Contacts of the helix formed by residues 116 - 127 (chain E) in PDB entry 2P5V
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E LEU* 3.6 15.7 - - - +
114E PHE* 3.3 2.4 - - - +
115E THR* 1.3 94.1 + - - +
117E MSE 1.3 64.9 + - - +
118E ASN* 3.3 18.6 + - - +
119E ALA* 3.1 19.2 + - - +
120E PHE 3.1 17.8 + - - -
1020E CL 3.8 15.3 - - + -
116H ASP* 5.9 2.2 - - + -
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Residues in contact with MSE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E LEU* 3.7 11.0 - - + +
116E ASP* 1.3 72.7 - - - +
118E ASN* 1.3 59.6 + - - +
120E PHE* 3.4 18.0 - - + +
121E SER* 2.8 32.8 + - - -
141E PHE* 4.1 14.1 - - - -
907E GOL 4.7 10.3 - - - +
1020E CL 3.2 18.2 - - + +
103G THR* 2.8 35.9 - - + -
67H GLY 4.7 4.3 - - - +
68H LEU* 3.8 21.3 - - + -
117H MSE 5.1 2.0 - - - -
141H PHE* 4.3 9.2 - - + -
142H VAL 4.0 19.7 - - - +
143H LEU* 3.3 22.2 - - + -
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Residues in contact with ASN 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E ASP* 3.3 18.2 + - - +
117E MSE 1.3 78.1 - - - +
119E ALA* 1.3 62.0 + - - +
121E SER* 3.3 2.8 + - - -
122E HIS* 3.1 23.9 + - - +
907E GOL 2.5 54.5 + - - -
67H GLY* 6.1 1.0 - - - -
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Residues in contact with ALA 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E PHE* 3.9 17.6 - - + -
115E THR* 3.7 22.9 - - + +
116E ASP* 3.1 10.6 + - - +
118E ASN* 1.3 75.0 - - - +
120E PHE* 1.3 66.5 + - - +
122E HIS* 3.3 9.8 + - - +
123E PHE* 3.0 21.7 + - - +
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Residues in contact with PHE 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E LEU* 3.9 11.4 - - + -
70E ALA* 3.5 21.3 - - + -
72E ILE* 3.9 13.9 - - + -
114E PHE* 3.5 32.9 - + + -
116E ASP 3.1 12.9 + - - +
117E MSE 3.4 31.6 - - + +
119E ALA* 1.3 75.3 - - - +
121E SER* 1.3 57.2 + - - +
123E PHE* 3.1 3.5 + - - +
124E VAL* 2.9 53.0 + - + +
139E SER* 3.3 28.3 - - - -
141E PHE* 3.6 21.1 - + - -
103G THR* 3.9 8.5 - - + -
143H LEU* 3.9 4.0 - - + -
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Residues in contact with SER 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E MSE 2.8 19.3 + - - -
118E ASN* 3.6 6.5 - - - -
119E ALA 3.3 0.2 - - - -
120E PHE* 1.3 76.6 - - - +
122E HIS* 1.3 62.7 + - - +
124E VAL 3.3 1.1 + - - +
125E LEU* 2.9 36.1 + - - +
907E GOL 4.5 5.9 + - - -
142H VAL 5.3 0.7 - - - -
143H LEU* 2.5 52.7 + - - -
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Residues in contact with HIS 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ASN 3.1 13.9 + - - +
119E ALA* 3.6 11.2 - - - +
121E SER* 1.3 77.1 - - - +
123E PHE* 1.3 63.3 + - + +
125E LEU* 5.8 0.4 - - - -
126E ASP* 2.5 66.9 + - + +
127E THR* 3.9 4.0 + - - -
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Residues in contact with PHE 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ILE* 4.0 22.4 - - + -
93E TRP* 3.8 35.4 - + - -
95E GLU* 3.8 30.7 - - + +
96E VAL* 3.8 13.0 - - + -
110E LEU* 5.2 0.9 - - + -
114E PHE* 3.5 32.5 - + + -
119E ALA 3.0 8.6 + - - +
120E PHE 3.4 5.8 - - - +
122E HIS* 1.3 79.2 - - + +
124E VAL* 1.3 68.0 + - + +
127E THR* 3.0 32.8 + - + -
128E LEU* 2.9 42.0 + - + -
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Residues in contact with VAL 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ILE* 5.2 0.9 - - + -
120E PHE* 2.9 56.5 + - + +
121E SER 3.9 2.7 - - - +
123E PHE* 1.3 82.1 - - + +
125E LEU* 1.3 58.7 + - - +
128E LEU* 3.8 17.3 - - + -
129E LEU* 2.6 61.6 + - + +
137E ALA* 5.7 1.6 - - + -
139E SER* 5.1 1.1 - - - +
143H LEU* 4.1 22.9 - - + -
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Residues in contact with LEU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E SER* 2.9 33.5 + - - +
124E VAL* 1.3 80.1 - - + +
126E ASP* 1.3 72.8 + - - +
129E LEU* 3.9 16.1 - - + +
130E SER* 3.7 17.8 + - - -
83G ARG* 3.8 30.4 - - - +
101G ALA* 5.0 2.2 - - + -
143H LEU* 4.1 17.9 - - + +
144H LYS* 4.0 32.3 - - + -
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Residues in contact with ASP 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E HIS* 2.5 53.9 + - + +
125E LEU* 1.3 84.2 - - - +
127E THR* 1.3 61.1 + - - +
130E SER* 2.8 18.5 + - - -
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Residues in contact with THR 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E TRP* 3.5 40.9 - - + +
122E HIS* 4.6 4.3 + - - -
123E PHE* 3.0 31.3 + - + -
126E ASP* 1.3 82.7 + - - +
128E LEU* 1.3 67.8 + - - +
130E SER* 3.4 3.3 + - - -
131E HIS* 3.3 19.2 + - - +
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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