Contacts of the helix formed by residues 116 - 127 (chain B) in PDB entry 5H4G
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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114B THR* 3.0 7.6 + - - +
115B ASP* 1.3 81.6 - - + +
117B PRO* 1.3 64.3 - - - +
118B LYS* 3.1 10.0 + - - +
119B ARG* 2.9 57.8 + - - +
120B TYR* 3.5 12.3 - - - -
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Residues in contact with PRO 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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114B THR* 3.6 19.9 - - + +
115B ASP 3.6 8.3 - - - +
116B ASP* 1.3 90.2 - - - +
118B LYS* 1.3 62.7 - - + +
120B TYR* 3.0 17.5 + - + +
121B GLU* 3.3 9.7 + - - +
130B THR* 3.9 22.3 + - - +
132B PRO* 3.9 35.9 - - + -
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Residues in contact with LYS 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 ASP* 3.1 10.1 + - - +
117B PRO* 1.3 79.1 - - - +
119B ARG* 1.3 62.4 + - - +
121B GLU* 3.1 28.1 + - + +
122B PRO* 4.1 2.6 - - - +
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Residues in contact with ARG 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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10B ASP* 3.3 24.5 + - - +
12B LEU* 4.7 19.3 - - - +
94B LEU* 3.2 25.1 - - + +
97B GLU* 6.3 0.6 - - - -
98B ASP* 3.2 35.0 + - - +
116B ASP* 2.9 51.8 + - - +
117B PRO 3.2 0.8 - - - -
118B LYS* 1.3 79.0 - - - +
120B TYR* 1.3 75.0 + - + +
121B GLU 3.3 0.2 - - - -
122B PRO* 3.6 9.4 - - - +
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Residues in contact with TYR 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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10B ASP* 2.7 31.1 + - - +
94B LEU* 4.5 4.7 - - + -
98B ASP* 3.7 36.0 + - + -
101B THR* 4.4 4.4 - - - +
102B ALA* 4.1 13.7 - - + -
112B LEU* 3.6 25.1 - - + -
114B THR* 3.5 33.9 - - + -
116B ASP 3.5 14.1 - - - -
117B PRO 3.0 8.0 + - - +
119B ARG* 1.3 92.5 + - + +
121B GLU* 1.3 66.9 + - - +
122B PRO* 3.2 4.9 - - - -
123B ILE* 2.9 25.1 + - + +
124B ARG* 3.7 2.9 + - - -
128B LEU* 3.8 15.5 - - + +
130B THR* 4.2 6.7 - - + +
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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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117B PRO 3.3 5.9 + - - +
118B LYS* 3.1 24.0 + - - +
120B TYR* 1.3 75.3 - - - +
122B PRO* 1.3 62.3 - - + +
124B ARG* 2.9 34.4 + - + +
125B ARG 4.6 0.2 + - - -
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Residues in contact with PRO 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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87B LEU* 3.5 24.2 - - + +
94B LEU* 4.4 10.5 - - + -
118B LYS 4.1 1.8 - - - +
119B ARG 3.6 13.9 - - - +
120B TYR 3.2 5.4 - - - -
121B GLU* 1.3 93.2 - - + +
123B ILE* 1.3 58.8 + - - +
124B ARG 3.2 0.7 - - - -
125B ARG* 3.2 41.2 + - - +
126B PHE* 4.0 1.7 - - - -
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Residues in contact with ILE 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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83B ILE* 4.2 10.3 - - + -
87B LEU* 3.8 15.3 - - + -
94B LEU* 4.0 29.4 - - + -
98B ASP 4.3 4.0 - - - +
99B ILE* 4.3 15.5 - - + +
102B ALA* 3.6 32.5 - - + -
103B THR* 5.8 0.2 - - - +
106B ILE* 4.1 17.9 - - + -
120B TYR* 2.9 15.5 + - + +
122B PRO* 1.3 76.8 - - - +
124B ARG* 1.4 65.3 + - - +
125B ARG 3.1 2.9 - - - -
126B PHE* 3.0 27.1 + - + +
127B GLY 3.8 2.8 + - - -
128B LEU* 3.8 10.5 + - + -
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Residues in contact with ARG 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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120B TYR 3.7 3.4 + - - +
121B GLU* 2.9 23.8 + - + +
123B ILE* 1.4 79.7 - - - +
125B ARG* 1.3 57.9 + - - +
127B GLY* 3.0 20.6 + - - -
128B LEU* 3.8 20.8 + - + +
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Residues in contact with ARG 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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86B ASN* 5.3 6.9 + - - +
87B LEU* 3.5 23.4 - - - +
121B GLU 4.6 0.4 + - - -
122B PRO* 3.2 30.7 + - - +
123B ILE 3.1 1.2 - - - -
124B ARG* 1.3 77.9 - - - +
126B PHE* 1.3 87.5 + - + +
127B GLY 3.6 0.9 + - - -
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Residues in contact with PHE 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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79B LYS* 4.4 20.3 + - - +
82B GLN* 5.0 2.5 - - + -
83B ILE* 3.7 57.4 - - + -
86B ASN* 3.8 37.9 - - + -
87B LEU* 4.1 5.8 - - + -
106B ILE* 3.7 18.5 - - + +
122B PRO 4.0 8.1 - - - -
123B ILE* 3.0 18.3 + - + +
125B ARG* 1.3 103.3 - - + +
127B GLY* 1.3 56.3 + - - +
128B LEU 3.6 1.6 - - - -
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Residues in contact with GLY 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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106B ILE* 4.0 11.0 - - - +
124B ARG 3.0 9.7 + - - -
125B ARG 3.4 2.0 + - - -
126B PHE* 1.3 78.4 - - - +
128B LEU* 1.3 66.6 + - - +
129B ASP* 3.5 10.8 + - - +
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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