Contacts of the helix formed by residues 352 - 366 (chain C) in PDB entry 1P5Q
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 ASN 352 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319C LEU* 3.6 17.5 - - + +
323C LEU* 3.5 24.6 - - + +
346C LEU* 3.8 13.2 - - + +
349C ASP* 3.0 31.3 + - + +
350C SER 3.6 0.8 - - - -
351C ASN* 1.3 75.3 - - - +
353C GLU* 1.3 63.0 + - - +
354C LYS* 2.8 20.3 + - - +
355C GLY* 2.7 24.3 + - - +
356C LEU* 2.9 30.3 + - - +
1008C SO4 3.8 11.3 + - - -
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Residues in contact with GLU 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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351C ASN 3.3 2.0 + - - -
352C ASN* 1.3 72.8 + - - +
354C LYS* 1.3 62.1 + - + +
356C LEU* 4.3 2.7 - - - +
357C SER* 2.5 35.2 + - - +
379C VAL* 4.6 3.1 - - + +
383C TYR* 3.1 54.5 + - + +
386C ASN* 2.5 35.1 + - - +
1008C SO4 5.0 2.0 + - - -
1009C SO4 4.0 9.2 + - - -
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Residues in contact with LYS 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LEU* 4.3 16.2 - - + -
352C ASN* 2.8 14.0 + - - +
353C GLU* 1.3 76.1 - - + +
355C GLY* 1.3 66.5 + - - +
357C SER* 2.9 7.6 + - - -
358C ARG* 2.7 70.6 + - - +
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Residues in contact with GLY 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LEU* 3.7 18.5 - - - +
342C CYS* 3.2 18.6 - - - +
345C ALA* 5.0 0.4 - - - -
346C LEU* 3.9 20.9 - - - -
352C ASN* 2.7 18.9 + - - -
353C GLU 3.5 0.2 - - - -
354C LYS* 1.3 71.1 - - - +
356C LEU* 1.3 61.2 + - - +
358C ARG* 5.1 0.2 - - - -
359C ARG* 3.1 21.1 + - - +
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Residues in contact with LEU 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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346C LEU* 3.9 24.2 - - + +
350C SER 4.3 8.3 - - - +
351C ASN 3.7 16.6 - - - +
352C ASN 2.9 23.1 + - - +
353C GLU* 4.3 1.6 - - - +
354C LYS 3.2 0.6 - - - -
355C GLY* 1.3 73.6 - - - +
357C SER* 1.3 54.2 + - - +
359C ARG* 3.3 6.1 + - - +
360C GLY 2.8 29.5 + - - -
375C ASP* 3.4 29.5 - - - +
378C LYS* 4.4 25.4 - - + +
379C VAL* 3.5 22.2 - - + -
382C LEU* 4.0 17.7 - - + -
383C TYR* 5.1 0.2 - - + -
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Residues in contact with SER 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C GLU* 2.5 26.7 + - - +
354C LYS* 2.9 8.7 + - - -
356C LEU* 1.3 75.3 - - - +
358C ARG* 1.3 62.2 + - - -
360C GLY* 3.1 2.4 + - - -
361C GLU* 2.8 37.2 + - - +
376C PHE* 4.0 10.5 - - - -
379C VAL* 4.0 19.6 - - - +
386C ASN* 4.5 5.9 + - - -
388C ALA* 6.5 0.7 - - - -
389C ALA* 5.8 0.5 - - - +
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Residues in contact with ARG 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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323C LEU* 2.8 38.0 + - - +
324C ASN* 4.3 2.2 + - - +
326C ALA* 4.3 7.0 - - + -
327C MET* 3.4 41.3 - - - +
330C LEU* 3.8 20.9 - - + +
338C ALA* 5.1 0.2 - - - +
342C CYS* 3.7 15.8 - - - -
354C LYS* 2.7 70.3 + - - +
355C GLY* 5.5 0.7 - - - -
357C SER* 1.3 72.1 - - - +
359C ARG* 1.3 60.1 + - - +
361C GLU* 3.4 10.5 - - + +
362C ALA* 2.9 28.2 + - - +
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Residues in contact with ARG 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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347A GLU* 4.6 7.9 + - - +
339C ILE* 4.0 19.7 - - + -
342C CYS* 3.3 19.2 - - + -
