Contacts of the helix formed by residues 360 - 371 (chain C) in PDB entry 1WUU
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 ALA 360 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335C VAL* 4.9 8.1 - - + -
336C PRO 4.2 18.4 - - - +
337C GLY* 4.4 13.5 - - - -
338C VAL* 5.6 0.2 - - + -
356C LEU* 3.8 9.6 - - + -
357C GLU* 2.7 15.6 + - + +
359C SER* 1.3 76.3 + - - +
361C ALA* 1.3 73.4 + - - +
362C PRO* 2.7 6.1 - - - -
363C HIS* 2.9 9.1 + - + +
364C ALA* 2.9 18.4 + - - +
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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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219C ALA* 5.0 2.9 - - + -
221C LEU* 4.6 0.6 - - - +
356C LEU* 3.5 14.3 - - + +
357C GLU 3.4 3.8 + - - -
358C ALA 3.0 12.5 + - - +
360C ALA* 1.3 83.1 - - - +
362C PRO* 1.3 63.2 - - + +
364C ALA* 3.2 3.8 + - - +
365C MSE 2.9 34.9 + - + +
380C LEU* 3.9 36.8 - - + -
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Residues in contact with PRO 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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1C HIS 4.8 5.3 + - - +
358C ALA 4.0 2.7 - - - +
359C SER* 3.7 13.0 - - - +
360C ALA 3.0 5.2 - - - -
361C ALA* 1.3 94.9 - - + +
363C HIS* 1.3 65.8 + - - +
365C MSE 3.2 16.8 + - + +
366C ARG* 3.1 39.6 + - - +
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Residues in contact with HIS 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C VAL* 2.9 30.6 - - + +
336C PRO* 3.7 20.7 + - + +
359C SER 5.3 0.4 + - - +
360C ALA* 2.9 13.3 + - + +
362C PRO* 1.3 72.7 - - - +
364C ALA* 1.3 67.1 + - - +
366C ARG* 3.1 21.7 + - + +
367C HIS* 2.9 43.8 + + + +
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Residues in contact with ALA 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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221C LEU* 4.2 9.9 - - + -
335C VAL* 4.0 20.6 - - + +
338C VAL* 4.3 9.4 - - + -
356C LEU* 3.9 19.7 - - + -
360C ALA* 2.9 10.1 + - + +
361C ALA 3.2 10.1 - - - +
363C HIS* 1.3 81.0 - - - +
365C MSE 1.3 62.0 + - - +
367C HIS* 4.0 0.3 - - - +
368C ILE* 2.9 37.9 + - + +
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Residues in contact with MSE 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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1C HIS* 4.1 20.3 - - + +
2C ALA* 3.8 25.4 - - - +
3C ALA* 3.9 9.6 - - + +
221C LEU* 4.2 11.9 - - + -
361C ALA* 2.9 24.7 + - + +
362C PRO* 3.2 12.7 + - + +
364C ALA* 1.3 76.3 - - - +
366C ARG* 1.3 61.7 + - - +
368C ILE* 4.8 0.4 - - - -
369C GLN* 3.1 20.8 + - - +
378C PHE* 3.2 50.1 - - + -
380C LEU* 3.5 28.3 - - + -
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Residues in contact with ARG 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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1C HIS 4.2 21.9 + - - +
362C PRO* 3.1 32.2 + - - +
363C HIS* 3.1 29.0 + - + +
365C MSE 1.3 75.7 - - - +
367C HIS* 1.3 68.3 + - - +
369C GLN* 3.2 4.4 + - - +
370C GLU* 2.7 44.6 + - + +
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Residues in contact with HIS 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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331C ALA* 3.5 19.5 + - - -
334C ALA* 3.7 22.9 - - + -
335C VAL* 3.5 24.6 - - + +
363C HIS* 2.9 24.8 + + - +
366C ARG* 1.3 77.5 - - - +
368C ILE* 1.3 52.1 + - - +
370C GLU* 2.7 33.3 + - - -
371C HIS* 2.7 62.9 + + + -
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Residues in contact with ILE 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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221C LEU* 4.2 18.6 - - + -
223C THR* 4.5 9.2 - - + +
328C LEU* 3.6 29.8 - - + +
331C ALA* 4.1 15.7 - - + +
332C ALA* 3.5 41.3 - - + +
335C VAL* 5.0 0.2 - - + -
354C THR* 5.2 0.4 - - - +
364C ALA* 2.9 28.6 + - + +
365C MSE 4.2 2.2 - - - +
367C HIS* 1.3 75.4 - - + +
369C GLN* 1.3 64.6 + - - +
371C HIS 3.3 2.3 + - - -
372C TYR* 3.0 22.2 + - + +
376C ALA* 5.4 0.4 - - + -
378C PHE* 4.2 17.0 - - + -
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Residues in contact with GLN 369 (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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1C HIS* 3.6 34.4 + - + +
365C MSE 3.1 17.9 + - - +
366C ARG* 3.7 2.9 - - - +
368C ILE* 1.3 77.1 - - - +
370C GLU* 1.3 65.6 + - - +
372C TYR* 3.0 24.1 + - - +
374C GLY 3.5 14.8 + - - -
375C THR* 3.8 7.7 - - - +
376C ALA* 3.3 44.2 + - - +
378C PHE* 4.1 8.5 - - + -
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Residues in contact with GLU 370 (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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366C ARG* 2.7 36.9 + - + +
367C HIS* 2.7 25.4 + - - +
369C GLN* 1.3 79.8 - - - +
371C HIS* 1.3 75.2 + - + +
372C TYR 3.6 2.9 + - - +
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Residues in contact with HIS 371 (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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327C GLN* 4.8 12.1 + - - +
331C ALA* 4.2 20.7 - - + +
367C HIS* 2.7 73.8 + + - +
368C ILE 3.5 3.1 - - - -
370C GLU* 1.3 91.6 + - + +
372C TYR* 1.3 57.6 + - - +
373C GLY 3.9 2.2 + - - -
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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