Contacts of the helix formed by residues 75 - 85 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLU* 1.3 98.6 - - + +
76A SER* 1.3 57.7 + - - +
77A VAL 3.5 1.3 + - - -
78A ILE* 3.6 4.5 + - - +
79A ASP* 3.0 41.7 + - - +
96A SER* 4.0 15.1 + - - +
97A ARG 3.4 13.9 - - - +
98A THR* 3.6 23.6 - - + +
33B ASP* 4.8 2.9 - - - +
38B GLN* 5.5 7.4 - - - +
40B ALA* 5.9 0.2 - - - -
41B PRO* 5.4 1.3 - - + -
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Residues in contact with SER 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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74A GLU* 2.7 37.5 + - - -
75A PRO* 1.3 70.7 - - - +
77A VAL* 1.3 62.8 + - - +
79A ASP* 3.5 1.4 + - - +
80A ASN* 3.0 37.0 + - - +
31B GLY 6.0 1.8 - - - -
33B ASP* 3.9 25.5 - - - +
38B GLN 5.2 0.9 - - - -
39B THR* 5.1 2.0 - - - -
40B ALA* 4.1 18.5 + - - +
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Residues in contact with VAL 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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13A GLN* 3.7 35.9 - - + +
16A ASN* 3.8 24.5 - - + +
17A GLN* 3.7 34.1 - - + +
72A ASP* 4.2 11.6 + - - +
74A GLU* 3.9 9.2 + - - +
75A PRO 3.5 0.2 - - - -
76A SER* 1.3 76.2 + - - +
78A ILE* 1.3 67.1 + - - +
80A ASN* 2.9 22.0 + - + +
81A VAL* 3.0 16.2 + - + +
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Residues in contact with ILE 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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16A ASN* 3.9 13.9 - - + +
70A MET* 3.6 28.7 - - + +
71A VAL 3.7 4.3 - - - +
72A ASP* 3.6 24.8 + - + +
74A GLU 5.2 0.2 + - - -
75A PRO 3.6 6.7 + - - +
77A VAL* 1.3 75.1 - - - +
79A ASP* 1.3 57.8 + - - +
81A VAL* 3.3 7.6 + - + +
82A LYS* 3.0 38.7 + - + +
94A LEU* 3.9 29.1 - - + +
95A ILE 3.3 26.0 - - - +
96A SER* 4.3 13.9 - - - +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 3.0 28.5 + - - +
76A SER 3.7 2.0 - - - +
78A ILE* 1.3 79.2 - - - +
80A ASN* 1.3 58.3 + - - +
82A LYS* 3.3 17.6 + - - +
83A ALA* 2.9 28.6 + - - +
96A SER* 5.2 2.9 + - - -
33B ASP* 2.4 46.8 - - - +
34B PRO* 4.6 0.6 - - - +
35B LEU* 3.8 21.7 - - + +
36B THR* 3.7 13.6 - - - +
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Residues in contact with ASN 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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17A GLN* 5.3 5.9 - - - +
76A SER* 3.0 22.3 + - - +
77A VAL* 2.9 20.2 + - + +
79A ASP* 1.3 71.5 - - - +
81A VAL* 1.3 60.2 + - + +
83A ALA* 3.2 6.3 + - - +
84A THR* 2.8 37.3 + - + +
28B LEU* 3.6 23.1 - - + +
32B ILE 4.8 1.6 - - - +
33B ASP* 4.6 3.1 - - - -
34B PRO* 3.4 21.0 - - - +
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Residues in contact with VAL 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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16A ASN* 4.3 6.5 - - + +
17A GLN* 5.9 0.2 - - - -
20A ALA* 3.7 28.0 - - + -
70A MET* 4.0 26.5 - - + -
77A VAL* 3.0 23.0 + - + +
78A ILE* 3.6 9.4 - - + +
80A ASN* 1.3 77.3 - - + +
82A LYS* 1.3 61.0 + - - +
84A THR* 3.7 6.4 + - - -
85A SER* 2.7 33.5 + - - +
89A PHE* 3.7 30.7 - - + -
94A LEU* 5.0 5.6 - - + -
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Residues in contact with LYS 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 ILE* 3.0 35.2 + - - +
79A ASP* 3.6 17.4 + - - +
80A ASN 3.2 0.2 - - - -
81A VAL* 1.3 77.4 - - - +
83A ALA* 1.3 64.4 + - - +
84A THR 3.2 0.5 + - - -
85A SER* 3.7 7.7 + - - -
86A GLY* 4.0 13.3 + - - +
91A PRO* 5.7 3.2 + - - -
94A LEU* 3.8 34.7 + - + -
96A SER* 5.8 1.8 + - - -
35B LEU* 3.9 19.7 - - + +
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Residues in contact with ALA 83 (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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79A ASP 2.9 17.0 + - - +
80A ASN 3.2 4.9 + - - +
82A LYS* 1.3 77.6 - - - +
84A THR* 1.3 62.4 + - + +
85A SER 3.6 0.7 + - - -
86A GLY 4.8 2.1 + - - -
24B LYS* 2.6 39.9 + - + +
34B PRO* 3.6 29.6 - - + -
35B LEU* 4.5 14.8 - - + +
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Residues in contact with THR 84 (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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20A ALA* 6.1 1.0 - - - +
35A LEU* 3.3 17.3 - - - +
80A ASN* 2.8 23.0 + - + +
81A VAL* 3.7 6.8 + - - -
83A ALA* 1.3 83.3 - - + +
85A SER* 1.3 59.0 + - - +
86A GLY 3.8 0.9 - - - -
24B LYS* 4.6 6.7 - - + +
28B LEU* 3.8 33.2 - - + -
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Residues in contact with SER 85 (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 PRO 3.7 8.0 - - - +
35A LEU* 3.6 13.9 - - - +
81A VAL* 2.7 22.7 + - - -
82A LYS* 4.4 3.3 - - - -
84A THR* 1.3 81.6 - - - +
86A GLY* 1.3 66.2 + - - +
87A SER 3.2 0.2 + - - -
88A LEU* 3.0 21.1 + - - +
89A PHE* 3.3 35.5 + - - -
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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