Contacts of the helix formed by residues 326 - 330 (chain C) in PDB entry 1FZB
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 CYS 326 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320C ASP* 2.8 23.2 + - - -
322C PHE* 3.5 8.5 - - - -
325C ASN* 1.3 70.4 - - - +
327C ALA* 1.3 60.9 + - - +
329C GLN* 2.8 8.5 + - - -
330C ASP* 2.6 34.2 + - - +
336C MET* 3.4 28.3 - - + -
338C LYS 3.5 2.5 - - - -
339C CYS* 2.0 65.7 - - - -
3G ARG* 4.8 0.4 - - - +
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Residues in contact with ALA 327 (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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313C SER* 3.7 24.0 - - - +
314C THR* 3.5 26.0 - - - +
315C TRP* 3.7 3.8 - - - +
320C ASP* 4.5 0.2 + - - -
325C ASN* 3.1 12.0 - - - +
326C CYS* 1.3 78.5 - - - +
328C GLU* 1.3 53.5 + - - +
331C GLY* 2.7 33.8 + - - +
332C SER 3.2 12.4 + - - +
334C TRP 5.6 0.2 - - - +
336C MET* 3.8 12.9 - - + +
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Residues in contact with GLU 328 (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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205C LYS* 4.4 13.2 + - - -
315C TRP* 3.8 32.4 - - + +
324C GLY 5.6 0.7 - - - +
325C ASN* 3.1 31.2 + - + +
327C ALA* 1.3 79.0 - - - +
329C GLN* 1.3 69.4 + - + +
331C GLY* 3.5 7.0 + - - -
361C ASN* 5.1 1.0 + - - -
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Residues in contact with GLN 329 (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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322C PHE* 3.5 20.1 - - - -
324C GLY* 4.1 10.7 + - - +
325C ASN 3.2 14.1 + - - +
326C CYS 2.8 6.1 + - - +
328C GLU* 1.3 82.1 - - + +
330C ASP* 1.3 63.4 + - - +
331C GLY* 3.0 8.2 + - - -
360C PRO* 4.5 8.8 - - - +
361C ASN* 3.6 42.3 + - + +
363C TYR* 3.9 13.3 + - - -
365C ASN* 4.8 0.9 - - - +
3G ARG* 2.6 37.8 + - - +
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Residues in contact with ASP 330 (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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326C CYS 2.6 17.8 + - - +
327C ALA 3.8 0.2 - - - -
329C GLN* 1.3 76.9 - - - +
331C GLY* 1.3 64.0 + - - +
332C SER* 3.8 1.1 - - - -
336C MET* 4.1 10.3 - - + +
339C CYS* 4.7 0.9 - - - +
340C HIS* 2.9 26.9 + - - -
343C HIS* 4.0 16.3 - - + -
347C VAL* 4.4 1.9 - - - +
361C ASN* 5.8 0.3 - - - +
363C TYR* 4.0 8.5 - - - +
364C ASP 3.0 19.2 - - - +
365C ASN* 3.2 32.4 - - + +
3G ARG* 3.3 28.5 + - - -
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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