Contacts of the helix formed by residues 73 - 80 (chain A) in PDB entry 2AF0
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 SER 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LYS 3.9 0.4 + - - -
72A PRO* 1.3 76.1 - - - +
74A PRO* 1.3 71.8 - - - +
75A GLU* 3.2 18.3 + - - +
76A GLU* 3.1 31.6 + - - +
77A ALA* 3.1 19.8 + - - +
198A LEU 4.5 1.1 - - - -
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Residues in contact with PRO 74 (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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72A PRO 4.2 3.4 - - - +
73A SER* 1.3 86.7 - - - +
75A GLU* 1.3 63.2 + - - +
77A ALA* 3.4 2.3 + - - +
78A GLN* 3.0 36.4 + - - +
198A LEU 3.3 16.8 - - - +
199A CYS* 3.5 18.1 - - - +
200A LYS 3.3 20.6 - - - +
201A LYS* 3.9 20.9 - - + -
202A PRO* 4.4 10.8 - - + -
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Residues in contact with GLU 75 (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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73A SER* 3.1 20.4 - - - +
74A PRO* 1.3 82.2 - - - +
76A GLU* 1.3 61.9 + - - +
78A GLN* 3.4 16.7 + - - +
79A LEU* 3.6 17.3 + - - +
201A LYS* 3.0 38.1 + - + +
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Residues in contact with GLU 76 (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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72A PRO* 3.4 20.4 - - + +
73A SER* 3.1 34.3 + - - +
75A GLU* 1.3 77.0 - - - +
77A ALA* 1.3 68.6 + - - +
79A LEU* 3.1 30.4 + - + +
80A TRP* 3.4 16.7 + - + +
90A SER* 4.2 10.9 + - - -
92A TYR* 3.5 23.3 - - - -
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Residues in contact with ALA 77 (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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72A PRO* 4.4 2.2 - - + -
73A SER 3.1 13.8 + - - +
74A PRO 3.7 6.5 - - - +
76A GLU* 1.3 76.8 - - - +
78A GLN* 1.3 56.4 + - - +
80A TRP* 3.0 44.0 + - + +
195A TYR* 2.6 24.6 + - + -
198A LEU* 3.8 24.0 - - + +
199A CYS* 3.8 9.6 - - - -
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Residues in contact with GLN 78 (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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74A PRO 3.0 18.8 + - - +
75A GLU* 3.6 11.9 - - - +
76A GLU 3.3 0.4 - - - -
77A ALA* 1.3 74.0 - - - +
79A LEU* 1.3 64.1 + - + +
80A TRP 3.1 1.4 + - - -
81A SER* 3.3 21.8 + - - -
82A GLU 4.6 0.3 + - - -
195A TYR* 3.6 5.8 - - - -
199A CYS* 2.8 39.9 + - + +
201A LYS* 4.3 20.4 + - - +
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Residues in contact with LEU 79 (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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75A GLU 3.6 15.5 - - - +
76A GLU* 3.1 20.3 + - + +
78A GLN* 1.3 77.6 - - + +
80A TRP* 1.3 64.1 + - + +
81A SER 3.1 2.6 + - - -
82A GLU* 3.2 30.9 + - + +
86A GLU* 4.3 8.6 - - + +
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Residues in contact with TRP 80 (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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72A PRO* 3.6 26.9 - - + -
76A GLU* 3.4 15.3 + - + +
77A ALA* 3.0 28.1 + - + +
79A LEU* 1.3 80.0 - - + +
81A SER* 1.3 50.5 + - - +
82A GLU 3.4 0.2 - - - -
83A ALA 3.6 6.7 - - - +
86A GLU* 4.1 7.2 - - + -
87A LEU* 3.7 46.2 - - + +
90A SER* 3.5 20.2 + - - -
92A TYR* 3.6 11.2 - - + -
93A GLY* 3.1 33.2 - - - -
96A ALA* 3.9 15.7 - - + -
186A TYR* 2.6 34.5 + - - -
189A PHE* 4.3 0.9 - + - -
190A LEU* 4.4 2.9 - - + -
195A TYR* 3.7 24.5 - + + +
198A LEU* 4.1 9.4 - - + -
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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