Contacts of the helix formed by residues 83 - 94 (chain A) in PDB entry 2DMZ
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 ALA 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ILE* 4.9 0.2 - - - -
82A PHE* 1.3 76.9 - - - +
84A ASN* 1.3 68.8 + - - +
85A HIS* 3.1 36.6 - - + +
86A ASP* 2.6 21.0 + - + +
87A VAL* 2.7 15.2 + - - +
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Residues in contact with ASN 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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33A ILE* 3.5 22.4 + - + +
34A VAL* 3.3 8.3 + - - +
35A GLY* 2.9 43.4 - - - +
48A ILE* 4.0 5.9 - - - +
82A PHE 4.3 0.4 + - - -
83A ALA* 1.3 71.8 - - - +
85A HIS* 1.3 61.3 + - - +
87A VAL* 3.2 5.6 + - - +
88A VAL* 3.0 33.2 + - + +
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Residues in contact with HIS 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 ALA* 3.1 27.2 - - + +
84A ASN* 1.3 78.0 + - - +
86A ASP* 1.3 84.5 + - + +
88A VAL* 3.1 20.1 + - - +
89A GLU* 3.2 17.7 + - - +
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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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82A PHE* 3.3 32.9 - - + -
83A ALA* 2.6 30.9 + - + +
85A HIS* 1.3 85.6 - - + +
87A VAL* 1.3 54.6 + - - +
89A GLU* 3.0 29.2 - - - +
90A VAL* 3.0 20.7 - - - +
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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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33A ILE* 3.9 21.3 - - + -
48A ILE* 4.1 14.6 - - + -
71A ILE* 5.9 0.4 - - + -
74A VAL* 4.5 11.9 - - + -
79A ILE* 4.0 29.8 - - + -
82A PHE* 3.8 20.6 - - + -
83A ALA 2.7 24.7 + - - +
84A ASN 3.5 6.1 - - - +
86A ASP* 1.3 72.8 - - - +
88A VAL* 1.3 64.8 + - - +
90A VAL* 3.2 8.6 + - - +
91A LEU* 3.2 28.6 + - + +
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Residues in contact with VAL 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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33A ILE* 4.3 12.3 - - + -
84A ASN* 3.0 21.2 + - + +
85A HIS* 3.1 11.4 + - - +
87A VAL* 1.3 76.1 - - - +
89A GLU* 1.3 64.4 + - - +
91A LEU* 3.1 25.1 + - + +
92A ARG* 3.2 31.5 + - + +
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Residues in contact with GLU 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 HIS* 3.2 7.5 + - - +
86A ASP* 3.0 46.3 - - - +
88A VAL* 1.3 79.8 - - - +
90A VAL* 1.3 60.5 + - + +
92A ARG* 3.3 11.9 + - - +
93A ASN* 2.8 45.6 + - - +
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Residues in contact with VAL 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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74A VAL* 3.9 13.0 - - + -
75A ASP* 3.8 9.1 - - - +
77A VAL* 3.6 49.4 - - + -
79A ILE* 4.4 2.0 - - + -
82A PHE* 4.3 10.3 - - + -
86A ASP* 3.0 25.8 - - - +
87A VAL* 3.3 11.2 - - + +
88A VAL 3.1 0.2 - - - -
89A GLU* 1.3 82.8 - - + +
91A LEU* 1.3 63.6 + - - +
93A ASN* 3.2 8.4 + - + +
94A ALA* 2.9 21.7 + - - +
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Residues in contact with LEU 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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23A ARG* 5.6 3.1 + - - -
29A LEU* 3.2 41.2 - - + +
31A ILE* 4.7 14.4 - - + +
33A ILE* 4.8 11.7 - - + -
74A VAL* 3.6 32.5 - - + -
87A VAL* 3.3 22.7 - - + +
88A VAL* 3.1 17.6 + - + +
90A VAL* 1.3 77.4 - - - +
92A ARG* 1.3 63.6 + - + +
94A ALA* 3.2 23.6 + - - +
98A VAL* 5.6 0.7 - - - +
100A LEU* 4.8 3.6 - - + -
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Residues in contact with ARG 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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23A ARG* 4.9 8.4 + - - +
88A VAL* 3.2 30.4 + - + +
89A GLU* 3.6 9.9 - - - +
91A LEU* 1.3 78.0 - - + +
93A ASN* 1.3 64.0 + - - +
94A ALA 3.3 7.6 - - - +
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Residues in contact with ASN 93 (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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89A GLU* 2.8 43.1 + - - +
90A VAL* 3.5 7.9 - - - +
92A ARG* 1.3 75.5 - - - +
94A ALA* 1.3 66.2 + - - +
95A GLY* 3.5 2.1 + - - -
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Residues in contact with ALA 94 (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 ARG* 3.7 12.0 + - - -
29A LEU* 6.5 0.2 - - + -
75A ASP* 3.5 31.2 - - + +
90A VAL 2.9 8.5 + - - +
91A LEU* 3.2 18.2 + - - +
92A ARG 3.3 8.8 - - - +
93A ASN* 1.3 79.8 - - - +
95A GLY* 1.3 63.4 + - - +
98A VAL* 3.9 22.6 - - + +
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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