Contacts of the helix formed by residues 58 - 66 (chain B) in PDB entry 6BAA
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 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B ARG 3.4 13.7 + - - +
55B PHE 4.4 3.4 - - - +
56B LEU 3.1 3.5 - - - -
57B GLN* 1.3 75.0 - - - +
59B VAL* 1.3 55.1 + - - +
60B PHE* 4.1 1.7 + - - +
61B THR* 2.6 43.5 + - - +
62B THR* 2.7 29.3 + - - +
173C GLN 5.7 0.3 - - - +
176C ARG* 4.1 30.1 - - + +
177C ARG* 3.1 26.2 + - - +
180C THR* 5.6 1.8 - - + -
206C ARG* 5.6 4.1 - - - +
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Residues in contact with VAL 59 (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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56B LEU 2.9 22.4 - - - +
57B GLN* 2.8 16.0 + - - +
58B ASP* 1.3 71.8 - - - +
60B PHE* 1.3 77.0 + - + +
62B THR* 3.2 7.2 - - - -
63B LEU* 2.8 45.6 + - + +
46F ILE* 6.0 7.0 - - + -
49F ILE* 4.2 15.9 - - + +
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Residues in contact with PHE 60 (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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57B GLN 5.8 0.9 - - - -
58B ASP* 3.4 1.5 + - - +
59B VAL* 1.3 87.2 - - + +
61B THR* 1.3 61.8 + - - +
62B THR 3.1 1.3 - - - -
63B LEU* 3.9 11.2 - - + +
64B VAL* 3.0 33.0 + - - +
162B ILE* 3.3 36.3 - - + -
166B CYS* 3.7 19.1 - - - -
169B MET* 4.3 4.5 - - + -
68C TRP* 3.9 36.8 - + - -
170C LYS 5.2 0.9 - - - -
171C THR* 3.7 42.0 - - + +
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Residues in contact with THR 61 (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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58B ASP* 2.6 38.3 + - - +
60B PHE* 1.3 77.4 - - - +
62B THR* 1.3 52.8 + - - +
64B VAL* 3.5 4.9 + - - +
65B ASP* 2.8 50.1 + - - +
174C ALA* 5.5 5.4 - - - +
177C ARG* 4.1 24.4 - - + +
208C SER* 5.0 0.7 - - - +
291C VAL* 4.6 1.0 - - + +
293C THR* 3.4 26.9 + - + +
294C THR* 4.8 10.1 - - - +
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Residues in contact with THR 62 (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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55B PHE* 3.6 21.5 + - + +
56B LEU* 5.2 4.4 - - + -
58B ASP* 2.7 18.5 + - - +
59B VAL* 3.2 11.7 - - - -
61B THR* 1.3 77.8 - - - +
63B LEU* 1.3 65.0 + - - +
65B ASP* 3.0 19.6 + - + +
66B LEU* 3.0 25.0 + - + +
49F ILE* 3.5 31.9 - - + +
53F SER* 5.4 7.6 - - - -
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Residues in contact with LEU 63 (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 VAL* 2.8 35.8 + - + +
60B PHE* 3.9 12.1 - - + +
61B THR 3.4 0.2 - - - -
62B THR* 1.3 72.7 - - - +
64B VAL* 1.3 63.1 + - - +
66B LEU* 3.2 21.9 + - + +
71B THR* 3.7 15.6 + - + +
74B ILE* 3.6 28.9 - - + -
75B PHE* 4.9 11.4 - - + -
162B ILE* 5.4 2.2 - - + -
166B CYS* 3.5 34.3 - - + -
170B LYS* 4.0 2.6 + - - +
49F ILE* 3.3 29.6 - - + -
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Residues in contact with VAL 64 (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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60B PHE 3.0 18.9 + - - +
61B THR* 3.7 6.5 - - - +
63B LEU* 1.3 77.2 - - + +
65B ASP* 1.3 58.9 + - - +
166B CYS* 4.2 9.0 - - - +
169B MET* 3.6 48.5 - - + +
170B LYS* 2.9 29.5 + - - +
173B GLN* 3.0 41.9 - - + +
293C THR* 4.2 9.2 - - - +
294C THR* 5.5 1.6 - - + -
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Residues in contact with ASP 65 (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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61B THR* 2.8 38.7 + - - +
62B THR* 3.0 10.3 + - - +
64B VAL* 1.3 76.9 - - - +
66B LEU* 1.3 64.9 + - + +
67B LYS* 3.7 2.3 + - - +
173B GLN* 5.0 2.0 - - - +
208C SER* 4.7 10.4 + - - -
292C GLU* 5.2 0.5 - - - +
293C THR* 2.7 32.2 - - - +
56F SER* 6.0 1.6 - - - -
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Residues in contact with LEU 66 (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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62B THR* 3.0 26.0 + - + +
63B LEU* 3.2 22.1 + - + +
65B ASP* 1.3 80.9 - - + +
67B LYS* 1.3 66.7 + - - +
70B HIS* 4.4 14.1 - - + +
71B THR* 4.0 4.3 - - - +
74B ILE* 3.3 34.3 - - + -
170B LYS* 2.6 31.7 + - - -
49F ILE* 4.5 11.4 - - + +
52F GLY* 4.3 28.7 - - - +
53F SER* 4.6 4.0 - - - +
56F SER* 5.1 7.2 - - - +
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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