Contacts of the helix formed by residues 116 - 127 (chain A) in PDB entry 2P6T
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 ASP 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.6 13.5 - - - -
114A PHE* 3.5 2.6 - - - +
115A THR* 1.3 88.2 - - + +
117A MSE 1.3 65.1 + - - +
118A ASN* 3.1 13.2 + - - +
119A ALA* 3.1 23.3 + - - +
120A PHE* 3.1 21.0 + - - +
116D ASP* 6.1 4.9 - - + -
803D GOL 6.0 5.3 - - - -
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Residues in contact with MSE 117 (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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68A LEU* 3.3 35.5 - - + +
116A ASP* 1.3 75.6 - - - +
118A ASN* 1.3 57.2 + - - +
120A PHE* 3.6 13.8 - - + +
121A SER* 3.0 24.6 + - - -
141A PHE* 2.8 52.7 - - + -
67D GLY 5.0 9.4 - - - +
68D LEU* 3.4 34.3 - - + -
117D MSE 4.3 4.0 - - + +
141D PHE* 4.3 9.4 - - + -
142D VAL 5.5 4.8 - - - +
143D LEU* 4.1 17.6 - - - +
901D GOL 5.0 6.3 - - - -
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Residues in contact with ASN 118 (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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116A ASP* 3.1 15.7 - - - +
117A MSE 1.3 76.1 - - - +
119A ALA* 1.3 66.4 + - - +
121A SER* 2.9 19.1 + - - -
122A HIS* 3.0 47.7 + - - -
62D GLU* 4.8 3.8 - - - +
143D LEU 5.2 0.9 - - - +
901D GOL 2.8 29.8 + - - +
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Residues in contact with ALA 119 (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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114A PHE* 4.1 8.0 - - + -
115A THR* 4.5 12.8 - - - +
116A ASP* 3.1 24.7 + - - +
118A ASN* 1.3 74.1 - - - +
120A PHE* 1.3 67.8 + - - +
122A HIS* 3.1 12.7 + - - +
123A PHE* 2.9 21.7 + - - +
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Residues in contact with PHE 120 (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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70A ALA* 3.7 18.4 - - + -
72A ILE* 3.9 9.6 - - + -
114A PHE* 3.4 41.8 - + + -
116A ASP 3.1 10.3 + - - +
117A MSE 3.6 34.8 - - + +
119A ALA* 1.3 73.8 - - - +
121A SER* 1.3 65.2 + - - +
123A PHE* 2.8 14.5 + + - +
124A VAL* 2.9 40.5 + - + +
139A SER* 3.3 36.1 - - - -
141A PHE* 3.5 11.9 - + - -
103C THR* 4.8 0.4 - - + -
143D LEU* 3.7 20.9 - - + -
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Residues in contact with SER 121 (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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117A MSE 3.0 15.6 + - - -
118A ASN* 2.9 18.5 + - - -
120A PHE* 1.3 75.5 - - - +
122A HIS* 1.3 66.2 + - - +
124A VAL* 3.5 0.5 + - - +
125A LEU* 3.0 38.8 + - - +
143D LEU* 2.5 53.7 + - - +
144D LYS* 4.6 0.2 - - - +
901D GOL 5.9 0.2 - - - -
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Residues in contact with HIS 122 (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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118A ASN* 3.0 46.0 + - - -
119A ALA* 3.1 9.9 + - - +
121A SER* 1.3 81.1 - - - +
123A PHE* 1.3 59.9 + - - +
125A LEU* 5.1 0.2 - - - -
126A ASP* 2.8 52.3 + - - +
127A THR* 4.2 0.3 - - - +
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Residues in contact with PHE 123 (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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72A ILE* 5.3 4.0 - - + -
93A TRP* 4.1 26.2 - + - -
95A GLU* 3.4 37.5 - - + +
96A VAL* 3.9 26.9 - - + -
110A LEU* 5.4 0.7 - - + -
114A PHE* 3.5 34.8 - + + -
119A ALA 2.9 7.4 + - - +
120A PHE* 2.8 14.7 + + - +
122A HIS* 1.3 71.1 - - - +
124A VAL* 1.3 75.0 + - + +
127A THR* 2.7 49.8 + - + +
128A LEU* 3.1 25.2 + - + -
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Residues in contact with VAL 124 (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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120A PHE* 2.9 59.5 + - + +
121A SER 4.2 1.6 - - - +
123A PHE* 1.3 77.2 - - + +
125A LEU* 1.3 61.6 + - - +
128A LEU* 3.8 22.9 - - + -
129A LEU* 2.8 54.3 + - + +
137A ALA* 4.4 0.7 - - + -
1160C LEU* 3.7 24.2 - - + +
143D LEU* 4.3 7.6 - - + -
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Residues in contact with LEU 125 (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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121A SER* 3.0 33.9 + - - +
122A HIS* 5.1 0.2 - - - -
124A VAL* 1.3 81.7 - - - +
126A ASP* 1.3 70.1 + - - +
129A LEU* 4.4 7.1 - - + +
130A SER* 4.0 13.2 + - - -
83C ARG* 3.4 46.7 + - - +
101C ALA* 5.2 3.8 - - + -
1160C LEU* 4.0 14.8 - - + -
143D LEU* 4.5 12.3 - - + -
144D LYS* 3.9 35.0 - - + +
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Residues in contact with ASP 126 (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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122A HIS* 2.8 43.5 + - - +
125A LEU* 1.3 82.6 - - - +
127A THR* 1.3 62.0 + - + +
130A SER* 3.3 15.7 + - - -
144D LYS* 5.8 2.4 + - - -
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Residues in contact with THR 127 (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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93A TRP* 3.5 33.0 + - + -
95A GLU* 5.4 0.2 - - - +
122A HIS 4.2 1.1 - - - +
123A PHE* 2.7 57.6 + - + +
125A LEU 3.5 1.0 - - - -
126A ASP* 1.3 82.1 - - + +
128A LEU* 1.3 62.6 + - - +
129A LEU 3.6 0.7 - - - -
130A SER* 3.8 4.3 - - - -
131A HIS* 3.3 20.1 + - - +
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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