Contacts of the helix formed by residues 323 - 331 (chain C) in PDB entry 1Z1G
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 SER 323 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B LYS* 3.6 16.6 + - - -
318C TYR 3.5 9.8 + - - +
319C GLU* 3.7 11.9 - - - -
322C ILE* 1.3 85.2 - - - +
324C ASP* 1.3 59.8 + - - +
325C LYS* 3.4 8.3 + - - +
326C PHE* 3.2 34.3 + - - +
327C ALA* 3.2 12.3 + - - +
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Residues in contact with ASP 324 (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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319C GLU* 3.7 21.1 + - + +
323C SER* 1.3 72.0 - - - +
325C LYS* 1.3 57.9 + - + +
327C ALA* 3.7 7.4 + - - +
328C GLN* 3.2 29.9 + - - +
339C ALA* 4.3 11.3 - - - +
343C ARG* 2.8 39.3 + - - -
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Residues in contact with LYS 325 (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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356B LYS* 4.8 8.7 - - - +
323C SER* 3.7 9.2 - - - +
324C ASP* 1.3 76.8 - - - +
326C PHE* 1.3 62.9 + - - +
328C GLN* 3.7 20.4 + - - +
329C HIS* 3.2 50.2 + - - +
336C ASP* 5.4 5.7 + - - -
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Residues in contact with PHE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ILE* 4.5 13.8 - - + +
354B GLU 4.1 19.7 - - - -
355B ILE* 5.3 4.7 - - - -
356B LYS* 4.9 12.8 + - - +
243C PRO* 6.0 3.4 - - + -
246C LEU* 3.5 36.3 - - + -
318C TYR* 3.3 46.0 - + + -
322C ILE* 5.1 15.7 - - + -
323C SER* 3.2 25.8 + - - +
325C LYS* 1.3 78.6 - - - +
327C ALA* 1.3 61.5 + - - +
329C HIS* 3.0 19.5 + - - +
330C LEU* 3.1 20.6 + - + +
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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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315C ALA* 3.8 31.4 - - + +
318C TYR* 4.1 15.0 - - + -
319C GLU* 4.3 6.3 - - + +
323C SER 3.2 9.1 + - - +
324C ASP* 3.9 9.2 - - - +
325C LYS 3.6 0.2 - - - -
326C PHE* 1.3 79.0 - - - +
328C GLN* 1.3 60.3 + - - +
330C LEU* 5.2 0.9 - - - -
331C LEU* 2.9 38.4 + - + +
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Residues in contact with GLN 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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324C ASP* 3.2 19.7 + - - +
325C LYS* 3.7 25.1 + - + +
327C ALA* 1.3 81.1 - - - +
329C HIS* 1.3 65.7 + - + +
330C LEU 3.6 0.2 + - - -
331C LEU* 3.7 6.0 + - - -
333C HIS* 3.2 50.5 - - + +
334C LYS 4.1 3.9 + - - +
335C SER 2.8 28.5 + - - -
336C ASP* 2.9 25.7 + - - +
339C ALA* 3.6 24.8 - - + +
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Residues in contact with HIS 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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351B ASP* 3.7 23.3 + - - -
352B LYS 5.5 4.8 + - - -
353B ILE* 4.2 24.4 - - + +
354B GLU* 6.1 2.6 - - - +
240C ILE* 3.8 15.8 - - - +
325C LYS* 3.2 43.5 + - + +
326C PHE* 3.0 7.2 + - - +
328C GLN* 1.3 83.0 - - + +
330C LEU* 1.3 63.1 + - - +
332C GLY* 3.5 9.0 + - - -
333C HIS 4.7 8.6 + - - -
334C LYS* 5.2 8.1 + - - -
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Residues in contact with LEU 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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353B ILE* 3.6 28.6 - - + +
208C VAL 3.8 1.8 - - - +
209C THR* 3.0 34.5 - - - +
210C GLY* 4.8 1.1 - - - -
211C GLN* 2.6 30.4 + - - -
240C ILE* 3.4 6.6 - - - +
242C ILE* 3.4 29.4 - - + -
243C PRO* 5.0 1.3 - - + -
246C LEU* 4.1 10.3 - - + -
318C TYR* 3.6 32.1 - - + +
326C PHE* 3.1 19.7 + - + +
327C ALA* 4.6 2.7 - - - +
328C GLN 3.5 0.2 - - - -
329C HIS* 1.3 72.7 - - - +
331C LEU* 1.3 57.6 + - + +
332C GLY 2.9 9.1 + - - -
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Residues in contact with LEU 331 (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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210C GLY* 4.1 13.5 - - - +
211C GLN* 4.1 0.7 - - - +
212C ARG* 4.6 0.9 + - - -
233C GLN* 3.2 6.6 + - - -
311C ARG* 2.7 51.0 + - - +
314C SER* 4.6 8.3 - - - +
315C ALA* 3.8 33.9 - - + -
318C TYR* 5.3 2.2 - - + -
327C ALA* 2.9 28.9 + - + +
329C HIS 3.4 0.6 - - - -
330C LEU* 1.3 81.0 - - + +
332C GLY* 1.3 62.6 + - - +
333C HIS* 3.5 32.7 - - + +
342C PHE* 4.5 13.0 - - + -
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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