Contacts of the helix formed by residues 116 - 127 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ASP* 6.1 4.9 - - + -
68D LEU* 3.4 16.7 - - - +
114D PHE* 4.1 0.3 - - - +
115D THR* 1.3 89.4 + - - +
117D MSE 1.3 66.3 + - - +
118D ASN* 3.3 14.4 + - - +
119D ALA* 3.0 29.1 + - - +
120D PHE 3.3 3.6 + - - -
803D GOL 3.3 30.5 - - - +
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Residues in contact with MSE 117 (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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67A GLY 4.9 6.5 - - - +
68A LEU* 4.2 22.0 - - + +
117A MSE 4.3 8.0 - - + +
141A PHE* 3.4 36.1 - - + -
142A VAL 4.5 15.7 - - - +
143A LEU* 4.0 17.7 - - + -
68D LEU* 3.3 24.1 - - + +
116D ASP* 1.3 74.1 - - - +
118D ASN* 1.3 65.1 + - - +
120D PHE* 3.3 6.5 + - - +
121D SER* 3.1 19.1 + - - -
141D PHE* 3.4 46.7 - - + -
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Residues in contact with ASN 118 (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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62A GLU* 5.9 3.2 - - - +
67A GLY 4.3 3.5 - - - +
116D ASP* 3.1 15.8 + - - +
117D MSE 1.3 75.3 - - - +
119D ALA* 1.3 68.6 + - - +
121D SER* 2.7 21.2 + - - -
122D HIS* 3.1 12.5 + - - +
161D CA 2.1 33.2 - - - -
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Residues in contact with ALA 119 (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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114D PHE* 3.8 20.3 - - + -
115D THR* 3.1 29.4 - - + +
116D ASP* 3.0 9.9 + - - +
118D ASN* 1.3 78.0 - - - +
120D PHE* 1.3 62.4 + - - +
122D HIS* 3.2 7.9 + - - +
123D PHE* 3.1 20.4 + - - +
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Residues in contact with PHE 120 (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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143A LEU* 3.6 20.6 - - + -
103B THR* 4.6 1.3 - - + -
1160B LEU* 4.2 2.9 - - - -
68D LEU* 3.9 15.7 - - + -
70D ALA* 3.7 19.7 - - + -
72D ILE* 3.8 18.6 - - + -
114D PHE* 3.4 34.7 - + + -
116D ASP 3.3 1.4 + - - -
117D MSE 3.3 10.0 + - - +
118D ASN 3.0 0.8 - - - -
119D ALA* 1.3 77.0 - - - +
121D SER* 1.3 59.6 + - - +
123D PHE* 3.2 1.4 + - - +
124D VAL* 2.9 58.8 + - + +
139D SER* 3.2 33.9 - - - -
141D PHE* 3.6 23.3 - + - -
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Residues in contact with SER 121 (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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143A LEU* 2.7 51.3 + - - +
117D MSE 3.1 9.9 + - - -
118D ASN* 2.7 18.8 + - - -
120D PHE* 1.3 71.8 - - - +
122D HIS* 1.3 60.5 + - - -
124D VAL* 4.0 0.2 - - - +
125D LEU* 3.0 48.8 + - - +
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Residues in contact with HIS 122 (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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118D ASN 3.1 9.0 + - - +
119D ALA* 3.5 12.1 - - - +
121D SER* 1.3 79.2 - - - +
123D PHE* 1.3 62.8 + - - +
125D LEU* 5.3 0.2 - - - -
126D ASP* 2.9 61.5 + - + +
127D THR* 4.8 0.2 + - - -
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Residues in contact with PHE 123 (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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72D ILE* 4.3 14.8 - - + -
93D TRP* 3.9 17.7 - + - -
95D GLU* 3.4 39.9 - - + +
96D VAL* 3.7 24.0 - - + -
110D LEU* 5.9 0.9 - - + -
112D ALA* 5.6 0.9 - - + -
114D PHE* 3.3 34.1 - + + -
119D ALA 3.1 5.1 + - - +
120D PHE 3.2 4.5 + - - +
122D HIS* 1.3 79.5 - - - +
124D VAL* 1.3 68.5 - - + +
127D THR* 2.9 52.7 + - + -
128D LEU* 3.0 26.3 + - + -
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Residues in contact with VAL 124 (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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143A LEU* 4.3 8.1 - - + -
1160B LEU* 3.8 23.1 - - + +
72D ILE* 4.7 4.7 - - + -
120D PHE* 2.9 56.0 + - + +
121D SER 4.0 2.5 - - - +
123D PHE* 1.3 82.1 - - + +
125D LEU* 1.3 61.5 + - + +
128D LEU* 4.0 14.6 - - + -
129D LEU* 2.9 51.5 + - + +
137D ALA* 5.1 0.2 - - + -
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Residues in contact with LEU 125 (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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143A LEU* 4.1 18.8 - - + -
144A LYS* 4.5 18.8 - - + -
83B ARG* 3.3 56.6 + - - +
101B ALA* 5.0 7.2 - - + -
108B TYR* 5.1 0.7 - - - +
1160B LEU* 4.5 17.3 - - + -
121D SER* 3.0 40.0 + - - +
122D HIS* 5.3 0.4 - - - -
124D VAL* 1.3 82.6 - - + +
126D ASP* 1.3 70.6 + - - +
127D THR 3.8 0.2 + - - -
129D LEU* 4.4 4.4 - - + +
130D SER* 4.1 10.9 + - - -
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Residues in contact with ASP 126 (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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122D HIS* 2.9 52.2 + - + +
125D LEU* 1.3 88.5 - - - +
127D THR* 1.3 63.7 + - - +
130D SER* 3.5 14.4 + - - -
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Residues in contact with THR 127 (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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93D TRP* 3.4 40.2 - - + +
122D HIS 4.8 0.2 + - - -
123D PHE* 2.9 36.2 + - + -
125D LEU 3.6 0.6 - - - -
126D ASP* 1.3 83.4 + - - +
128D LEU* 1.3 69.6 + - - +
129D LEU 3.4 0.9 - - - -
130D SER* 3.0 17.7 + - - -
131D HIS* 3.1 9.9 + - - +
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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