Contacts of the helix formed by residues 325 - 329 (chain C) in PDB entry 1PRC
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 TYR 325 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C PRO 4.3 1.9 + - - -
41C ALA* 3.6 8.6 - - - -
42C LEU* 2.8 35.7 + - + +
72C ARG* 3.4 32.1 - - - -
73C THR* 5.1 2.0 - - + -
76C ALA* 3.4 29.3 - - + +
79C GLU* 5.0 1.4 + - - -
80C TRP* 3.4 31.0 - + - -
131C THR* 5.3 0.9 - - + -
321C ARG* 3.0 27.5 + - + +
322C LEU* 3.9 5.9 - - - +
324C ASP* 1.3 88.8 - - + +
326C PRO* 1.3 58.7 - - - +
327C GLU* 2.7 34.7 + - - +
328C LEU* 2.9 28.4 + - + +
329C GLY 4.5 0.9 - - - +
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Residues in contact with PRO 326 (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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72C ARG* 5.3 0.9 - - - +
322C LEU 3.8 8.9 - - - +
323C LYS* 3.6 14.1 - - - +
324C ASP 3.5 7.6 - - - +
325C TYR* 1.3 87.0 - - - +
327C GLU* 1.3 64.0 + - + +
328C LEU 2.9 6.7 + - - -
329C GLY* 3.0 20.0 + - - +
330C PRO* 4.6 6.1 - - + +
331C ILE* 5.3 1.7 - - - +
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Residues in contact with GLU 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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62C LEU* 3.9 13.5 - - + +
65C LEU* 4.1 29.9 - - + +
69C GLU* 4.4 7.4 - - - +
72C ARG* 3.5 22.7 + - - -
73C THR* 2.7 36.6 + - - +
115C ARG* 3.0 31.7 + - - +
325C TYR* 2.7 28.6 + - - +
326C PRO* 1.3 71.5 - - + +
328C LEU* 1.3 64.3 + - + +
329C GLY 3.4 0.4 - - - -
331C ILE* 5.5 0.2 - - - -
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Residues in contact with LEU 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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62C LEU* 5.1 1.6 - - + -
73C THR* 5.2 5.6 - - + -
77C ILE* 6.3 0.4 - - + -
80C TRP* 4.2 24.0 - - + -
111C LEU* 3.8 28.5 - - + -
114C THR* 4.1 23.1 - - + -
115C ARG* 3.4 22.2 - - + -
118C ASN* 3.1 24.5 + - - +
130C VAL 4.9 0.4 - - - +
131C THR* 4.7 13.0 - - + -
325C TYR* 2.9 27.0 + - + +
327C GLU* 1.3 95.7 - - + +
329C GLY* 1.3 56.8 - - - +
610C HEC 4.4 6.1 - - + -
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Residues in contact with GLY 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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115C ARG 4.6 0.2 - - - -
118C ASN* 3.7 13.0 - - - -
119C THR* 3.9 6.1 - - - -
322C LEU* 3.6 25.3 - - - +
325C TYR 4.5 0.7 - - - +
326C PRO* 3.0 13.2 + - - +
327C GLU 3.4 1.4 + - - -
328C LEU* 1.3 81.7 - - - +
330C PRO* 1.3 77.0 - - - +
331C ILE* 4.0 6.4 - - - +
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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