343C ASN* 2.8 29.0 + - - -
346C LEU* 3.5 24.9 - - - +
355C GLY 3.1 19.5 + - - +
356C LEU* 3.7 6.9 - - - +
358C ARG* 1.3 74.6 - - - +
360C GLY* 1.3 66.3 + - - +
362C ALA* 3.2 5.6 + - - +
363C HIS* 3.0 43.4 + - - +
375C ASP* 2.6 37.9 + - - +
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Residues in contact with GLY 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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356C LEU 2.8 16.0 + - - -
357C SER 3.5 3.4 - - - -
359C ARG* 1.3 78.3 - - - +
361C GLU* 1.3 56.2 + - - +
363C HIS 3.3 0.9 + - - -
364C LEU* 2.9 27.4 + - - +
372C ALA* 3.3 13.9 - - - +
375C ASP* 3.3 19.5 + - - -
376C PHE* 3.4 16.8 - - - -
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Residues in contact with GLU 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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330C LEU* 4.4 14.4 - - + -
357C SER* 2.8 27.3 + - - +
358C ARG* 3.4 13.5 - - + +
359C ARG 3.2 0.2 - - - -
360C GLY* 1.3 76.4 - - - +
362C ALA* 1.3 57.9 + - - +
364C LEU* 3.3 3.6 + - - +
365C ALA* 2.9 30.7 + - - +
376C PHE* 3.6 11.2 - - - -
388C ALA* 4.7 5.0 - - - +
392C GLN* 2.2 50.5 + - - +
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Residues in contact with ALA 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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330C LEU* 4.0 9.4 - - + +
335C PHE* 3.7 17.8 - - + +
338C ALA* 4.1 12.6 - - + -
339C ILE* 3.5 26.2 - - + -
358C ARG 2.9 16.8 + - - +
359C ARG* 3.5 7.2 - - - +
361C GLU* 1.3 78.2 - - - +
363C HIS* 1.3 61.6 + - - +
365C ALA* 3.3 3.8 + - - +
366C VAL* 3.3 25.3 + - - +
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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
----------------------------------------------------------
339C ILE* 3.5 30.3 - - + +
359C ARG* 3.0 37.6 + - - +
360C GLY 3.7 0.9 - - - +
362C ALA* 1.3 72.1 - - - +
364C LEU* 1.3 66.1 + - - +
366C VAL* 3.4 8.4 + - - +
367C ASN 3.2 4.3 + - - -
368C ASP* 2.9 31.9 + - - +
371C LEU* 3.8 42.5 - - + +
372C ALA* 3.5 21.1 - - + +
375C ASP* 3.4 17.5 + - - -
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Residues in contact with LEU 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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360C GLY 2.9 16.7 + - - +
361C GLU* 3.7 6.1 - - - +
363C HIS* 1.3 77.1 - - - +
365C ALA* 1.3 63.4 + - - +
367C ASN* 3.0 14.2 + - - +
368C ASP 4.9 0.7 - - - +
369C PHE* 3.2 34.8 - - + -
372C ALA* 3.3 6.9 - - + +
376C PHE* 4.5 2.5 - - + -
392C GLN* 4.1 28.7 - - + +
395C VAL* 4.2 27.8 - - + -
396C CYS* 3.9 15.5 - - - -
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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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335C PHE* 3.4 38.6 - - + -
361C GLU 2.9 17.7 + - - +
362C ALA 3.4 6.3 - - - +
363C HIS 3.2 0.2 - - - -
364C LEU* 1.3 77.6 - - - +
366C VAL* 1.3 59.1 + - - +
367C ASN* 3.2 11.6 + - - +
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Residues in contact with VAL 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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335C PHE* 3.5 38.1 - - + -
336C SER* 6.2 0.2 - - - +
339C ILE* 5.3 6.5 - - + -
362C ALA 3.3 14.6 - - - +
363C HIS* 3.6 10.8 - - - +
365C ALA* 1.3 76.0 - - - +
367C ASN* 1.3 64.5 + - - +
368C ASP* 3.2 20.1 + - + +
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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