Contacts of the helix formed by residues 88 - 99 (chain A) in PDB entry 2DAZ
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 SER 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A MET* 3.3 18.8 - - - +
53A ILE* 4.6 1.2 - - - +
87A ARG* 1.3 75.3 - - - +
89A HIS* 1.3 62.3 + - - +
90A GLN* 3.9 20.7 + - - -
91A ASN* 2.6 48.9 + - - +
92A ALA 3.5 1.7 + - - -
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Residues in contact with HIS 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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42A LEU* 3.5 43.1 + - + +
43A ALA* 4.5 3.7 - - - +
44A GLY* 4.1 23.6 + - - -
53A ILE* 3.8 25.2 - - + +
87A ARG 3.8 2.0 + - - -
88A SER* 1.3 73.5 - - - +
90A GLN* 1.3 104.0 + - + +
92A ALA* 3.0 19.1 + - - +
93A SER* 3.4 4.5 + - - -
121A PRO 6.1 0.7 - - - -
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Residues in contact with GLN 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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88A SER* 2.8 19.2 + - - +
89A HIS* 1.3 107.9 + - + +
91A ASN* 1.3 62.0 + - - +
93A SER* 2.6 27.7 + - - -
94A ALA* 3.4 4.7 + - - +
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Residues in contact with ASN 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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87A ARG* 3.8 42.8 - - + +
88A SER* 2.6 49.5 + - - +
90A GLN* 1.3 72.0 - - - +
92A ALA* 1.3 68.0 + - - +
94A ALA* 2.7 21.7 + - - +
95A ILE* 3.0 15.1 + - + +
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Residues in contact with ALA 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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42A LEU* 3.9 14.8 - - + -
53A ILE* 4.0 10.5 - - + +
76A LEU* 4.8 1.3 - - + -
79A ILE* 4.7 6.1 - - + +
84A LEU* 3.9 38.0 - - + +
88A SER 3.5 1.6 + - - -
89A HIS 3.0 11.7 + - - +
91A ASN* 1.3 77.0 - - - +
93A SER* 1.3 65.6 + - - +
95A ILE* 2.9 16.6 + - - +
96A ILE* 3.1 16.5 + - + +
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Residues in contact with SER 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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42A LEU* 4.6 8.1 - - - +
89A HIS 3.4 5.3 + - - -
90A GLN* 2.6 24.5 + - - -
91A ASN 3.2 0.2 - - - -
92A ALA* 1.3 77.2 - - - +
94A ALA* 1.3 66.4 + - - +
96A ILE* 3.1 15.6 + - - +
97A LYS* 3.0 30.6 + - - +
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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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90A GLN 4.0 4.3 - - - +
91A ASN* 2.7 24.3 + - - +
93A SER* 1.3 76.5 + - - +
95A ILE* 1.3 60.5 + - + +
97A LYS* 3.1 20.8 + - - +
98A THR* 3.2 18.0 + - - +
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Residues in contact with ILE 95 (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 ILE* 3.6 26.7 - - + +
80A ASN* 4.6 7.0 - - + +
82A GLN* 3.9 34.1 - - + +
83A ILE 5.2 0.2 - - - +
84A LEU* 2.9 38.1 - - + -
87A ARG* 4.6 13.0 - - - +
91A ASN* 3.0 8.6 + - + +
92A ALA* 2.9 13.7 + - - +
94A ALA* 1.3 75.6 - - + +
96A ILE* 1.3 58.0 + - - +
98A THR* 2.7 23.9 + - - +
99A ALA* 2.9 13.3 + - - +
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Residues in contact with ILE 96 (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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33A LYS* 3.5 18.3 - - + -
38A LEU* 3.4 53.2 - - + +
40A LEU* 5.8 2.7 - - + -
42A LEU* 6.1 2.2 - - + -
76A LEU* 5.5 2.9 - - + -
79A ILE* 3.6 38.8 - - + -
92A ALA* 3.1 11.4 + - + +
93A SER* 3.1 16.0 + - - +
95A ILE* 1.3 74.1 - - - +
97A LYS* 1.3 67.1 + - - +
99A ALA* 2.9 27.4 + - - +
103A VAL* 4.7 1.8 - - + -
105A LEU* 4.6 1.1 - - + -
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Residues in contact with LYS 97 (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 LYS* 4.5 7.5 + - - +
93A SER* 3.0 20.9 + - - +
94A ALA* 3.1 13.7 + - - +
96A ILE* 1.3 80.0 - - - +
98A THR* 1.3 62.5 + - + +
99A ALA 3.6 4.9 - - - +
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Residues in contact with THR 98 (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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94A ALA 3.2 10.9 + - - +
95A ILE* 2.7 25.7 + - - +
97A LYS* 1.3 76.8 - - + +
99A ALA* 1.3 64.7 + - - +
100A PRO* 3.7 2.1 - - - +
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Residues in contact with ALA 99 (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 LYS* 3.0 22.9 + - - -
80A ASN* 3.7 21.5 - - + +
95A ILE 2.9 14.0 + - - +
96A ILE* 2.9 16.4 + - - +
97A LYS 3.6 2.8 - - - +
98A THR* 1.3 81.4 + - - +
100A PRO* 1.3 71.8 - - + +
103A VAL* 3.5 20.6 - - + -
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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