 2.6 34.4 + - - -
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Residues in contact with GLN 366 (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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180C LYS 5.2 4.4 + - - -
182C VAL* 3.3 44.7 + - + +
184C VAL* 3.7 9.4 - - + +
185C ASP* 3.7 21.1 - - + +
362C LEU 3.1 11.8 + - - +
363C LYS 3.0 7.9 + - - +
365C ALA* 1.3 75.3 - - - +
367C THR* 1.3 66.4 + - - +
369C SER* 3.4 5.3 + - - -
370C SER* 3.2 27.5 + - - +
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Residues in contact with THR 367 (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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363C LYS* 3.0 18.5 + - - +
364C ASP* 3.8 6.3 + - - -
366C GLN* 1.3 78.1 - - - +
368C ASN* 1.3 69.8 + - - +
369C SER 3.3 1.3 + - - -
370C SER 3.7 3.7 - - - +
371C SER* 3.1 34.9 + - - -
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Residues in contact with ASN 368 (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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339C ALA* 4.0 16.5 - - - +
342C TYR* 5.9 6.5 - - + -
343C ALA* 4.1 15.5 - - + +
364C ASP* 3.0 27.7 + - - +
365C ALA 3.9 0.7 - - - -
367C THR* 1.3 88.8 - - - +
369C SER* 1.3 59.2 + - - +
370C SER 3.7 0.2 - - - -
374C VAL* 3.6 16.0 - - - +
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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