Contacts of the helix formed by residues 79 - 90 (chain A) in PDB entry 2X2P
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 GLY 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR* 3.6 13.2 - - - -
68A ALA* 3.9 13.0 - - - -
69A SER 4.9 2.2 - - - -
70A GLY* 4.9 1.1 - - - -
77A MET 3.1 0.4 + - - -
78A PHE* 1.3 77.6 - - - +
80A ALA* 1.4 57.7 + - - +
81A SER* 3.1 3.4 - - - -
82A ALA* 3.0 22.3 + - - +
83A ASP* 3.6 0.5 - - - +
96A LYS* 3.4 24.0 - - - -
1119A FMN 2.8 13.9 + - - -
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Residues in contact with ALA 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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42A THR* 4.1 2.2 - - - +
46A GLY* 3.4 25.4 - - - +
76A ASP 5.1 2.0 - - - +
77A MET* 3.1 27.1 + - + +
78A PHE 3.2 1.7 - - - -
79A GLY* 1.4 73.4 - - - +
81A SER* 1.3 64.6 + - - +
82A ALA 3.2 0.2 - - - -
83A ASP* 3.1 17.5 + - + +
84A LYS* 3.1 33.2 + - - +
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Residues in contact with SER 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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40A THR* 3.5 9.5 - - - +
41A TYR 3.4 17.4 + - - -
42A THR* 2.8 23.0 + - - +
46A GLY 3.7 6.3 + - - -
47A ASN 3.8 13.5 - - - -
48A VAL* 3.9 17.5 - - - -
68A ALA* 3.4 12.0 - - - +
80A ALA* 1.3 78.5 - - - +
82A ALA* 1.4 62.1 + - - -
84A LYS* 3.4 2.5 + - - +
85A ILE* 3.1 30.6 + - - +
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Residues in contact with ALA 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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66A VAL* 3.8 21.3 - - + +
68A ALA* 3.7 21.3 - - + +
79A GLY 3.0 12.7 + - - +
81A SER* 1.4 78.9 + - - +
83A ASP* 1.3 60.2 + - - +
85A ILE 3.4 0.2 + - - -
86A SER* 2.8 34.3 + - - -
93A ILE* 3.9 27.4 - - + -
96A LYS* 4.5 2.7 - - + -
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Residues in contact with ASP 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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76A ASP 5.7 1.2 - - - +
78A PHE 4.3 0.2 - - - +
80A ALA* 3.1 20.7 + - + +
82A ALA* 1.3 75.1 - - - +
84A LYS* 1.3 64.0 + - + +
86A SER* 3.8 1.1 - - - -
87A THR* 2.9 33.9 + - - +
93A ILE* 3.4 20.4 - - - +
96A LYS* 2.6 30.8 + - - -
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE 4.9 2.2 + - - -
46A GLY* 2.8 32.1 + - - +
47A ASN* 3.8 17.9 + - - +
48A VAL* 4.1 20.2 - - + +
80A ALA* 3.1 17.1 + - - +
81A SER 3.7 6.5 - - - +
82A ALA 3.3 0.2 - - - -
83A ASP* 1.3 78.5 - - + +
85A ILE* 1.3 57.4 + - - +
87A THR* 3.5 4.0 + - - -
88A LYS* 3.0 30.9 + - - +
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Residues in contact with ILE 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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38A LEU* 3.8 14.8 - - + -
40A THR* 4.1 8.7 - - + -
48A VAL* 4.0 26.9 - - + -
53A LEU* 5.7 1.6 - - + -
56A LEU* 3.8 33.2 - - + -
63A LEU* 4.1 12.1 - - + -
66A VAL* 3.9 28.5 - - + -
81A SER 3.1 18.3 + - - +
82A ALA 4.0 2.2 - - - +
84A LYS* 1.3 72.8 - - - +
86A SER* 1.3 66.7 + - - +
88A LYS* 4.7 0.7 - - - -
89A TYR* 3.0 39.4 + - + +
91A VAL* 4.3 1.0 - - + +
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Residues in contact with SER 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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66A VAL* 4.1 2.4 - - - +
82A ALA 2.8 18.2 + - - -
83A ASP 3.8 2.9 - - - -
85A ILE* 1.3 78.4 - - - +
87A THR* 1.3 57.7 + - - +
90A GLU* 2.8 30.5 + - - -
91A VAL* 2.6 30.4 + - - -
92A PRO* 4.3 0.7 - - - +
93A ILE* 3.6 27.0 + - - +
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Residues in contact with THR 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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83A ASP* 2.9 20.2 + - - +
84A LYS* 3.9 4.7 - - - -
86A SER* 1.3 78.7 + - - +
88A LYS* 1.4 64.4 + - - +
90A GLU* 3.9 13.3 + - - +
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Residues in contact with LYS 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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53A LEU* 5.9 6.0 - - + +
57A GLU* 6.3 1.0 - - - +
84A LYS 3.0 19.0 + - - +
85A ILE* 4.0 2.7 - - - +
87A THR* 1.4 81.7 - - - +
89A TYR* 1.3 99.1 + - + +
90A GLU* 3.4 5.6 + - - +
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Residues in contact with TYR 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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53A LEU* 5.1 4.3 + - + +
56A LEU* 3.8 39.5 + - + +
57A GLU* 4.1 6.6 + - - +
60A ASN* 3.5 39.7 + - + +
63A LEU* 4.1 21.8 - - + -
85A ILE* 3.0 32.0 + - + +
88A LYS* 1.3 113.5 + - + +
90A GLU* 1.3 73.8 + - - +
91A VAL* 3.4 9.0 + - + +
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Residues in contact with GLU 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 SER 2.8 14.5 + - - -
87A THR 3.9 13.8 - - - +
88A LYS 3.4 5.1 - - - +
89A TYR* 1.3 83.1 - - - +
91A VAL* 1.3 58.4 + - - +
92A PRO* 4.9 0.3 - - - +
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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