Contacts of the helix formed by residues 72 - 82 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B SER* 5.0 6.5 - - - -
71B GLY* 1.3 75.3 - - - +
73B GLU* 1.3 66.4 + - - +
74B THR* 3.6 6.6 + - - -
75B GLU* 3.0 46.3 + - - +
76B VAL* 2.9 22.1 + - - +
192B SER* 3.5 31.5 + - - -
194B SER* 6.0 1.8 - - - -
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Residues in contact with GLU 73 (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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34B GLY* 5.4 4.7 + - - -
68B SER* 5.5 1.4 + - - -
71B GLY 3.8 0.8 + - - -
72B SER* 1.3 73.9 - - - +
74B THR* 1.3 62.3 + - - +
76B VAL* 3.6 5.4 + - - +
77B LEU* 3.2 22.3 + - - +
88B THR* 4.7 3.9 + - - +
89B ILE* 3.8 37.5 - - + +
90B SER* 3.4 28.8 - - - +
91B ASP* 3.9 10.0 + - - +
172B GLN* 4.1 9.3 - - - +
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 3.1 5.7 + - - -
73B GLU* 1.3 77.9 - - - +
75B GLU* 1.3 66.7 + - + +
77B LEU* 3.4 9.8 + - + +
78B GLU* 3.3 28.8 + - + +
173B HIS* 4.0 30.9 + - + +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLY* 3.7 7.8 - - - -
72B SER* 3.0 41.1 + - - +
74B THR* 1.3 78.1 - - + +
76B VAL* 1.3 63.0 + - - +
78B GLU* 3.2 10.8 + - - +
79B GLN* 3.2 32.9 + - - +
192B SER* 5.5 0.5 + - - -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA* 3.8 15.0 - - + -
70B LEU* 3.7 30.5 - - + +
71B GLY* 3.6 15.3 - - - +
72B SER 2.9 19.5 + - - +
73B GLU* 4.0 4.5 - - - +
75B GLU* 1.3 74.1 - - - +
77B LEU* 1.3 64.8 + - - +
79B GLN* 3.0 14.7 + - - +
80B ALA* 3.0 20.3 + - - +
86B ILE* 3.8 13.9 - - + -
88B THR* 3.6 29.4 - - - +
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Residues in contact with LEU 77 (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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73B GLU 3.2 14.6 + - - +
74B THR* 3.6 12.1 - - + +
75B GLU 3.3 0.4 - - - -
76B VAL* 1.3 75.6 - - - +
78B GLU* 1.3 67.4 + - - +
80B ALA* 3.2 5.5 + - + +
81B LYS* 2.9 27.0 + - - +
88B THR* 4.4 9.8 - - + +
89B ILE 6.0 0.2 - - - +
90B SER* 4.3 12.6 - - - +
94B ALA* 6.2 3.1 - - + -
95B LEU* 4.0 15.0 - - + -
98B ILE* 4.9 4.7 - - + -
138B ILE* 3.7 34.1 - - + -
240B VAL* 3.5 32.3 - - + -
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Residues in contact with GLU 78 (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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74B THR* 3.3 19.0 + - + +
75B GLU* 3.2 9.8 + - - +
76B VAL 3.1 0.8 - - - -
77B LEU* 1.3 88.1 - - - +
79B GLN* 1.3 64.7 + - + +
81B LYS* 3.2 35.7 + - - -
82B PHE* 3.2 43.2 + - + -
98B ILE* 6.0 1.0 - - - +
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Residues in contact with GLN 79 (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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70B LEU* 3.5 27.9 + - - +
71B GLY* 5.3 0.2 - - - -
75B GLU* 3.2 24.6 + - - +
76B VAL* 3.0 15.7 + - - +
78B GLU* 1.3 76.1 - - + +
80B ALA* 1.3 63.4 + - - +
82B PHE* 3.3 11.4 + - - +
83B GLY 3.4 0.7 + - - -
84B ALA* 3.2 26.1 + - + +
86B ILE* 3.6 22.8 - - + +
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Residues in contact with ALA 80 (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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76B VAL 3.0 11.5 + - - +
77B LEU* 3.5 13.7 - - + +
79B GLN* 1.3 75.7 - - - +
81B LYS* 1.3 66.2 + - - +
83B GLY* 3.0 14.9 + - - -
84B ALA* 3.9 11.6 + - - +
86B ILE* 4.2 22.8 - - + +
88B THR* 4.7 6.5 - - + -
138B ILE* 6.5 0.2 - - + -
240B VAL 5.7 0.2 - - - -
241B ALA* 4.5 4.0 - - - -
242B GLY* 3.3 29.2 + - - +
245B PHE* 5.2 0.2 - - - +
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Residues in contact with LYS 81 (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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77B LEU 2.9 15.2 + - - +
78B GLU* 3.2 36.7 + - - +
79B GLN 3.4 0.4 - - - -
80B ALA* 1.3 76.8 - - - +
82B PHE* 1.3 81.0 + - + +
83B GLY* 3.5 1.2 + - - -
98B ILE* 5.5 4.0 - - - +
136B HIS 4.6 8.7 - - - +
137B ASP* 3.7 46.7 - - + +
138B ILE* 4.5 16.8 - - + +
242B GLY* 4.2 3.4 - - - -
244B ALA* 4.8 8.1 - - - +
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Residues in contact with PHE 82 (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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78B GLU* 3.2 44.2 + - + +
79B GLN* 3.3 5.1 + - - +
80B ALA 3.1 1.0 - - - -
81B LYS* 1.3 96.6 - - + +
83B GLY* 1.3 56.0 + - - +
84B ALA 3.7 2.4 + - - -
244B ALA* 5.4 1.3 - - - -
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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