Contacts of the helix formed by residues 357 - 362 (chain A) in PDB entry 3RGZ
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 PRO 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A VAL* 4.2 35.2 - - + +
355A GLU 3.6 7.4 - - - +
356A LEU* 1.3 91.8 - - + +
358A MET* 1.3 59.7 + - - +
359A ASP* 3.4 2.5 - - - -
360A THR* 3.2 16.4 + - - +
361A LEU* 2.8 42.5 + - + +
372A LEU* 5.0 3.4 - - + -
377A PHE* 4.8 10.8 - - + -
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Residues in contact with MET 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A LEU* 3.1 28.3 + - - +
357A PRO* 1.3 69.9 - - - +
359A ASP* 1.3 60.7 + - - +
361A LEU* 4.2 5.4 - - + +
362A LEU* 2.6 65.8 + - + +
382A PRO* 3.3 35.0 - - + -
384A SER* 3.3 13.9 - - - +
385A LEU* 3.7 33.7 - - + +
388A LEU* 4.3 11.7 - - + -
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Residues in contact with ASP 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A PRO 3.4 0.6 - - - -
358A MET* 1.3 78.0 - - - +
360A THR* 1.3 61.5 + - - +
362A LEU* 4.4 6.5 - - - +
363A LYS* 3.4 42.5 + - - +
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Residues in contact with THR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A VAL* 4.8 7.3 + - + -
333A PRO 4.1 4.6 + - - +
334A PRO* 3.6 22.5 + - - +
336A PHE* 3.6 20.0 - - + -
337A GLY* 3.4 29.9 - - - +
357A PRO* 3.2 18.8 + - - +
358A MET 3.1 0.2 - - - -
359A ASP* 1.3 78.3 - - - +
361A LEU* 1.3 67.0 + - + +
363A LYS* 3.2 18.7 + - - +
364A MET* 3.8 15.7 - - + +
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A VAL* 6.3 0.9 - - + -
345A LEU* 3.9 28.0 - - + -
356A LEU* 4.4 9.0 - - + -
357A PRO* 2.8 46.8 + - + +
358A MET* 3.9 11.7 - - + +
360A THR* 1.3 77.8 - - + +
362A LEU* 1.3 57.3 + - - +
364A MET* 3.0 34.8 + - + +
367A LEU* 4.1 6.2 - - + +
370A LEU* 3.9 32.3 - - + -
372A LEU* 4.9 2.0 - - + -
385A LEU* 5.8 0.2 - - + -
388A LEU* 3.4 29.5 - - + +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A MET* 2.6 43.9 + - + +
359A ASP* 4.4 6.5 - - - +
361A LEU* 1.3 72.7 - - - +
363A LYS* 1.3 61.6 + - + +
364A MET 3.2 0.8 - - - -
365A ARG* 4.2 14.6 + - - +
384A SER* 3.6 45.3 - - - +
387A ASN* 3.8 20.9 - - + +
388A LEU* 4.1 13.9 - - + +
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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