Contacts of the helix formed by residues 127 - 136 (chain D) in PDB entry 2AOB
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 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.9 8.9 - - - -
2601C S1S 3.3 7.9 - - - -
125D PHE* 3.3 7.9 + - - +
126D ASN* 1.3 79.0 - - - +
128D LEU* 1.3 63.5 + - - +
129D ASN* 3.6 10.5 + - - -
130D GLU* 2.8 37.5 + - - +
131D LEU* 3.1 18.9 + - - +
2701D S1S 3.5 26.9 - - - -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C TRP* 3.8 10.8 - - + -
61C PHE* 4.8 0.2 - - + -
85C ILE* 4.1 28.0 - - + -
95C PHE* 3.9 24.2 - - + -
110C VAL* 3.9 16.4 - - + -
118C TYR* 3.5 20.0 - - + -
2601C S1S 2.8 49.2 + - + +
127D SER* 1.3 72.1 - - - +
129D ASN* 1.3 57.6 + - - +
131D LEU* 3.2 8.5 + - + +
132D VAL* 2.8 35.3 + - - +
2701D S1S 3.8 21.1 - - + -
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Residues in contact with ASN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 5.7 8.6 - - + +
57C PRO* 4.3 16.9 + - - +
60C TRP* 3.8 25.6 - - + +
2601C S1S 4.6 0.8 + - - +
127D SER* 3.2 10.4 + - - +
128D LEU* 1.3 80.0 - - - +
130D GLU* 1.3 68.2 + - - +
132D VAL* 3.3 3.8 + - - +
133D ASP* 3.1 40.7 + - - +
2701D S1S 5.8 6.3 - - + +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2401C S1S 3.1 39.7 + - - +
2501C S1S 4.3 9.1 - - - +
125D PHE* 4.1 9.5 - - + -
126D ASN* 3.7 16.4 + - - +
127D SER* 2.8 36.8 + - - +
129D ASN* 1.3 81.0 - - - +
131D LEU* 1.3 63.4 + - - +
133D ASP* 3.3 7.3 + - - +
134D TYR* 3.2 22.2 + - - +
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE* 5.4 4.5 - - + -
97C LEU* 5.0 6.5 - - + -
110C VAL* 4.0 15.7 - - + -
118C TYR* 3.7 12.6 - - + -
119C PHE* 3.6 38.4 - - - +
120C LEU* 4.1 15.9 - - + -
125D PHE* 3.6 24.0 - - + -
127D SER 3.1 12.9 + - - +
128D LEU* 3.5 12.3 - - + +
130D GLU* 1.3 73.9 - - - +
132D VAL* 1.3 74.2 + - + +
134D TYR* 3.3 2.8 + - - +
135D HIS* 3.1 41.3 + - + +
148D LEU* 5.3 0.9 - - + -
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C TRP* 4.1 20.2 - - + +
83C PHE* 3.6 28.9 - - + -
85C ILE* 3.6 29.4 - - + -
128D LEU 2.8 20.3 + - - +
129D ASN* 3.6 7.4 - - - +
131D LEU* 1.3 78.6 - - + +
133D ASP* 1.3 63.9 + - - +
135D HIS* 3.0 13.5 + - - -
136D ARG* 3.1 33.7 + - - +
148D LEU* 3.7 12.3 - - + +
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Residues in contact with ASP 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ASN* 3.1 32.8 + - - +
130D GLU* 3.8 7.5 - - - +
131D LEU 3.3 0.2 - - - -
132D VAL* 1.3 74.2 - - - +
134D TYR* 1.3 66.8 + - - +
136D ARG* 3.1 44.0 + - - +
137D SER* 4.2 4.5 + - - -
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Residues in contact with TYR 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C TYR* 3.1 20.8 + - - -
135C HIS* 5.7 0.3 - - - -
138C THR* 3.6 16.3 - - + +
2401C S1S 3.8 28.1 - - + +
123D VAL* 3.6 26.7 - - + +
125D PHE* 3.1 33.0 - + + -
130D GLU 3.2 9.0 + - - +
131D LEU 3.6 6.1 - - - +
133D ASP* 1.3 77.8 - - - +
135D HIS* 1.3 76.5 + + - +
136D ARG 3.2 0.2 - - - -
137D SER* 3.2 9.7 + - - -
138D THR* 3.1 48.1 + - + -
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Residues in contact with HIS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 3.9 19.5 + - + +
121C TRP* 4.8 9.0 - + - -
134C TYR* 5.8 0.4 - - - -
123D VAL* 5.4 3.2 - - + +
125D PHE* 4.5 6.8 - + - -
131D LEU* 3.1 38.3 + - + +
132D VAL 3.0 4.5 + - - -
134D TYR* 1.3 97.8 - + + +
136D ARG* 1.3 63.2 + - - +
137D SER 3.2 1.1 - - - -
138D THR* 2.9 27.7 + - + +
139D SER 3.1 18.8 + - - -
140D VAL* 3.5 25.9 - - + +
147D PHE* 3.7 2.6 - - - -
148D LEU* 2.8 35.3 + - + -
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C TRP* 4.2 14.1 - - - +
83C PHE* 4.6 6.1 - - - -
132D VAL* 3.1 30.9 + - - +
133D ASP* 3.1 35.8 + - - +
134D TYR 3.2 0.2 - - - -
135D HIS* 1.3 78.3 - - - +
137D SER* 1.3 61.4 + - - +
147D PHE* 3.7 8.9 - - - +
148D LEU* 3.6 21.7 + - + +
149D ARG* 2.8 31.4 + - - +
150D ASP* 3.4 38.8 + - - +
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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