Contacts of the helix formed by residues 80 - 90 (chain A) in PDB entry 3DAG
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLU 4.0 1.8 + - - +
79A PHE* 1.3 71.9 - - - +
81A PRO* 1.4 79.1 - - - +
82A LYS* 3.2 21.4 + - - +
83A GLU* 2.9 48.3 + - - +
84A VAL* 3.0 22.9 + - - +
96A ILE* 5.9 1.4 - - - +
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Residues in contact with PRO 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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35A PRO* 3.2 38.8 - - + +
36A GLU* 4.1 9.2 - - + +
38A ALA* 4.1 1.0 - - + +
39A LEU* 3.8 29.4 - - + -
79A PHE 3.5 9.1 - - - +
80A ASP* 1.4 89.1 - - - +
82A LYS* 1.3 58.0 + - + +
84A VAL* 3.7 2.2 - - + +
85A MET* 2.9 34.1 + - - +
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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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35A PRO* 4.1 31.0 - - + -
80A ASP* 3.1 16.1 + - - +
81A PRO* 1.3 78.9 - - + +
83A GLU* 1.3 58.8 + - + +
85A MET* 3.5 8.9 + - - +
86A GLU* 2.9 38.9 + - + +
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Residues in contact with GLU 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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80A ASP* 2.9 39.8 + - - +
82A LYS* 1.3 74.5 - - + +
84A VAL* 1.3 65.5 + - - +
86A GLU* 3.6 12.7 - - - +
87A ALA* 3.0 24.8 + - - +
96A ILE* 4.3 17.5 - - + +
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Residues in contact with VAL 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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22A PHE* 4.4 7.9 - - + -
26A CYS* 3.9 11.0 - - - -
38A ALA* 4.2 13.0 - - + +
39A LEU* 3.6 22.7 - - + -
79A PHE* 4.2 11.7 - - + -
80A ASP 3.0 16.8 + - - +
81A PRO 3.7 7.2 - - - +
83A GLU* 1.3 76.3 - - - +
85A MET* 1.3 60.9 + - - +
87A ALA* 3.4 1.4 + - - +
88A HIS* 2.8 52.7 + - + +
96A ILE* 4.1 21.8 - - + -
100A ILE* 4.2 9.6 - - + -
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Residues in contact with MET 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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26A CYS* 3.7 16.8 - - + +
29A ALA* 3.9 6.5 - - + +
30A LYS* 3.7 42.8 - - + +
35A PRO* 3.8 32.8 - - + -
38A ALA* 3.3 17.7 - - + -
81A PRO 2.9 20.7 + - - +
82A LYS* 3.7 8.7 - - - +
84A VAL* 1.3 76.8 - - - +
86A GLU* 1.3 56.9 + - + +
88A HIS 3.3 0.5 + - - -
89A LEU* 2.8 44.5 + - + +
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Residues in contact with GLU 86 (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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82A LYS* 2.9 30.8 + - + +
83A GLU* 3.6 12.7 - - - +
85A MET* 1.3 76.3 - - + +
87A ALA* 1.3 60.2 + - - +
89A LEU* 5.2 1.6 - - - -
90A SER* 2.9 32.6 + - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLU 3.0 16.6 + - - +
84A VAL 3.7 1.6 - - - +
85A MET 3.3 0.2 - - - -
86A GLU* 1.3 76.9 - - - +
88A HIS* 1.3 58.8 + - - +
90A SER* 3.1 7.3 + - - -
92A ASN* 2.9 37.4 + - - +
95A SER* 3.5 22.4 - - - +
96A ILE* 3.6 26.5 - - + -
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Residues in contact with HIS 88 (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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21A ASN* 3.4 12.4 - - + +
22A PHE* 2.9 31.4 + - + -
23A MET* 3.4 44.3 - - + +
26A CYS* 3.7 17.7 - - + -
84A VAL* 2.8 47.8 + - + +
87A ALA* 1.3 77.4 - - - +
89A LEU* 1.3 57.5 + - - +
91A GLY* 3.0 17.3 + - - -
93A PRO* 3.6 22.3 - - + +
96A ILE* 4.0 12.0 - - + +
97A MET* 3.8 17.7 - - - -
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Residues in contact with LEU 89 (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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23A MET* 4.4 7.4 - - - -
26A CYS* 3.9 23.6 - - + +
27A GLU* 3.8 29.8 - - + +
30A LYS* 3.8 41.7 - - + +
85A MET* 2.8 33.3 + - + +
86A GLU* 4.7 1.6 - - - +
88A HIS* 1.3 73.7 - - - +
90A SER* 1.3 58.2 + - - +
91A GLY 3.3 1.6 + - - -
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Residues in contact with SER 90 (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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86A GLU 2.9 22.8 + - - -
87A ALA* 3.1 7.1 + - - -
89A LEU* 1.3 77.6 - - - +
91A GLY* 1.3 55.5 + - - +
92A ASN* 3.0 27.0 + - - +
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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