Contacts of the helix formed by residues 83 - 92 (chain A) in PDB entry 2DNO
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 THR 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LYS 4.0 9.6 - - - +
81A GLN 3.6 10.3 - - - +
82A GLN* 1.3 80.1 - - - +
84A ASP* 1.3 75.2 + - - +
85A GLU* 2.7 17.0 + - - +
86A ASP* 2.7 24.3 + - - -
87A VAL* 2.9 15.6 + - - -
102A VAL* 4.5 5.8 - - - -
104A ARG* 5.5 8.1 - - - +
110A SER* 6.2 0.7 - - - -
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Residues in contact with ASP 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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83A THR* 1.3 78.1 + - - +
85A GLU* 1.3 69.6 + - - +
87A VAL* 4.6 2.0 - - - -
88A ARG* 2.7 52.9 + - - +
100A CYS* 4.4 21.2 - - + +
102A VAL* 3.7 27.0 - - + +
104A ARG* 5.1 11.3 + - - +
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Residues in contact with GLU 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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83A THR* 2.7 14.6 + - - +
84A ASP* 1.3 88.5 + - - +
86A ASP* 1.3 61.1 + - - +
88A ARG* 3.6 3.9 - - - +
89A LYS* 2.9 36.7 + - + +
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Residues in contact with ASP 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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81A GLN 3.2 8.6 - - - +
82A GLN* 3.0 36.7 + - - +
83A THR* 2.7 34.4 + - - +
85A GLU* 1.3 76.0 - - - +
87A VAL* 1.3 52.2 + - - +
89A LYS* 3.1 3.7 + - - +
90A MET* 2.5 42.2 + - + +
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Residues in contact with VAL 87 (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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75A VAL* 5.0 2.7 - - + -
78A LEU* 3.7 33.9 - - + -
82A GLN* 4.5 9.4 - - + +
83A THR* 2.9 24.7 + - - +
84A ASP* 4.2 4.3 - - - +
86A ASP* 1.3 72.3 - - - +
88A ARG* 1.3 54.5 + - - +
90A MET* 3.9 9.6 - - + -
91A PHE* 2.6 64.0 + - + +
100A CYS* 4.7 6.5 - - - -
102A VAL* 5.5 0.9 - - + -
114A ALA* 5.0 9.0 - - + -
116A VAL* 4.0 22.0 - - + -
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Residues in contact with ARG 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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84A ASP* 2.7 34.4 + - - +
85A GLU* 3.6 3.8 - - - +
87A VAL* 1.3 74.3 - - - +
89A LYS* 1.3 54.1 + - + +
91A PHE 3.1 0.7 + - - -
92A GLU* 2.7 61.8 + - + +
97A ILE* 3.3 27.6 + - + +
100A CYS* 4.7 15.2 - - + -
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Residues in contact with LYS 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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85A GLU* 2.9 22.6 + - + +
86A ASP* 3.9 3.1 - - - +
88A ARG* 1.3 74.9 - - + +
90A MET* 1.3 55.4 - - - +
91A PHE 3.4 0.2 - - - -
92A GLU* 4.2 8.3 - - + -
93A PRO* 2.9 23.4 - - - +
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Residues in contact with MET 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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82A GLN* 3.0 33.4 - - - +
86A ASP* 2.5 22.6 + - + +
87A VAL* 3.5 11.0 - - + +
89A LYS* 1.3 74.5 - - - +
91A PHE* 1.3 80.2 + - + +
93A PRO* 3.4 14.5 - - - +
94A PHE* 4.0 14.0 - - - -
131A LEU* 4.0 7.3 - - + +
135A ARG* 3.3 42.2 - - - +
137A LEU* 4.2 12.8 - - + -
144A LEU* 4.3 12.1 - - + -
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Residues in contact with PHE 91 (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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73A LEU* 5.4 1.1 - - + -
75A VAL* 3.1 46.9 - - + -
87A VAL* 2.6 42.8 + - + +
90A MET* 1.3 87.0 - - + +
92A GLU* 1.3 65.0 + - - +
93A PRO* 3.1 2.7 - - - -
94A PHE* 3.0 10.2 + - - +
97A ILE* 3.5 16.4 - - + -
116A VAL* 3.8 18.2 - - + -
118A PHE* 3.0 35.2 - + + -
127A ALA* 4.8 1.1 - - + -
131A LEU* 3.6 29.6 - - + -
144A LEU* 3.9 18.2 - - + -
146A VAL* 4.0 13.2 - - + -
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Residues in contact with GLU 92 (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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88A ARG* 2.7 48.1 + - + +
89A LYS* 4.2 7.0 - - + +
91A PHE* 1.3 66.7 - - - +
93A PRO* 1.3 60.9 - - + +
94A PHE 2.6 6.6 + - - -
95A GLY 2.4 47.2 + - - +
96A THR* 3.6 13.3 + - - +
97A ILE* 2.9 40.9 + - + +
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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