Contacts of the helix formed by residues 333 - 346 (chain C) in PDB entry 5ZR1
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 333 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C LEU* 3.5 21.4 - - + +
45C LEU* 4.3 20.2 - - + -
49C GLU* 4.2 9.9 - - - +
57C ARG* 4.1 6.7 + - - +
331C GLN 3.9 0.6 + - - -
332C ASN* 1.3 71.4 - - - +
334C PHE* 1.3 61.2 + - + +
335C SER 3.1 5.6 + - - -
336C VAL* 3.5 20.8 + - - +
350C TYR* 3.9 27.8 + - + -
353C ILE* 6.4 1.1 - - + -
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Residues in contact with PHE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C TYR* 4.4 3.1 - - - -
332C ASN* 3.2 6.4 - - + +
333C ALA* 1.3 80.0 - - + +
335C SER* 1.3 60.9 + - - +
336C VAL 3.2 2.5 - - - +
337C PHE* 3.4 31.6 + + + -
346C LEU* 5.0 0.9 - - + -
350C TYR* 3.4 52.5 - + + -
353C ILE* 3.6 18.6 - - + -
354C LEU* 3.6 28.5 - - + -
392C PHE* 5.6 3.6 - + - -
465C LEU* 3.6 39.9 - - + +
466C PHE* 3.2 36.5 - + + -
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Residues in contact with SER 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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57C ARG* 3.7 11.2 - - - -
60C LEU* 3.4 20.6 - - - +
328C TYR* 3.2 38.7 + - - -
329C PHE* 3.6 24.6 - - - -
332C ASN* 2.9 19.9 + - - +
333C ALA 3.1 1.8 - - - -
334C PHE* 1.3 77.4 - - - +
336C VAL* 1.3 59.8 + - - +
337C PHE 3.2 3.6 + - - -
338C ILE* 3.7 10.3 - - - +
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Residues in contact with VAL 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 5.0 0.2 - - - +
53C ASN* 3.5 37.9 - - + +
56C LYS* 4.4 9.2 - - + -
57C ARG* 3.7 22.9 - - + +
60C LEU* 4.9 5.4 - - - -
333C ALA 3.5 18.6 - - - +
335C SER* 1.3 76.8 - - - +
337C PHE* 1.3 78.7 + - + +
338C ILE 3.4 2.5 - - - -
339C ASP* 2.9 21.9 - - - +
342C ASN* 3.4 23.1 - - + +
350C TYR* 4.7 7.9 - - - +
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Residues in contact with PHE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C PHE* 3.4 41.9 + + - +
335C SER 3.2 2.2 - - - -
336C VAL* 1.3 96.4 - - + +
338C ILE* 1.3 61.9 + - - +
339C ASP 3.7 4.5 - - - -
342C ASN* 3.2 30.7 - - + -
343C VAL* 4.5 6.1 - - + -
345C PHE* 4.9 4.5 - + + -
346C LEU* 3.6 32.5 - - + -
350C TYR* 3.8 23.1 - + - -
392C PHE* 3.8 17.5 - + + -
396C LEU* 3.3 28.1 - - + +
466C PHE* 3.4 18.6 - - + -
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Residues in contact with ILE 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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60C LEU* 3.7 28.3 - - + -
64C LEU* 3.8 13.9 - - + -
290C GLY 5.5 0.7 - - - +
291C LYS* 3.4 67.9 - - + +
292C LEU* 5.0 5.2 - - + -
328C TYR* 4.9 4.5 - - + +
329C PHE* 4.3 7.6 - - + -
334C PHE 4.7 0.7 - - - +
335C SER* 3.7 16.6 - - - +
336C VAL 3.4 0.2 - - - -
337C PHE* 1.3 82.0 - - - +
339C ASP* 1.3 63.1 + - - +
340C PRO* 4.1 4.4 - - - +
396C LEU* 4.7 7.6 - - - +
466C PHE* 3.8 17.5 - - + -
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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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56C LYS* 3.5 17.3 + - - -
60C LEU* 4.4 22.0 - - + +
63C GLN* 5.3 3.1 + - - +
336C VAL 2.9 23.2 - - - +
