Contacts of the helix formed by residues 116 - 127 (chain B) in PDB entry 2H5X
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 GLY 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B THR* 3.8 5.3 - - - +
114B GLY 3.8 4.4 + - - -
115B ILE* 1.3 76.6 - - - +
117B LYS* 1.3 66.2 + - - +
118B ARG 3.3 2.9 - - - -
119B GLY* 3.4 5.9 + - - +
120B ALA* 3.0 23.7 + - - +
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Residues in contact with LYS 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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106B VAL* 5.3 5.0 - - + +
110B THR* 3.8 16.5 - - + +
116B GLY* 1.3 71.4 - - - +
118B ARG* 1.3 66.3 + - + +
120B ALA* 3.5 3.1 + - - +
121B GLU* 3.1 32.3 + - - +
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Residues in contact with ARG 118 (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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116B GLY* 3.3 0.6 - - - -
117B LYS* 1.3 79.3 - - + +
119B GLY* 1.3 58.2 + - - +
121B GLU* 2.6 37.0 + - - +
122B ARG* 2.9 45.7 + - + +
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Residues in contact with GLY 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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115B ILE* 4.6 5.2 - - - -
116B GLY* 3.4 9.9 + - - +
118B ARG* 1.3 77.1 - - - +
120B ALA* 1.3 63.1 + - - +
122B ARG* 3.0 25.8 + - - +
123B MET* 2.8 34.5 + - - +
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Residues in contact with ALA 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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106B VAL* 4.1 12.3 - - + +
109B LEU* 3.7 25.1 - - + +
110B THR* 4.0 12.8 - - + -
115B ILE* 3.7 2.9 - - + +
116B GLY 3.0 17.9 + - - +
117B LYS 3.6 6.1 - - - +
119B GLY* 1.3 74.3 - - - +
121B GLU* 1.3 58.0 + - - +
123B MET* 3.5 15.5 + - - +
124B VAL* 2.8 35.4 + - - +
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Residues in contact with GLU 121 (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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106B VAL* 4.8 18.7 - - + +
117B LYS* 3.1 22.3 - - - +
118B ARG* 2.6 27.1 + - - +
120B ALA* 1.3 69.8 - - - +
122B ARG* 1.3 62.8 + - - +
124B VAL* 3.3 7.4 + - - +
125B LEU* 2.8 24.5 + - - +
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Residues in contact with ARG 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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77B VAL* 4.7 9.6 - - + -
78B SER* 4.7 21.8 + - - -
118B ARG* 2.9 57.5 + - - +
119B GLY* 3.0 37.2 + - - +
121B GLU* 1.3 74.3 - - + +
123B MET* 1.3 55.3 + - - +
125B LEU* 2.9 10.0 + - - +
126B GLU* 2.7 44.1 + - + +
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Residues in contact with MET 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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74B LEU* 5.2 14.6 - - - -
77B VAL* 4.2 26.5 - - + -
80B VAL* 4.2 20.0 - - + -
84B LEU* 5.5 0.9 - - + -
101B LEU* 4.2 15.7 - - + -
109B LEU* 4.1 14.1 - - + -
115B ILE* 3.2 54.1 - - + -
119B GLY 2.8 13.7 + - - +
120B ALA* 3.6 12.3 - - - +
122B ARG* 1.3 75.9 - - - +
124B VAL* 1.3 57.4 + - - +
126B GLU* 4.4 1.3 - - - -
127B LEU* 2.7 39.5 + - + +
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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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101B LEU* 3.6 11.7 - - + +
104B GLY* 3.5 27.8 - - - +
106B VAL* 5.1 5.2 - - + +
109B LEU* 3.8 18.2 - - + -
120B ALA 2.8 26.3 + - - +
121B GLU* 3.7 7.0 - - - +
123B MET* 1.3 74.2 - - - +
125B LEU* 1.3 59.6 + - - +
127B LEU 2.5 20.4 - - - +
128B ARG* 3.1 40.7 - - - +
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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 GLU 2.8 14.2 + - - +
122B ARG* 3.3 11.7 - - - +
124B VAL* 1.3 78.7 - - - +
126B GLU* 1.3 75.8 + - - +
127B LEU 4.4 1.0 - - - +
128B ARG* 4.6 7.3 - - - +
129B ASP* 5.0 3.3 - - - +
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Residues in contact with GLU 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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76B SER* 4.6 9.1 - - - +
77B VAL* 3.7 32.9 - - + -
78B SER* 5.3 4.4 + - - +
122B ARG* 2.7 28.3 + - + +
123B MET 3.6 2.0 - - - +
125B LEU* 1.3 88.6 - - - +
127B LEU* 1.3 63.4 + - + +
128B ARG 3.9 1.0 + - - -
129B ASP* 5.1 1.7 + - - +
130B LYS* 4.1 19.7 + - - +
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Residues in contact with LEU 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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70B LEU* 5.4 1.6 - - + -
73B THR* 3.3 44.2 - - + +
74B LEU* 3.8 29.2 - - + -
76B SER* 4.0 4.3 - - - +
77B VAL* 4.0 15.7 - - + -
101B LEU* 3.9 28.2 - - + +
123B MET* 2.7 23.3 + - + +
124B VAL* 2.5 28.6 - - - +
126B GLU* 1.3 73.3 - - + +
128B ARG* 1.3 59.0 + - - +
130B LYS* 3.7 28.3 - - - +
131B VAL* 4.7 4.0 - - + -
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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