Contacts of the helix formed by residues 116 - 127 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.5 15.3 - - - +
114B PHE* 3.3 2.5 - - - +
115B THR* 1.3 91.3 + - - +
117B MSE 1.3 65.2 + - - +
118B ASN* 3.2 16.8 - - - +
119B ALA* 3.1 19.8 + - - +
120B PHE 3.0 17.5 + - - -
1012B CL 3.8 15.5 - - + -
116G ASP* 5.9 2.5 - - + -
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Residues in contact with MSE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.7 7.9 - - + -
116B ASP* 1.3 73.1 - - - +
118B ASN* 1.3 56.9 + - - +
120B PHE* 3.2 28.4 + - - +
121B SER* 2.8 36.6 + - - -
141B PHE* 3.4 33.4 - - + -
1012B CL 3.5 12.5 - - + +
67G GLY 4.7 4.0 - - - +
68G LEU* 3.6 21.1 - - + -
117G MSE 3.4 32.8 - - + -
141G PHE* 3.9 13.7 - - + -
142G VAL 4.6 10.3 - - - +
143G LEU* 4.8 3.1 - - - -
906G GOL 4.2 12.3 - - - +
103H THR* 4.1 10.8 - - - -
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Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 3.2 17.8 + - - +
117B MSE 1.3 78.8 - - - +
119B ALA* 1.3 52.2 + - - +
121B SER* 3.5 3.3 + - - -
122B HIS* 2.3 61.1 + - + -
67G GLY* 5.7 0.2 - - - -
906G GOL 3.1 45.2 + - - -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 4.0 15.4 - - + -
115B THR* 3.5 25.4 - - - +
116B ASP* 3.1 8.5 + - - +
118B ASN* 1.3 77.0 - - - +
120B PHE* 1.3 66.9 + - - +
122B HIS* 3.3 8.7 + - - +
123B PHE* 3.1 22.0 + - - +
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.9 11.2 - - + -
70B ALA* 3.6 19.1 - - + -
72B ILE* 3.8 13.2 - - + -
114B PHE* 3.4 32.2 - + + -
116B ASP 3.0 12.8 + - - +
117B MSE 3.4 18.8 - - - +
119B ALA* 1.3 77.1 - - - +
121B SER* 1.3 56.2 + - - +
123B PHE* 3.1 3.6 + - - +
124B VAL* 2.9 60.4 + - + +
139B SER* 3.3 23.6 - - - -
141B PHE* 3.4 32.3 - + - -
143G LEU* 3.9 13.5 - - + -
103H THR* 4.2 4.5 - - + -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B MSE 2.8 20.9 + - - -
118B ASN* 3.7 7.6 - - - -
120B PHE* 1.3 70.3 - - - +
122B HIS* 1.3 63.1 + - - +
124B VAL* 4.5 0.4 - - - -
125B LEU* 2.9 41.5 + - - +
142G VAL 5.3 1.1 - - - -
143G LEU* 2.6 54.0 + - - -
906G GOL 5.4 3.1 - - - -
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ASN* 2.3 52.7 + - + -
119B ALA* 3.6 9.4 - - - +
120B PHE 3.3 0.4 - - - -
121B SER* 1.3 79.4 + - - +
123B PHE* 1.3 58.7 + - - +
126B ASP* 2.9 54.3 + - - +
127B THR* 3.9 0.7 + - - -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 4.1 22.0 - - + -
93B TRP* 3.7 33.0 - + - -
95B GLU* 3.8 27.1 - - + +
96B VAL* 3.8 14.4 - - + -
110B LEU* 5.4 0.7 - - + -
114B PHE* 3.6 32.8 - + + -
119B ALA 3.1 8.3 + - - +
120B PHE 3.1 6.5 + - - +
122B HIS* 1.3 77.3 - - - +
124B VAL* 1.3 67.4 + - + +
127B THR* 2.8 55.7 + - + -
128B LEU* 2.9 24.8 + - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 5.8 0.2 - - + -
120B PHE* 2.9 58.9 + - + +
121B SER* 4.0 4.9 - - - +
123B PHE* 1.3 81.3 - - + +
125B LEU* 1.3 60.8 + - - +
128B LEU* 3.9 17.9 - - + -
129B LEU* 2.8 57.1 + - + +
137B ALA* 5.5 2.9 - - + -
139B SER* 5.2 1.1 - - - +
143G LEU* 4.1 17.9 - - + -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER* 2.9 38.6 + - - +
124B VAL* 1.3 75.8 - - - +
126B ASP* 1.3 71.6 + - - +
129B LEU* 3.9 18.4 - - + +
130B SER* 3.9 14.6 + - - -
143G LEU* 4.1 22.4 - - + +
144G LYS* 4.0 33.0 - - + -
83H ARG* 3.9 27.4 - - - +
101H ALA* 5.1 1.6 - - + -
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B HIS* 2.9 39.9 + - - +
125B LEU* 1.3 86.2 - - - +
127B THR* 1.3 60.7 + - - +
130B SER* 2.7 18.9 + - - -
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B TRP* 3.4 41.0 - - + +
122B HIS 3.9 0.4 + - - -
123B PHE* 2.8 33.8 + - + -
126B ASP* 1.3 83.7 + - - +
128B LEU* 1.3 63.8 + - - +
130B SER* 3.4 8.7 + - - -
131B HIS* 3.4 14.7 + - - +
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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