Contacts of the helix formed by residues 72 - 81 (chain B) in PDB entry 1XOX
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 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA* 3.8 16.2 - - - +
37B ARG* 5.9 1.1 - - - -
70B ASP 3.9 2.5 + - - +
71B ASP* 1.3 68.9 + - - +
73B PRO* 1.3 60.8 - - + +
74B ILE* 4.8 1.1 - - + +
75B GLU* 3.7 29.3 - - + +
76B GLU* 2.8 35.0 + - - +
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Residues in contact with PRO 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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32B ALA 3.2 19.7 - - - +
37B ARG* 2.9 41.3 - - + +
38B MET* 3.6 12.3 - - + -
41B ALA* 3.5 8.7 - - + +
43B PHE* 3.2 32.6 - - + -
67B TRP* 4.0 4.3 - - + -
71B ASP 3.1 1.7 - - - +
72B ASP* 1.3 82.0 - - + +
74B ILE* 1.3 66.7 + - + +
76B GLU* 2.8 20.1 + - + +
77B HIS* 3.0 13.3 + - - +
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Residues in contact with ILE 74 (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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40B GLU* 4.0 25.8 - - + +
41B ALA* 3.1 26.9 - - + +
72B ASP* 5.8 1.3 - - + -
73B PRO* 1.3 81.9 - - + +
75B GLU* 1.3 68.0 + - + +
77B HIS* 4.4 0.2 - - - +
78B LYS* 3.2 41.3 + - - +
87B LEU* 3.7 39.1 - - + +
90B LYS* 6.3 0.4 - - - +
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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
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72B ASP* 3.5 28.9 + - + +
73B PRO 3.1 0.6 - - - -
74B ILE* 1.3 82.6 - - + +
76B GLU* 1.3 53.8 + - - +
78B LYS* 4.2 10.0 - - - +
79B LYS* 2.8 58.5 + - - +
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Residues in contact with GLU 76 (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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43B PHE* 4.1 0.2 - - + -
64B LEU* 3.9 22.9 - - + -
67B TRP* 3.4 29.2 - - + -
71B ASP* 3.4 27.5 - - - +
72B ASP 2.8 15.7 + - - +
73B PRO 2.8 9.0 + - - +
75B GLU* 1.3 74.2 - - - +
77B HIS* 1.3 68.8 + - - +
79B LYS* 3.1 21.6 + - - +
80B HIS* 3.2 45.1 + - - -
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Residues in contact with HIS 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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41B ALA 3.9 4.1 + - - +
43B PHE* 3.7 22.8 - - + -
57B CYS* 3.5 3.9 - - + -
60B CYS* 2.8 17.9 - - - +
62B LYS* 4.6 14.0 - - + +
64B LEU* 4.6 6.3 - - - -
73B PRO 3.0 6.8 + - - +
74B ILE 4.4 2.2 - - - +
76B GLU* 1.3 78.0 - - - +
78B LYS* 1.3 53.4 + - - +
80B HIS* 3.0 5.9 + - - +
81B SER* 2.5 64.8 + - - +
83B GLY* 3.4 8.8 + - - -
84B CYS* 3.1 28.1 - - + +
87B LEU* 3.9 6.1 - - + +
998B ZN 2.1 38.1 - - - -
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Residues in contact with LYS 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 ILE* 3.2 34.2 + - - +
75B GLU* 4.2 8.8 - - - +
77B HIS* 1.3 79.3 - - - +
79B LYS* 1.3 65.2 + - - +
81B SER* 2.9 22.5 + - - -
82B SER* 3.3 26.7 + - - +
87B LEU* 3.9 16.1 - - + +
88B SER* 5.5 4.4 + - - -
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Residues in contact with LYS 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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75B GLU* 2.8 43.9 + - - +
76B GLU* 3.1 16.4 + - - +
78B LYS* 1.3 74.2 - - - +
80B HIS* 1.3 76.4 + - + +
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Residues in contact with HIS 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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62B LYS* 3.7 33.1 - - + -
64B LEU* 4.0 17.4 - - + +
76B GLU* 3.2 39.4 + - - +
77B HIS* 3.0 7.4 + - - +
78B LYS 3.7 0.2 - - - -
79B LYS* 1.3 90.6 - - + +
81B SER* 1.3 68.6 + - - +
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Residues in contact with SER 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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62B LYS* 5.2 8.7 - - - -
77B HIS* 2.5 53.3 + - - +
78B LYS* 2.9 8.2 + - - -
80B HIS* 1.3 79.0 + - - +
82B SER* 1.3 58.1 + - - +
83B GLY* 3.2 8.3 - - - -
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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