Contacts of the helix formed by residues 98 - 110 (chain B) in PDB entry 2O52
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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PHE* 3.4 21.5 + - - -
71A ARG* 4.0 21.1 - - - +
16B SER* 3.0 13.9 + - - -
94B GLU 3.3 9.1 + - - -
95B THR 2.6 21.3 + - - -
96B TYR 3.1 0.2 - - - -
97B ASN* 1.3 77.4 - - - +
99B LEU* 1.3 64.2 + - - +
100B ALA 3.3 2.2 - - - -
101B ALA* 3.2 16.5 + - - +
102B TRP* 3.3 18.3 + - - -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 3.6 34.7 - - + +
87B VAL 3.8 17.9 - - - +
88B TYR* 3.7 18.4 - - + -
95B THR 3.9 6.1 - - - +
96B TYR* 3.2 47.0 + - + +
97B ASN 3.4 0.8 - - - -
98B SER* 1.3 79.2 + - - +
100B ALA* 1.3 58.2 + - - +
102B TRP* 3.3 5.8 + - + +
103B LEU* 2.8 30.2 + - - +
118B LEU* 3.8 15.9 - - + -
139B PHE* 4.0 21.3 - - + -
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASN 4.8 3.6 + - - +
98B SER 3.3 0.8 + - - -
99B LEU* 1.3 78.0 - - - +
101B ALA* 1.3 52.5 + - - +
103B LEU* 3.6 9.3 - - + +
104B THR* 2.7 41.0 + - - +
139B PHE* 4.3 19.4 - - + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG* 3.4 49.8 - - + +
72A SER* 4.7 4.7 - - - +
98B SER 3.2 10.4 + - - +
100B ALA* 1.3 75.2 - - - +
102B TRP* 1.3 59.4 + - - +
104B THR* 3.5 6.6 + - - -
105B ASP* 3.0 37.8 + - - +
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Residues in contact with TRP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE 3.0 20.2 + - - -
71A ARG* 3.8 24.9 - - + +
72A SER* 4.7 5.8 - - - -
14B ILE* 3.7 16.4 - - + +
15B GLY* 3.5 44.9 - - - +
16B SER* 3.5 1.5 - - - +
64B THR* 6.1 1.6 - - + -
68B GLU* 4.0 26.0 - - + -
73B VAL* 4.0 16.6 - - + -
78B TYR* 3.2 28.0 - - - -
86B LEU* 3.6 20.6 - - + -
98B SER* 3.3 30.0 + - - -
99B LEU* 3.3 5.5 + - + +
101B ALA* 1.3 77.0 - - - +
103B LEU* 1.3 57.5 + - - +
105B ASP* 3.4 12.2 + - - +
106B ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 5.3 0.7 - - - -
86B LEU* 4.1 11.6 - - + +
99B LEU 2.8 20.3 + - - +
100B ALA* 3.7 6.3 - - + +
102B TRP* 1.3 70.3 - - - +
104B THR* 1.3 64.9 + - - +
106B ALA* 3.2 7.9 + - + +
107B ARG* 3.0 63.9 + - + +
116B VAL* 4.0 33.9 - - + -
139B PHE* 4.7 9.0 - - + -
143B ASN* 3.8 33.4 - - + +
145B LEU* 4.3 11.0 - - + -
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Residues in contact with THR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ALA* 2.7 25.6 + - - +
101B ALA* 3.7 7.7 - - - -
103B LEU* 1.3 72.0 - - - +
105B ASP* 1.3 62.1 + - - +
107B ARG* 3.3 6.4 + - - +
108B THR* 2.8 46.1 + - - +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A SER* 3.3 30.2 + - - -
78B TYR* 3.7 24.0 + - + +
101B ALA 3.0 22.7 + - - +
102B TRP* 3.6 13.1 - - - +
104B THR* 1.3 78.2 - - - +
106B ALA* 1.3 58.4 + - - +
108B THR* 4.5 4.0 - - - -
109B LEU* 2.8 50.6 + - + +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 3.8 18.2 - - + -
78B TYR* 3.9 14.2 - - + -
84B ALA* 5.2 0.2 - - + -
102B TRP 3.0 14.4 + - - +
103B LEU* 3.4 11.9 - - + +
105B ASP* 1.3 75.7 - - - +
107B ARG* 1.3 56.6 + - + +
110B ALA* 2.8 35.8 + - - +
111B SER 3.4 0.7 + - - +
114B ILE* 4.1 23.1 - - + -
116B VAL* 4.9 8.1 - - + -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 3.0 54.5 + - + +
104B THR* 4.0 5.6 - - - +
106B ALA* 1.3 78.0 - - - +
108B THR* 1.3 60.4 + - - +
111B SER* 3.1 11.7 - - - +
112B PRO* 3.0 53.0 + - + +
114B ILE* 4.2 13.4 + - + -
116B VAL* 5.4 1.0 - - - +
143B ASN* 3.7 28.1 + - - +
145B LEU* 4.1 8.1 - - - +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ARG* 6.0 3.4 - - - +
104B THR* 2.8 33.5 + - - +
105B ASP* 3.9 4.0 - - - -
107B ARG* 1.3 79.3 - - - +
109B LEU* 1.3 75.0 + - + +
110B ALA 4.8 2.1 - - - +
111B SER* 4.8 0.4 - - - -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL 5.1 4.5 - - - +
75B ARG* 4.0 35.3 - - + +
78B TYR* 3.4 49.5 - - + +
79B ARG* 3.8 18.2 + - - +
105B ASP* 2.8 34.6 + - + +
108B THR* 1.3 87.8 - - + +
110B ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TYR* 3.6 25.9 - - + +
79B ARG* 6.1 0.7 - - - -
80B GLY* 4.7 9.5 + - - +
81B ALA* 4.1 9.9 - - + +
106B ALA* 2.8 15.2 + - - +
108B THR 4.8 1.4 - - - +
109B LEU* 1.3 81.3 - - - +
111B SER* 1.3 64.7 + - - +
114B ILE* 3.6 27.1 - - + -
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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