Contacts of the helix formed by residues 349 - 354 (chain C) in PDB entry 3THT
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 349 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242C HIS* 3.1 9.9 - - - +
341C CYS* 3.8 2.9 - - - -
345C TYR 3.4 11.3 + - - +
346C PRO* 3.5 11.4 - - + +
347C LEU 3.3 1.8 - - - -
348C VAL* 1.3 75.8 - - - +
350C ASP* 1.3 60.7 + - - +
351C SER* 3.3 22.9 - - - -
352C GLN* 3.3 27.4 - - + +
353C ARG* 2.9 28.0 + - - +
401C ZN 2.5 33.7 - - - -
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Residues in contact with ASP 350 (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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241C THR* 3.3 20.6 - - + +
242C HIS* 3.8 4.6 + - - +
243C SER* 2.6 35.4 + - - -
348C VAL 3.6 4.8 + - - +
349C CYS* 1.3 68.4 - - - +
351C SER* 1.3 75.9 + - - -
352C GLN 2.8 10.3 + - - -
353C ARG* 4.0 9.9 - - - +
354C LYS* 3.1 28.5 + - + +
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Residues in contact with SER 351 (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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243C SER* 3.6 20.2 - - - -
340C PRO* 3.6 15.3 - - - +
341C CYS* 2.8 43.7 + - - -
349C CYS* 3.3 7.3 - - - -
350C ASP* 1.3 83.6 + - - +
352C GLN* 1.3 58.0 + - - +
354C LYS* 3.8 14.3 - - - +
355C GLU* 3.2 16.7 - - - +
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Residues in contact with GLN 352 (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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341C CYS 3.2 24.7 + - - -
342C ASN* 3.8 14.2 - - - +
343C CYS 3.9 9.8 + - - +
346C PRO* 3.7 31.9 - - + +
349C CYS* 3.2 26.4 + - + +
350C ASP 2.8 2.0 + - - -
351C SER* 1.3 78.9 + - - +
353C ARG* 1.3 63.5 + - - +
354C LYS 2.7 6.9 + - - -
355C GLU* 2.8 43.7 + - - +
356C ASN* 5.1 1.0 - - - +
401C ZN 4.2 1.4 - - - -
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Residues in contact with ARG 353 (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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346C PRO 4.4 5.0 + - - +
347C LEU* 3.4 31.3 + - - +
349C CYS 2.9 16.3 + - - +
350C ASP* 3.3 9.3 + - - +
352C GLN* 1.3 75.0 - - - +
354C LYS* 1.3 61.3 + - - +
356C ASN* 3.3 25.7 + - - +
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Residues in contact with LYS 354 (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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350C ASP* 3.1 21.0 + - + +
351C SER* 3.8 13.5 - - - +
352C GLN 2.7 0.8 + - - -
353C ARG* 1.3 72.8 - - - +
355C GLU* 1.3 54.0 + - + +
356C ASN* 2.6 22.5 + - - -
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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