Contacts of the helix formed by residues 96 - 107 (chain A) in PDB entry 2OUX
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 TYR 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASP* 5.6 4.3 + - - -
67A ASP* 2.9 37.9 + - + -
94A GLU 5.8 0.7 - - - -
95A MSE 1.3 71.6 - - - +
97A THR* 1.3 67.5 + - - +
98A ASP* 3.4 15.7 - - - +
99A ASN* 2.9 21.2 + - - +
100A ALA 2.9 9.9 + - - -
143A THR* 4.1 0.4 - - - +
145A GLU* 3.5 24.7 - - + +
167A ASP 5.0 2.9 + - - -
168A MSE 3.4 23.1 + - - -
169A ALA 3.7 12.6 + - - -
170A GLU* 3.1 40.2 + - + +
191B ARG* 5.0 2.3 + - - -
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Residues in contact with THR 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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95A MSE 3.4 2.8 + - - -
96A TYR* 1.3 70.2 - - - +
98A ASP* 1.3 65.2 + - - +
100A ALA* 3.0 0.9 + - - +
101A VAL* 2.9 25.6 + - + +
126A GLU* 3.7 31.8 - - + +
127A ILE* 3.2 31.2 - - + +
130A LEU* 3.8 18.2 - - + -
143A THR* 3.6 4.0 + - - -
144A THR* 3.1 14.2 + - - +
145A GLU* 2.7 20.8 + - - -
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Residues in contact with ASP 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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96A TYR* 3.4 13.9 - - - +
97A THR* 1.3 74.5 - - - +
99A ASN* 1.3 89.2 + - - +
101A VAL* 3.6 5.3 + - - +
102A ASP* 3.2 30.8 + - - +
130A LEU* 4.9 2.2 - - - -
140A ALA 5.4 2.7 - - - +
141A ILE* 4.3 8.4 - - - +
142A MSE 3.1 27.1 + - - +
143A THR* 3.1 16.5 + - - -
251A ASP* 3.1 8.1 - - - +
402A MG 4.0 0.3 - - - -
406A MG 2.1 30.1 - - - -
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Residues in contact with ASN 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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67A ASP* 2.9 48.7 + - - +
71A GLU* 5.4 1.4 - - - +
95A MSE 3.6 26.5 - - + +
96A TYR* 2.9 13.8 + - - +
98A ASP* 1.3 96.6 + - - +
100A ALA* 1.3 65.5 - - - +
102A ASP* 3.4 10.4 + - - +
103A LEU* 3.0 18.5 + - - +
170A GLU* 5.0 1.4 + - - -
251A ASP* 5.0 5.7 - - - +
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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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92A LEU* 3.7 26.9 - - + +
95A MSE 4.1 12.9 - - + +
96A TYR 2.9 11.2 + - - +
97A THR* 3.0 1.5 + - - +
99A ASN* 1.3 74.5 - - - +
101A VAL* 1.3 66.4 + - - +
103A LEU* 3.1 5.3 + - - +
104A LEU* 3.0 30.0 + - + +
127A ILE* 3.1 30.5 - - + -
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Residues in contact with VAL 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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97A THR* 2.9 18.7 + - + +
98A ASP* 3.8 5.6 - - - +
100A ALA* 1.3 76.1 - - - +
102A ASP* 1.3 68.6 + - - +
104A LEU* 3.4 5.4 + - - +
105A ASN* 2.9 46.5 + - - +
127A ILE* 3.5 33.2 - - + +
130A LEU* 4.0 23.1 - - + +
131A LEU* 3.6 23.5 - - + +
140A ALA* 5.7 1.1 - - - +
402A MG 4.5 4.9 - - - -
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Residues in contact with ASP 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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71A GLU* 3.0 36.4 - - + +
98A ASP* 3.2 15.6 + - - +
99A ASN* 3.7 8.9 - - - +
100A ALA 3.2 0.6 - - - -
101A VAL* 1.3 75.8 - - - +
103A LEU* 1.3 68.5 + - - +
105A ASN* 3.2 16.3 + - - +
106A MSE 3.3 16.6 + - - +
402A MG 2.2 31.3 - - - -
409A MG 4.2 4.7 - - - -
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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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66A PHE* 4.2 16.8 - - + +
69A ILE 6.0 0.9 - - - +
71A GLU* 4.3 13.4 - - + +
76A MSE 3.5 35.2 - - + -
80A LEU* 3.5 29.8 - - + -
91A MSE 6.2 0.2 - - + -
92A LEU* 4.0 18.8 - - + -
95A MSE 4.5 10.3 - - + -
99A ASN 3.0 13.5 + - - +
100A ALA* 3.4 8.3 - - - +
102A ASP* 1.3 75.2 - - - +
104A LEU* 1.3 58.3 + - - +
106A MSE 2.8 24.0 + - - +
107A LEU* 3.2 20.5 + - + -
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Residues in contact with LEU 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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92A LEU* 3.9 32.8 - - + -
100A ALA* 3.0 18.5 + - + +
101A VAL* 3.7 7.2 - - - +
103A LEU* 1.3 75.6 - - - +
105A ASN* 1.3 58.8 + - - +
106A MSE 3.0 5.4 + - - -
107A LEU* 3.2 37.4 + - + +
112A LYS* 3.7 43.2 - - + +
115A TYR* 4.7 3.1 - - + -
116A LEU* 4.4 15.3 - - + +
119A LEU* 6.3 1.1 - - + -
127A ILE* 3.8 30.1 - - + -
131A LEU* 4.8 5.8 - - + -
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Residues in contact with ASN 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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101A VAL* 2.9 43.9 + - - +
102A ASP* 3.2 9.6 + - - +
104A LEU* 1.3 73.7 - - - +
106A MSE 1.3 74.3 + - + +
107A LEU 4.2 3.5 - - - +
109A LYS* 5.9 0.3 + - - -
112A LYS* 3.7 12.4 - - - -
131A LEU* 3.4 18.9 + - - +
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Residues in contact with MSE 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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71A GLU* 3.2 35.0 - - + +
72A ASP* 4.0 22.2 - - - +
76A MSE 5.3 5.2 - - + -
77A LYS* 3.8 16.5 - - - +
102A ASP 3.4 13.0 - - - +
103A LEU* 2.8 13.8 + - + +
105A ASN* 1.3 106.8 - - + +
107A LEU* 1.3 66.8 + - + +
108A ASP* 4.8 0.2 - - - +
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Residues in contact with LEU 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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76A MSE 4.5 2.0 - - + -
77A LYS* 3.4 39.9 - - + +
80A LEU* 3.5 16.6 - - + -
103A LEU* 3.6 27.4 - - + +
104A LEU* 3.2 27.8 + - + +
105A ASN 4.2 3.5 - - - +
106A MSE 1.3 83.5 + - - +
108A ASP* 1.3 66.8 + - - +
109A LYS* 3.7 4.2 + - - +
111A GLN* 3.7 14.8 - - + +
112A LYS* 4.3 3.3 - - - +
115A TYR* 3.5 36.1 - - + -
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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