Contacts of the helix formed by residues 364 - 368 (chain C) in PDB entry 3R9A
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 LEU 364 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C LEU 6.0 0.9 - - - +
27C GLY 3.8 10.1 - - - +
28C PRO* 3.9 6.1 - - + -
29C GLY* 3.7 33.4 - - - +
31C SER* 4.1 13.2 - - - -
186C ALA 4.5 3.1 - - - +
209C LLP 3.8 26.5 - - + +
210C ALA* 3.7 17.7 - - + +
212C ASN* 3.2 10.9 + - - -
291C HIS* 3.9 0.7 - - - -
320C THR* 3.6 33.0 - - + +
321C VAL* 5.3 2.5 - - + -
362C GLY* 4.0 2.8 + - - -
363C LEU* 1.3 77.3 - - - +
365C GLY* 1.3 67.2 + - - +
367C ASN* 3.0 22.1 + - + +
368C ALA* 3.7 5.1 - - - +
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Residues in contact with GLY 365 (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 ALA* 3.2 25.6 + - - +
212C ASN* 3.3 2.9 - - - -
287C SER* 5.8 0.4 - - - -
290C GLN* 3.0 21.1 + - - -
291C HIS* 3.1 22.3 + - - -
364C LEU* 1.3 69.1 - - - +
366C CYS* 1.3 57.6 + - - -
368C ALA* 2.9 18.7 + - - +
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Residues in contact with CYS 366 (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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32C ASN* 4.2 4.7 - - - -
33C LEU 4.9 0.9 - - - -
34C PRO* 3.6 33.2 - - + -
212C ASN* 2.8 26.9 + - - +
290C GLN* 4.5 4.7 - - - +
365C GLY* 1.3 71.4 - - - -
367C ASN* 1.3 70.7 + - - +
369C THR* 3.3 22.4 - - - +
372C ASN* 4.8 0.5 + - - -
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Residues in contact with ASN 367 (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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24C LEU* 4.5 1.6 - - - +
25C LEU 3.0 26.0 + - - +
26C LEU* 4.1 9.6 - - + +
31C SER* 4.4 3.6 - - - -
32C ASN* 3.1 45.4 + - - +
362C GLY 5.6 0.2 - - - +
363C LEU* 4.0 6.0 - - - +
364C LEU* 3.0 20.9 + - + +
366C CYS* 1.3 88.0 - - - +
368C ALA* 1.3 57.3 + - - +
369C THR* 2.9 8.2 + - - -
372C ASN* 2.8 37.1 + - - +
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Residues in contact with ALA 368 (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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290C GLN* 3.0 27.6 + - - +
291C HIS* 3.9 16.6 - - + -
294C ALA* 3.9 16.2 - - + +
363C LEU* 3.7 36.8 - - + +
364C LEU 3.7 2.5 + - - +
365C GLY 2.9 13.8 + - - +
366C CYS 3.3 0.2 - - - -
367C ASN* 1.3 73.1 - - - +
369C THR* 1.3 59.7 + - - +
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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