Contacts of the helix formed by residues 332 - 340 (chain B) in PDB entry 1ATT
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 VAL 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B PHE* 4.0 12.3 - - + -
84B ILE* 3.8 36.3 - - + -
88B PHE* 4.6 2.2 - - + -
330B PHE* 3.9 9.2 + - + -
331B SER* 1.3 69.9 - - - +
333B LYS* 1.3 62.6 + - - +
335B GLN* 3.2 5.8 + - - +
336B LEU* 3.1 41.3 + - + +
345B PHE* 5.5 0.2 - - - -
368B ALA* 2.9 22.2 + - + +
369B PHE 4.0 6.1 - - - +
370B HIS* 3.8 28.0 - - + +
387B THR* 5.1 2.9 - - + -
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Residues in contact with LYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B SER* 2.9 19.8 + - - +
332B VAL* 1.3 76.5 - - - +
334B GLU* 1.3 74.4 + - - +
336B LEU* 3.5 2.3 + - - +
337B GLN* 3.0 53.0 + - - +
345B PHE* 3.5 41.2 - - + -
365B VAL 4.9 0.4 + - - -
366B SER 2.8 26.4 + - - +
367B ASP* 3.6 23.9 + - - +
368B ALA* 3.7 5.6 + - - +
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B SER* 3.4 20.9 + - - +
332B VAL 3.4 0.2 - - - -
333B LYS* 1.3 93.5 - - - +
335B GLN* 1.3 70.8 + - + +
337B GLN* 3.0 22.3 + - - +
338B ASP* 2.9 21.2 + - - +
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Residues in contact with GLN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PHE* 3.3 31.4 - - + -
66B HIS* 2.8 36.0 + - + +
67B LEU* 3.5 26.8 - - + +
70B SER* 2.9 34.1 + - - -
330B PHE* 4.9 2.2 - - + -
331B SER 4.8 7.4 - - - +
332B VAL 3.2 5.4 + - - +
334B GLU* 1.3 84.0 - - + +
336B LEU* 1.3 59.3 + - - +
338B ASP* 2.9 18.0 - - - +
339B MET* 2.9 24.2 + - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 3.6 31.4 - - + -
63B PHE* 4.3 2.5 - - + -
84B ILE* 4.8 0.9 - - + -
88B PHE* 3.5 39.5 - - + -
106B VAL* 3.7 17.9 - - + -
107B PHE* 3.6 12.6 - - + -
332B VAL* 3.1 27.8 + - + +
335B GLN* 1.3 79.7 - - - +
337B GLN* 1.3 54.2 + - - +
339B MET* 3.1 11.6 + - - +
340B GLY 2.9 10.9 + - - -
341B LEU* 2.7 36.9 + - + +
345B PHE* 3.9 12.3 - - + -
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Residues in contact with GLN 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B LYS* 3.0 53.0 + - - +
334B GLU* 3.0 14.4 + - - +
336B LEU* 1.3 76.5 - - - +
338B ASP* 1.3 58.0 + - + +
340B GLY* 3.2 17.8 + - - -
341B LEU 3.1 17.0 + - - +
342B GLU* 3.6 33.3 - - - +
345B PHE* 4.0 12.3 - - + -
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Residues in contact with ASP 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B HIS* 3.7 24.5 + - - -
334B GLU 2.9 19.2 + - - +
335B GLN* 2.9 29.9 - - - +
337B GLN* 1.3 74.1 - - - +
339B MET* 1.3 63.7 + - - +
340B GLY* 3.2 1.3 - - - -
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Residues in contact with MET 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 3.6 31.0 - - + -
62B ALA* 4.2 13.0 - - + +
63B PHE* 3.6 49.1 - - - +
66B HIS* 3.8 24.2 - - + +
106B VAL* 3.8 24.0 - - + +
108B LYS* 4.8 4.9 - - - +
335B GLN 2.9 19.7 + - - +
336B LEU* 3.1 14.3 + - + +
338B ASP* 1.3 80.2 - - - +
340B GLY* 1.4 54.5 + - - +
341B LEU 4.0 0.4 - - - -
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Residues in contact with GLY 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLN* 3.3 19.4 + - - +
106B VAL* 3.8 10.7 - - - +
336B LEU 2.9 3.4 + - - -
337B GLN 3.2 5.5 + - - -
338B ASP 3.2 4.4 - - - -
339B MET* 1.4 80.0 - - - +
341B LEU* 1.3 59.7 + - - -
342B GLU* 2.9 12.8 + - - +
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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