Contacts of the helix formed by residues 116 - 127 (chain C) in PDB entry 5T5W
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C ARG* 1.3 82.5 - - - +
117C ARG* 1.3 66.0 + - - -
118C LEU 3.1 4.5 + - - -
119C HIS* 3.3 12.0 + - - +
120C ARG* 3.3 11.8 + - - +
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Residues in contact with ARG 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C TRP* 3.7 47.0 + - + +
51C GLN* 2.8 48.3 + - - +
52C LEU* 3.7 16.9 - - + +
116C GLY* 1.3 73.0 - - - -
118C LEU* 1.3 62.4 + - - +
120C ARG* 4.1 5.3 - - - +
121C TRP* 3.3 22.9 + - - +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C TRP* 4.6 1.8 - - + -
52C LEU* 3.8 18.4 - - + +
56C GLU* 3.8 45.5 - - + +
59C VAL* 4.4 12.3 - - + -
60C ALA* 3.7 32.5 - - + +
116C GLY* 3.1 1.0 - - - -
117C ARG* 1.3 80.6 - - - +
119C HIS* 1.3 66.8 + - - +
121C TRP* 4.4 6.3 - - + -
122C LEU* 2.9 49.8 + - + +
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Residues in contact with HIS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG* 3.8 33.4 - - + +
116C GLY 3.3 10.5 + - - +
118C LEU* 1.3 79.1 - - - +
120C ARG* 1.3 62.3 + - + +
122C LEU* 3.9 7.8 - - - +
123C HIS* 3.0 43.9 + + + +
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Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG 5.6 1.1 - - - +
116C GLY 3.3 12.1 + - - +
117C ARG* 4.4 4.9 - - - +
119C HIS* 1.3 84.0 - - + +
121C TRP* 1.3 58.6 + - - +
123C HIS* 3.4 8.7 + - - +
124C ARG* 3.1 35.1 + - - +
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Residues in contact with TRP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 3.6 15.3 - - + -
43C PHE* 3.5 30.7 - + - -
45C ARG* 3.5 25.5 - - + +
47C TRP* 3.5 28.0 - + + +
60C ALA* 4.0 19.3 + - + -
64C GLU* 2.8 34.4 + - + +
117C ARG 3.3 19.4 + - - +
118C LEU* 3.8 5.2 - - + +
119C HIS 3.3 0.4 - - - -
120C ARG* 1.3 74.7 - - - +
122C LEU* 1.3 68.3 + - + +
123C HIS 3.0 1.5 + - - -
124C ARG* 3.2 39.6 + - + +
125C LEU* 3.1 49.7 + - + +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C VAL* 3.8 33.9 - - + +
60C ALA* 4.2 3.6 - - - -
63C ALA* 3.5 30.5 - - + +
118C LEU* 2.9 42.5 + - + +
119C HIS* 4.0 6.3 - - - +
121C TRP* 1.3 77.4 - - + +
123C HIS* 1.3 61.2 + - - +
125C LEU* 4.0 6.1 - - - +
126C GLN* 3.2 24.1 + - - +
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Residues in contact with HIS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C HIS* 3.0 33.0 + + + +
120C ARG* 3.6 10.1 + - - +
121C TRP 3.0 0.2 - - - -
122C LEU* 1.3 75.2 - - - +
124C ARG* 1.3 63.2 + - - +
126C GLN* 3.1 11.8 + - - +
127C GLU* 2.9 58.4 + - + +
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Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C SER* 5.4 8.3 - - - +
41C ARG 4.0 17.2 + - - -
42C LEU* 4.0 21.8 + - + +
44C PRO 5.4 0.2 + - - -
45C ARG* 4.9 4.9 - - - +
46C THR* 5.3 7.3 + - - +
47C TRP* 5.9 0.8 - - - +
120C ARG* 3.1 21.6 + - - +
121C TRP* 3.2 39.4 + - + +
123C HIS* 1.3 80.6 - - - +
125C LEU* 1.3 64.9 + - - +
127C GLU* 3.6 4.5 - - - +
128C ALA* 3.2 29.4 + - + +
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 3.9 13.5 - - + -
43C PHE* 4.1 4.7 - - + -
63C ALA* 3.6 34.3 - - + +
64C GLU* 3.6 13.2 - - + +
67C LEU* 3.8 34.3 - - + +
121C TRP* 3.1 68.1 + - + +
122C LEU* 4.0 4.5 - - - +
124C ARG* 1.3 77.2 - - - +
126C GLN* 1.3 60.9 + - - +
128C ALA* 4.1 3.3 - - - +
129C PRO* 3.4 18.2 - - - +
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Residues in contact with GLN 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LEU 3.2 18.0 + - - +
123C HIS* 3.1 12.5 + - - +
125C LEU* 1.3 77.6 - - - +
127C GLU* 1.3 88.8 + - - +
128C ALA 3.4 2.2 + - - -
129C PRO* 3.9 8.4 - - - +
130C LYS* 5.2 3.8 + - - +
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C HIS* 2.9 47.0 + - + +
124C ARG* 3.4 5.4 + - - +
126C GLN* 1.3 104.1 + - - +
128C ALA* 1.3 57.6 + - - +
129C PRO 3.9 0.2 - - - -
130C LYS* 4.5 13.7 - - - +
131C LYS* 3.7 20.4 + - - +
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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