Contacts of the helix formed by residues 342 - 349 (chain A) in PDB entry 3A61
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 ASP 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A GLY* 4.0 6.8 - - - +
210A HIS* 3.1 26.8 + - - +
272A ARG* 2.7 37.0 + - - +
276A TRP* 3.6 10.4 + - - -
337A GLY* 3.2 19.7 + - - +
339A GLY 3.1 10.1 + - - +
340A PRO 4.4 5.4 - - - +
341A GLY* 1.3 73.4 - - - +
343A ALA* 1.3 71.8 + - - +
344A GLY 2.4 18.2 + - - -
345A GLU* 2.8 19.8 + - - +
346A VAL 3.7 1.7 + - - -
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Residues in contact with ALA 343 (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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203A SER 3.8 0.7 - - - +
207A GLY* 3.7 16.4 - - - -
276A TRP* 3.5 30.0 - - + -
342A ASP* 1.3 85.7 + - - +
344A GLY* 1.3 56.7 + - - +
345A GLU 3.6 0.2 - - - -
346A VAL* 4.1 2.5 - - - -
347A GLN* 2.9 58.7 + - + +
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Residues in contact with GLY 344 (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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341A GLY* 2.7 13.9 + - - -
342A ASP 2.4 11.7 + - - -
343A ALA* 1.3 70.6 - - - +
345A GLU* 1.3 69.6 + - - +
347A GLN* 3.8 5.3 - - - +
348A ALA* 2.9 21.4 + - - +
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Residues in contact with GLU 345 (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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336A LEU* 3.3 31.8 - - + +
337A GLY* 3.8 7.0 + - - +
339A GLY* 3.0 38.4 + - - -
340A PRO* 4.3 2.1 - - - +
341A GLY* 3.7 12.3 + - - -
342A ASP 2.8 14.4 + - - +
344A GLY* 1.3 74.2 - - - +
346A VAL* 1.3 64.2 + - - +
348A ALA* 2.8 19.9 + - - +
349A HIS* 3.3 4.7 + - - +
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Residues in contact with VAL 346 (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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203A SER* 5.0 2.2 - - - -
276A TRP* 3.8 37.7 - - + -
279A LEU* 4.6 10.5 - - + -
323A LEU* 4.8 3.8 - - + -
327A LEU* 4.1 12.6 - - + -
336A LEU* 4.0 20.6 - - + +
337A GLY* 3.8 20.2 - - - -
342A ASP 3.7 1.6 + - - +
343A ALA 4.2 4.9 - - - +
344A GLY 3.3 0.6 - - - -
345A GLU* 1.3 77.5 - - - +
347A GLN* 1.3 69.7 + - + +
348A ALA 2.8 1.7 + - - -
349A HIS* 2.9 18.7 + - - +
352A PHE* 3.7 23.9 - - + -
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Residues in contact with GLN 347 (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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203A SER* 3.3 33.2 + - - +
204A MET* 3.3 35.9 - - - +
207A GLY* 5.4 0.2 - - - -
343A ALA* 2.9 32.1 + - + +
344A GLY* 3.9 4.5 - - - +
346A VAL* 1.3 79.2 - - + +
348A ALA* 1.3 60.4 + - - +
349A HIS 3.6 0.3 + - - -
352A PHE* 3.7 15.9 - - - +
357A TRP* 3.1 54.7 + - + +
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Residues in contact with ALA 348 (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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344A GLY 2.9 12.0 + - - +
345A GLU* 2.8 17.7 + - - +
346A VAL 2.8 1.6 + - - -
347A GLN* 1.3 76.8 - - - +
349A HIS* 1.3 65.1 + - - +
350A PRO* 3.4 4.2 - - - +
352A PHE 5.8 0.3 - - - -
353A ARG* 5.7 1.2 + - - -
357A TRP* 5.6 0.7 - - - +
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Residues in contact with HIS 349 (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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319A GLU* 3.5 23.5 + - + -
322A ASP* 3.5 18.6 - - + +
323A LEU* 3.1 50.0 + - + -
326A LYS* 4.6 4.3 - - + -
336A LEU* 4.4 16.6 - - + -
345A GLU 3.3 1.8 + - - +
346A VAL 2.9 13.2 + - - +
347A GLN 3.8 4.3 - - - +
348A ALA* 1.3 80.9 - - - +
350A PRO* 1.3 95.1 - - + +
351A PHE* 2.7 30.3 + - + +
352A PHE* 3.0 13.1 + - + +
353A ARG 4.2 1.0 + - - -
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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