Contacts of the helix formed by residues 75 - 85 (chain B) in PDB entry 2BTO
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 PRO 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU 4.0 1.3 - - - +
74B GLU* 1.4 96.2 - - - +
76B SER* 1.3 56.1 + - - +
77B VAL 3.2 2.9 + - - -
78B ILE* 3.4 4.4 + - - +
79B ASP* 2.9 45.2 + - - +
96B SER* 4.0 18.4 - - - +
97B ARG 3.8 18.6 - - - +
98B THR* 3.6 17.5 - - + +
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 6.3 0.2 - - - -
74B GLU* 2.9 36.3 + - - -
75B PRO* 1.3 74.1 - - - +
77B VAL* 1.3 61.3 + - - +
79B ASP* 3.5 8.5 - - - +
80B ASN* 3.1 37.8 + - - +
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Residues in contact with VAL 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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13B GLN* 3.7 42.8 - - + +
16B ASN* 3.8 24.0 - - + -
17B GLN* 3.6 31.6 - - + +
72B ASP* 4.1 13.9 - - - +
74B GLU* 4.2 4.6 + - + +
75B PRO 3.3 0.6 - - - -
76B SER* 1.3 81.7 - - - +
78B ILE* 1.3 58.7 + - - +
80B ASN* 3.1 11.9 + - + +
81B VAL* 3.0 28.6 + - + +
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Residues in contact with ILE 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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16B ASN* 4.2 13.0 - - + +
70B MET* 3.5 33.7 - - + +
71B VAL 4.0 0.7 - - - -
72B ASP* 3.7 20.6 - - + +
74B GLU 5.2 0.8 + - - -
75B PRO 3.4 5.8 + - - +
77B VAL* 1.3 75.0 - - - +
79B ASP* 1.3 66.7 + - - +
81B VAL* 3.3 6.9 + - + +
82B LYS* 3.0 34.0 + - + +
94B LEU* 3.9 24.9 - - + +
95B ILE 3.4 29.6 - - - +
96B SER* 4.1 14.8 - - - +
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Residues in contact with ASP 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 PRO* 2.9 34.6 + - - +
76B SER* 3.5 9.7 + - - +
78B ILE* 1.3 76.8 - - - +
80B ASN* 1.3 59.8 + - - +
82B LYS* 3.4 19.0 + - - +
83B ALA* 3.0 26.7 + - - +
96B SER* 5.6 0.7 + - - -
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Residues in contact with ASN 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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17B GLN* 5.3 7.0 - - - +
76B SER* 3.1 26.1 + - - +
77B VAL* 3.1 14.2 + - + +
79B ASP* 1.3 76.0 - - - +
81B VAL* 1.3 64.1 + - + +
83B ALA* 3.1 9.0 + - - +
84B THR* 2.8 33.3 + - + +
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Residues in contact with VAL 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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16B ASN* 4.5 6.7 - - + +
17B GLN* 5.9 0.7 - - - -
20B ALA* 4.2 22.0 - - + -
70B MET* 3.9 24.7 - - + -
77B VAL* 3.0 18.7 + - + +
78B ILE* 3.5 11.9 - - - +
80B ASN* 1.3 77.4 - - + +
82B LYS* 1.3 55.6 + - - +
84B THR* 3.1 7.0 + - - -
85B SER* 2.7 49.7 + - - +
89B PHE* 3.8 23.6 - - + -
94B LEU* 4.7 7.4 - - + -
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Residues in contact with LYS 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 ILE* 3.0 23.5 + - + +
79B ASP* 3.5 21.7 + - - +
80B ASN 3.3 0.2 - - - -
81B VAL* 1.3 76.4 - - - +
83B ALA* 1.3 61.8 + - - +
85B SER* 3.9 7.3 + - - -
86B GLY* 4.3 14.0 + - - +
91B PRO* 5.5 9.4 - - - +
94B LEU* 4.1 29.8 + - + -
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Residues in contact with ALA 83 (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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79B ASP 3.0 14.3 + - - +
80B ASN* 3.1 15.2 + - - +
82B LYS* 1.3 78.6 - - - +
84B THR* 1.3 62.8 + - + +
85B SER 3.9 0.3 + - - -
86B GLY 4.9 1.6 + - - -
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Residues in contact with THR 84 (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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20B ALA* 5.6 3.6 - - - +
35B LEU* 3.3 20.0 - - - +
80B ASN* 2.8 19.7 + - + +
81B VAL* 3.4 9.7 + - - -
83B ALA* 1.3 80.5 - - + +
85B SER* 1.3 58.1 + - - +
86B GLY 3.7 1.6 - - - -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 6.4 0.9 - - - -
34B PRO 4.5 4.3 - - - -
35B LEU* 3.7 11.3 - - - +
81B VAL* 2.7 27.4 + - - -
82B LYS* 4.3 2.8 + - - -
83B ALA 3.6 0.4 - - - -
84B THR* 1.3 82.4 - - - +
86B GLY* 1.3 69.1 + - - +
88B LEU* 3.1 23.6 + - - +
89B PHE* 3.5 34.7 + - - -
94B LEU* 5.8 0.2 - - - +
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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