Contacts of the helix formed by residues 72 - 82 (chain A) in PDB entry 4O8M
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 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A SER* 5.0 6.1 - - - -
71A GLY* 1.3 75.0 - - - -
73A GLU* 1.3 65.7 + - - +
74A THR* 3.6 6.9 + - - -
75A GLU* 3.0 46.2 + - - +
76A VAL* 2.9 21.9 + - - +
192A SER* 3.6 31.5 + - - -
194A SER* 5.9 1.8 - - - -
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Residues in contact with GLU 73 (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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34A GLY* 5.3 4.7 + - - -
68A SER* 5.4 2.2 + - - -
71A GLY 3.9 0.6 + - - -
72A SER* 1.3 73.1 - - - +
74A THR* 1.3 62.5 + - - +
76A VAL* 3.5 5.2 + - - +
77A LEU* 3.1 21.8 + - - +
88A THR* 4.7 4.1 + - - +
89A ILE* 3.6 38.1 - - + +
90A SER* 3.3 29.1 - - - +
91A ASP* 3.8 10.0 + - - +
172A GLN* 3.9 11.3 - - - +
192A SER* 5.8 0.2 - - - -
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Residues in contact with THR 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 SER* 3.2 5.9 + - - +
73A GLU* 1.3 78.0 - - - +
75A GLU* 1.3 67.4 + - + +
77A LEU* 3.4 9.1 + - - +
78A GLU* 3.3 25.1 + - + +
94A ALA* 5.5 4.5 - - - +
173A HIS* 3.9 34.2 + - + +
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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
----------------------------------------------------------
71A GLY* 3.8 6.9 - - - -
72A SER* 3.0 43.6 + - - +
74A THR* 1.3 79.6 - - + +
76A VAL* 1.3 63.8 + - - +
78A GLU* 3.2 11.7 + - - +
79A GLN* 3.1 29.8 + - - +
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Residues in contact with VAL 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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32A ALA* 3.8 11.4 - - + -
70A LEU* 4.0 24.0 - - + +
71A GLY 3.7 18.2 - - - +
72A SER 2.9 21.1 + - - +
73A GLU* 3.9 5.2 - - - +
75A GLU* 1.3 75.5 - - - +
77A LEU* 1.3 66.0 + - - +
79A GLN* 3.1 8.7 + - - +
80A ALA* 3.0 20.4 + - - +
86A ILE* 3.7 23.6 - - + -
88A THR* 3.6 28.5 - - - +
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Residues in contact with LEU 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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73A GLU 3.1 14.1 + - - +
74A THR* 3.6 10.8 - - - +
75A GLU 3.3 0.2 - - - -
76A VAL* 1.3 75.6 - - - +
78A GLU* 1.3 58.0 + - - +
80A ALA* 3.2 6.9 + - + +
81A LYS* 2.9 31.2 + - - +
88A THR* 4.4 10.2 - - + +
90A SER* 4.2 10.3 - - - +
94A ALA* 6.1 4.0 - - + -
95A LEU* 3.8 23.3 - - + -
98A ILE* 4.9 4.3 - - + -
138A ILE* 4.0 29.6 - - + -
240A VAL* 3.6 30.5 - - + -
241A ALA 6.1 0.2 - - - -
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Residues in contact with GLU 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 THR* 3.3 15.3 + - + +
75A GLU* 3.2 13.2 + - - +
76A VAL 3.1 0.8 - - - -
77A LEU* 1.3 79.9 - - - +
79A GLN* 1.3 62.3 + - + +
81A LYS* 3.2 34.4 + - - +
82A PHE* 3.1 57.2 + - + -
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Residues in contact with GLN 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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30A MET* 5.4 1.7 - - - +
70A LEU* 3.2 31.1 + - - +
71A GLY* 5.0 0.2 - - - -
75A GLU* 3.1 21.4 + - - +
76A VAL* 3.1 18.2 + - - +
78A GLU* 1.3 76.9 - - + +
80A ALA* 1.3 62.8 + - - +
82A PHE* 3.3 12.4 + - - +
83A GLY 3.3 0.9 + - - -
84A ALA* 3.2 24.6 + - + +
86A ILE* 3.7 21.2 - - + +
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Residues in contact with ALA 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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76A VAL 3.0 12.3 + - - +
77A LEU* 3.4 14.4 - - + +
79A GLN* 1.3 75.3 - - - +
81A LYS* 1.3 65.7 + - - +
83A GLY* 2.8 15.8 + - - -
84A ALA* 3.8 12.6 + - - +
86A ILE* 4.3 22.6 - - + +
88A THR* 4.8 5.4 - - + -
138A ILE* 6.2 0.2 - - + -
241A ALA* 4.6 3.8 - - - -
242A GLY* 3.3 29.9 + - - +
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Residues in contact with LYS 81 (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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77A LEU* 2.9 18.6 + - - +
78A GLU* 3.2 31.4 + - - +
80A ALA* 1.3 76.5 - - - +
82A PHE* 1.3 74.5 + - + +
83A GLY* 3.2 1.3 + - - -
98A ILE* 4.9 8.9 - - - +
136A HIS 4.7 4.8 + - - +
137A ASP* 4.1 31.5 - - + +
138A ILE* 3.8 29.4 - - + +
242A GLY* 4.2 9.9 - - - -
244A ALA* 4.7 10.2 - - - +
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Residues in contact with PHE 82 (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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78A GLU* 3.1 47.8 + - + +
79A GLN* 3.7 6.3 - - - +
80A ALA 3.0 1.4 - - - -
81A LYS* 1.3 92.6 - - + +
83A GLY* 1.3 55.8 + - - +
84A ALA 3.6 2.0 + - - -
244A ALA* 5.4 1.6 - - - -
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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