337C PHE 4.8 0.4 - - - -
338C ILE* 1.3 79.4 + - - +
340C PRO* 1.3 70.3 - - + +
341C VAL* 3.2 13.8 + - + +
342C ASN* 3.0 23.4 + - - +
343C VAL* 4.0 6.9 - - - +
396C LEU* 5.0 0.9 - - - -
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Residues in contact with PRO 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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338C ILE 4.1 3.6 - - - +
339C ASP* 1.3 86.0 - - + +
341C VAL* 1.3 65.2 + - + +
342C ASN 3.2 0.7 - - - -
343C VAL* 3.3 27.4 + - + +
344C ASP* 4.7 5.2 + - - +
396C LEU* 4.3 17.0 - - + -
397C VAL* 5.6 8.1 - - + -
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Residues in contact with VAL 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LYS* 4.6 9.0 - - - +
339C ASP* 3.8 23.1 - - + +
340C PRO* 1.3 81.8 - - + +
342C ASN* 1.3 71.2 + - - +
343C VAL 3.4 0.6 + - - -
344C ASP* 4.2 16.8 + - - +
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Residues in contact with ASN 342 (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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53C ASN* 5.8 2.6 + - - -
56C LYS* 3.3 30.9 - - - +
336C VAL* 3.4 24.5 - - + +
337C PHE* 3.2 21.8 - - + -
339C ASP* 3.0 31.2 + - - +
340C PRO 3.2 0.6 - - - -
341C VAL* 1.3 82.2 + - - +
343C VAL* 1.3 64.1 + - - +
344C ASP 3.2 2.5 - - - -
345C PHE* 3.3 21.9 - - + +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C PHE* 4.5 11.2 - - + -
339C ASP 4.0 3.4 - - - +
340C PRO* 3.3 31.6 - - + +
341C VAL 3.4 1.2 - - - -
342C ASN* 1.3 76.2 - - - +
344C ASP* 1.3 61.2 + - - +
345C PHE 3.1 7.1 + - - -
346C LEU* 3.6 19.4 + - + +
392C PHE* 4.9 11.2 - - + -
393C VAL* 3.7 37.2 - - + +
396C LEU* 3.7 28.5 - - + -
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Residues in contact with ASP 344 (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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340C PRO 4.9 5.4 - - - +
341C VAL* 4.3 14.2 - - - +
342C ASN* 3.2 1.6 - - - +
343C VAL* 1.3 80.4 - - - +
345C PHE* 1.3 56.8 + - - +
346C LEU 3.6 0.9 - - - -
393C VAL* 6.0 1.2 - - - +
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Residues in contact with PHE 345 (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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50C SER* 3.5 22.9 - - - -
52C VAL* 4.3 14.6 - - + -
53C ASN* 3.2 32.8 - - - -
337C PHE* 4.9 3.1 - + + -
342C ASN* 3.3 24.4 - - + +
343C VAL 3.1 1.0 - - - -
344C ASP* 1.3 77.1 - - - +
346C LEU* 1.3 67.4 + - - +
347C ASN* 3.6 12.4 + - + +
350C TYR* 4.3 17.0 - + - -
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Residues in contact with LEU 346 (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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334C PHE* 5.0 1.3 - - + -
337C PHE* 3.6 32.5 - - + -
342C ASN 4.6 0.4 + - - -
343C VAL* 3.6 15.2 + - + +
344C ASP 3.6 1.6 - - - -
345C PHE* 1.3 78.9 - - - +
347C ASN* 1.3 69.8 + - - +
350C TYR* 3.6 20.9 - - + -
351C LEU* 4.4 9.6 - - + -
354C LEU* 5.9 2.2 - - + -
389C GLU* 3.7 52.2 - - + +
392C PHE* 4.0 24.2 - - + -
393C VAL* 5.5 2.5 - - + -
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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