Contacts of the helix formed by residues 98 - 110 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A SER* 2.7 21.5 + - - -
94A GLU 3.2 11.5 + - - -
95A THR 2.8 12.1 + - - -
96A TYR 3.1 0.4 - - - -
97A ASN* 1.3 77.0 - - - +
99A LEU* 1.3 63.5 + - - +
100A ALA 3.4 0.9 - - - -
101A ALA* 3.1 17.4 + - - +
102A TRP* 3.2 22.3 + - - -
70B PHE* 3.5 14.1 - - - -
71B ARG* 3.3 28.5 - - - +
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Residues in contact with LEU 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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86A LEU* 3.5 30.7 - - + +
87A VAL 4.2 7.2 - - - +
88A TYR* 4.0 18.8 - - + -
95A THR 4.0 2.9 - - - +
96A TYR* 3.1 52.1 + - + +
97A ASN 3.3 0.6 - - - -
98A SER* 1.3 77.7 + - - +
100A ALA* 1.3 58.2 + - - +
102A TRP* 3.3 7.8 + - + +
103A LEU* 2.9 30.5 + - - +
118A LEU* 3.6 25.6 - - + -
139A PHE* 3.7 26.5 - - + -
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Residues in contact with ALA 100 (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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97A ASN 4.5 5.6 + - - +
98A SER 3.3 0.8 + - - -
99A LEU* 1.3 78.7 - - - +
101A ALA* 1.3 57.1 + - - +
103A LEU* 3.7 7.1 - - - +
104A THR* 2.9 36.6 + - - +
139A PHE* 4.0 17.8 - - + -
143A ASN* 6.2 0.2 - - - +
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Residues in contact with ALA 101 (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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98A SER 3.1 10.3 + - - +
100A ALA* 1.3 75.9 - - - +
102A TRP* 1.3 60.4 + - - +
104A THR* 3.4 5.3 + - - -
105A ASP* 2.9 36.8 + - - +
71B ARG* 4.1 29.6 - - + -
72B SER* 4.6 10.5 - - - +
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Residues in contact with TRP 102 (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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14A ILE* 3.7 15.7 - - + +
15A GLY* 3.5 39.9 - - - -
16A SER* 3.5 5.6 - - - +
64A THR* 6.3 1.3 - - + -
68A GLU* 3.9 24.9 - - + -
73A VAL* 4.1 13.5 - - + -
78A TYR* 3.4 27.4 - - - -
86A LEU* 3.5 21.1 - - + -
98A SER* 3.2 32.3 + - - -
99A LEU* 3.3 5.3 + - + +
101A ALA* 1.3 77.0 - - - +
103A LEU* 1.3 56.0 + - - +
105A ASP* 3.4 12.5 + - - +
106A ALA* 2.8 29.8 + - - +
70B PHE 2.8 29.6 + - - -
71B ARG* 3.7 18.7 - - + +
72B SER* 4.8 4.5 - - - -
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Residues in contact with LEU 103 (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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14A ILE* 5.3 0.2 - - - -
86A LEU* 4.0 9.8 - - + +
99A LEU 2.9 16.8 + - - +
100A ALA* 3.7 6.3 - - - +
102A TRP* 1.3 74.1 - - - +
104A THR* 1.3 60.7 + - - +
106A ALA* 3.3 4.0 + - - +
107A ARG* 3.0 71.3 + - - +
116A VAL* 4.0 23.8 - - + -
139A PHE* 5.0 6.1 - - + -
143A ASN* 3.8 30.7 - - + +
145A LEU* 3.9 21.1 - - + -
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Residues in contact with THR 104 (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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100A ALA* 2.9 24.6 + - - +
101A ALA* 3.8 5.6 - - - -
103A LEU* 1.3 69.5 - - - +
105A ASP* 1.3 65.1 + - - +
107A ARG* 3.2 6.1 + - - +
108A THR* 2.8 45.0 + - - +
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Residues in contact with ASP 105 (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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78A TYR* 3.8 23.3 + - + +
101A ALA* 2.9 24.0 + - - +
102A TRP* 3.5 13.7 - - - +
104A THR* 1.3 77.6 - - - +
106A ALA* 1.3 59.6 + - - +
108A THR* 4.7 2.5 - - - -
109A LEU* 2.8 48.3 + - + +
72B SER* 3.1 32.2 + - - -
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Residues in contact with ALA 106 (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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14A ILE* 3.5 21.5 - - + -
78A TYR* 3.7 14.5 - - + -
102A TRP 2.8 20.7 + - - +
103A LEU* 3.6 7.2 - - - +
104A THR 3.3 0.2 - - - -
105A ASP* 1.3 72.0 - - - +
107A ARG* 1.3 59.0 + - - +
110A ALA* 2.9 35.7 + - - +
111A SER 3.4 1.0 + - - +
114A ILE* 4.0 20.6 - - + +
116A VAL* 5.0 6.7 - - + -
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Residues in contact with ARG 107 (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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103A LEU* 3.0 49.4 + - + +
104A THR* 3.8 6.1 - - - +
106A ALA* 1.3 76.3 - - - +
108A THR* 1.3 60.2 + - - +
111A SER* 3.1 29.0 - - - +
112A PRO* 3.2 28.4 + - + +
114A ILE* 4.1 20.8 + - + -
116A VAL* 5.1 2.4 - - - +
143A ASN* 3.2 27.5 + - - +
144A GLU* 4.6 9.3 + - - +
145A LEU* 3.5 14.3 - - - +
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Residues in contact with THR 108 (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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104A THR* 2.8 33.2 + - - +
105A ASP* 4.0 2.9 - - - -
107A ARG* 1.3 80.3 - - - +
109A LEU* 1.3 72.9 + - + +
110A ALA 3.7 2.6 - - - -
111A SER* 5.2 0.7 - - - -
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Residues in contact with LEU 109 (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 VAL 5.1 4.0 - - - +
75A ARG* 4.0 47.7 - - + +
78A TYR* 3.6 40.0 - - + +
79A ARG* 3.6 22.7 - - - +
105A ASP* 2.8 30.0 + - + +
108A THR* 1.3 90.3 - - + +
110A ALA* 1.3 65.9 + - - +
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Residues in contact with ALA 110 (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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12A LEU* 4.7 0.7 - - + -
78A TYR* 3.4 26.8 - - + +
79A ARG* 4.5 1.8 - - - +
80A GLY* 4.6 7.9 + - - +
81A ALA 4.0 10.1 - - - +
106A ALA 2.9 16.9 + - - +
108A THR 4.8 1.1 - - - +
109A LEU* 1.3 81.1 - - - +
111A SER* 1.3 66.0 + - - +
114A ILE* 3.6 25.8 - - + -
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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