Contacts of the helix formed by residues 347 - 355 (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 ASN 347 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C LYS 4.8 11.3 + - - -
345C PHE* 4.3 12.9 - - + +
346C LEU* 1.3 76.2 - - - +
348C ASP* 1.3 79.9 + - - +
349C ASP* 4.5 9.4 - - + +
350C TYR* 3.5 29.8 - - + +
351C LEU* 3.3 28.6 + - - +
389C GLU* 5.7 0.2 - - - -
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Residues in contact with ASP 348 (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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347C ASN* 1.3 84.2 + - - +
349C ASP* 1.3 61.0 + - - +
350C TYR 3.2 1.6 - - - -
351C LEU* 2.9 29.1 + - - +
352C LYS* 3.1 13.7 + - - +
382C THR* 5.4 4.2 + - - -
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Residues in contact with ASP 349 (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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45C LEU* 3.6 29.9 - - + +
48C LYS* 3.3 35.7 - - + +
347C ASN* 3.6 8.1 - - - +
348C ASP* 1.3 75.2 - - - +
350C TYR* 1.3 66.0 + - - +
352C LYS* 3.4 29.7 + - - +
353C ILE* 3.4 23.3 + - - +
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Residues in contact with TYR 350 (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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45C LEU* 3.6 26.9 - - + -
49C GLU* 3.9 13.4 + - + +
53C ASN* 3.2 27.9 + - - -
333C ALA* 3.9 23.0 + - + -
334C PHE* 3.4 24.1 - + + -
336C VAL* 4.7 1.9 - - - +
337C PHE* 3.8 18.2 - + - -
345C PHE* 4.3 14.4 - + - -
346C LEU* 3.6 24.5 - - + -
347C ASN* 3.5 35.1 - - + +
349C ASP* 1.3 79.4 - - - +
351C LEU* 1.3 60.3 + - - +
353C ILE* 3.4 7.4 - - + +
354C LEU* 3.2 26.4 + - - +
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Residues in contact with LEU 351 (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* 4.4 11.0 - - + -
347C ASN 3.3 17.4 + - - +
348C ASP* 2.9 24.6 + - - +
350C TYR* 1.3 77.0 - - - +
352C LYS* 1.3 58.8 + - - +
353C ILE 3.4 0.2 - - - -
354C LEU* 3.4 13.2 - - + +
355C SER* 3.2 24.3 + - - -
382C THR* 5.8 4.2 - - - +
385C ASN* 4.5 12.3 - - - +
388C LEU* 3.9 34.2 - - + +
389C GLU* 4.1 36.8 - - + +
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Residues in contact with LYS 352 (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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348C ASP* 3.1 13.0 + - - +
349C ASP* 3.4 25.8 + - - +
350C TYR 3.3 0.6 - - - -
351C LEU* 1.3 77.6 - - - +
353C ILE* 1.3 62.9 + - - +
355C SER* 4.5 6.8 + - - -
356C ARG* 3.5 32.6 + - - +
415F ASP* 5.3 5.4 - - - +
418F TYR* 5.5 5.7 - - - -
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Residues in contact with ILE 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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45C LEU* 3.7 26.9 - - + -
333C ALA* 6.4 0.9 - - + -
334C PHE* 3.6 21.2 - - + -
349C ASP* 3.4 19.1 + - - +
350C TYR* 3.4 10.5 - - + +
352C LYS* 1.3 80.2 - - + +
354C LEU* 1.3 65.5 + - - +
355C SER 3.3 1.8 - - - -
356C ARG* 3.2 34.2 - - - +
465C LEU* 6.1 0.7 - - + -
412F LEU* 3.7 17.0 - - + +
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Residues in contact with LEU 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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334C PHE* 3.6 25.8 - - + -
346C LEU* 5.9 2.2 - - + -
350C TYR 3.2 23.0 + - - +
351C LEU* 3.4 32.3 - - + +
353C ILE* 1.3 78.1 - - - +
355C SER* 1.3 77.5 + - - +
356C ARG 3.2 0.2 - - - -
357C CYS* 3.2 23.0 + - - +
388C LEU* 4.4 6.5 - - + +
392C PHE* 3.6 46.4 - - + -
462C PHE* 3.5 25.9 - - + -
465C LEU* 4.6 7.0 - - + -
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Residues in contact with SER 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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351C LEU 3.2 19.1 + - - -
352C LYS* 4.8 4.5 - - - -
353C ILE 3.3 1.2 - - - -
354C LEU* 1.3 80.8 - - - +
356C ARG* 1.3 55.8 + - - +
357C CYS 3.2 6.1 + - - +
360C PHE* 3.2 36.1 - - - -
361C MET* 4.4 1.9 - - - +
381C LEU* 6.2 0.4 - - - -
388C LEU* 3.4 22.5 - - - +
418F TYR* 3.4 32.0 - - - -
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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