Contacts of the helix formed by residues 58 - 68 (chain C) in PDB entry 6ACQ
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 GLU 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C VAL* 3.6 3.8 - - - -
57C ILE* 1.3 83.6 - - - +
59C GLU* 1.3 67.2 + - - +
60C ALA* 3.9 13.2 - - + +
61C THR* 2.7 29.6 + - - +
62C LYS 2.9 9.2 + - - -
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Residues in contact with GLU 59 (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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52C VAL* 3.4 28.4 - - + +
58C GLU* 1.3 70.2 - - - +
60C ALA* 1.3 61.7 + - - +
62C LYS* 3.3 30.4 + - - +
63C VAL* 3.2 34.1 + - + +
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Residues in contact with ALA 60 (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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58C GLU* 2.9 11.2 + - + +
59C GLU* 1.3 76.2 - - - +
61C THR* 1.3 66.6 + - - +
63C VAL* 3.0 25.4 - - - +
64C GLU* 3.2 17.8 + - - +
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Residues in contact with THR 61 (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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22C ALA 6.0 0.7 - - - +
57C ILE* 4.0 18.9 - - + +
58C GLU* 2.7 33.8 + - - +
60C ALA* 1.3 76.2 - - - +
62C LYS* 1.3 59.2 + - - -
64C GLU* 3.4 17.6 + - - +
65C ILE* 3.2 41.0 + - + +
68C ARG* 5.8 1.3 - - - +
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Residues in contact with LYS 62 (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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45C ASN* 2.6 33.1 + - - +
48C LEU* 3.7 32.1 - - + +
49C SER* 3.7 21.9 + - - +
52C VAL* 4.1 3.6 - - + -
57C ILE* 3.8 19.3 - - + +
58C GLU 2.9 6.3 + - - +
59C GLU* 3.5 37.5 - - - +
60C ALA 3.1 0.2 - - - -
61C THR* 1.3 78.9 - - - +
63C VAL* 1.3 62.3 + - + +
65C ILE* 3.6 2.7 + - - +
66C LEU* 3.1 38.1 + - + +
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Residues in contact with VAL 63 (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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59C GLU* 3.2 27.7 + - + +
60C ALA* 3.0 23.8 - - - +
62C LYS* 1.3 80.5 - - + +
64C GLU* 1.3 66.0 + - + +
65C ILE 3.2 0.2 - - - -
66C LEU* 3.5 9.7 + - + +
67C THR* 2.8 31.9 + - - +
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Residues in contact with GLU 64 (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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60C ALA* 3.2 20.7 + - - +
61C THR* 3.4 19.9 - - - +
63C VAL* 1.3 77.7 - - - +
65C ILE* 1.3 63.1 + - - +
67C THR* 3.1 20.7 + - - +
68C ARG* 3.3 41.1 + - - +
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Residues in contact with ILE 65 (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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18C GLN* 4.7 4.9 - - + +
21C ALA* 3.7 20.4 - - + +
22C ALA* 3.7 35.9 - - + +
48C LEU* 3.7 34.1 - - + -
57C ILE* 5.2 4.0 - - + -
61C THR* 3.2 36.4 + - + +
62C LYS* 3.8 4.9 - - - +
63C VAL 3.2 0.2 - - - -
64C GLU* 1.3 78.7 - - - +
66C LEU* 1.3 64.4 + - - +
68C ARG* 3.2 26.7 + - - +
69C ILE* 3.4 17.2 - - + +
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Residues in contact with LEU 66 (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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41C LEU* 5.1 8.1 - - + +
44C ILE* 4.3 17.5 - - + -
45C ASN* 3.8 32.1 - - + +
48C LEU* 3.9 16.6 - - + -
62C LYS* 3.1 38.8 + - + +
63C VAL* 3.9 11.0 - - + +
65C ILE* 1.3 80.7 - - - +
67C THR* 1.3 61.6 + - - +
69C ILE* 3.4 27.3 + - + +
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Residues in contact with THR 67 (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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63C VAL* 2.8 22.8 + - - +
64C GLU* 3.2 10.1 - - - +
65C ILE 3.1 0.4 - - - -
66C LEU* 1.3 78.3 - - - +
68C ARG* 1.3 60.2 + - + +
69C ILE 3.1 9.1 + - - +
70C SER* 5.0 2.9 + - - -
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Residues in contact with ARG 68 (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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21C ALA* 2.8 27.3 + - + -
22C ALA 4.1 8.9 + - - -
24C GLY* 3.8 21.7 - - - +
25C PHE 3.4 21.1 - - - +
26C GLU* 3.5 15.3 - - + +
27C VAL* 2.8 29.1 + - - +
61C THR* 5.8 1.6 - - - +
64C GLU* 3.3 45.3 + - - +
65C ILE* 3.2 24.1 + - - +
67C THR* 1.3 80.9 - - + +
69C ILE* 1.3 58.4 + - - +
70C SER* 4.2 2.6 + - - -
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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