Contacts of the helix formed by residues 114 - 125 (chain C) in PDB entry 5MGS
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 PRO 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C ASN* 1.3 99.1 - - + +
115C TRP* 1.3 66.1 + - - +
116C ASN* 3.3 15.5 - - - +
117C ASN* 3.3 20.8 + - - +
118C SER* 2.9 22.9 + - - -
153C TRP* 3.6 0.2 - - - -
202C CYS 3.6 9.2 - - - +
203C SER* 3.9 16.6 - - - +
204C THR 3.4 10.3 - - - +
205C GLU* 3.9 19.4 - - + +
503C NAG 5.3 6.3 - - - +
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Residues in contact with TRP 115 (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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114C PRO* 1.3 70.5 - - - +
116C ASN* 1.3 65.5 + - + +
118C SER* 3.1 4.2 + - - -
119C LEU* 2.9 49.5 + - + -
129C LEU* 3.7 13.7 - - + +
153C TRP* 3.4 36.9 - + + +
154C ILE 2.9 25.0 + - - -
156C LEU 4.0 7.2 + - - -
157C ASN* 3.6 19.5 - - + -
168C ILE* 3.7 29.4 - - + -
189C CYS* 3.4 35.2 - - + -
202C CYS* 3.0 17.4 + - + +
502C NAG 3.5 43.5 - - - -
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Residues in contact with ASN 116 (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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114C PRO* 3.7 16.8 - - - +
115C TRP* 1.3 91.6 - - + +
117C ASN* 1.3 61.7 + - - +
119C LEU* 3.3 7.1 + - + +
120C ALA* 3.0 27.6 + - - +
202C CYS* 4.9 1.4 + - - +
502C NAG 5.4 5.8 - - - +
503C NAG 1.4 65.7 + - - +
119D LEU* 4.6 4.9 - - + +
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Residues in contact with ASN 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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113C ASN* 3.3 34.6 + - - +
114C PRO* 3.3 21.6 + - + +
116C ASN* 1.3 82.2 + - - +
118C SER* 1.3 59.4 + - - +
120C ALA* 3.5 7.1 + - - +
121C ASP* 2.9 27.4 + - - +
503C NAG 2.9 40.8 + - - +
166D LYS* 4.9 5.2 + - - +
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Residues in contact with SER 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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113C ASN* 3.4 12.0 - - - +
114C PRO 2.9 15.0 + - - -
115C TRP* 3.1 10.1 + - - -
117C ASN* 1.3 72.3 - - - +
119C LEU* 1.3 65.8 + - - +
121C ASP* 3.3 2.9 + - - +
122C CYS* 3.1 27.5 + - - -
129C LEU* 4.3 7.0 - - - -
153C TRP* 3.3 18.9 - - - -
208C TRP* 3.5 36.3 - - - -
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Residues in contact with LEU 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 TRP* 2.9 37.0 + - + +
116C ASN* 3.3 8.7 + - - +
118C SER* 1.3 74.8 - - - +
120C ALA* 1.3 59.3 + - - +
122C CYS* 3.2 2.8 + - - -
123C SER* 2.9 29.5 + - - -
129C LEU* 3.8 21.5 - - + +
168C ILE* 3.9 18.8 - - + -
502C NAG 5.2 2.5 - - - +
116D ASN* 4.6 4.7 - - + +
119D LEU* 3.8 25.8 - - + -
120D ALA* 4.3 17.0 - - + +
123D SER* 3.6 33.4 - - - +
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Residues in contact with ALA 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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116C ASN 3.0 15.9 + - - +
117C ASN* 3.7 5.8 - - - +
119C LEU* 1.3 78.4 - - - +
121C ASP* 1.3 54.6 + - - +
123C SER* 3.7 4.8 - - - -
124C THR* 2.7 39.5 + - - -
503C NAG 3.8 22.7 - - + -
119D LEU* 4.1 12.7 - - + +
168D ILE* 3.7 24.9 - - + +
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Residues in contact with ASP 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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107C LEU* 5.3 0.9 - - - +
113C ASN* 5.0 1.8 - - - +
117C ASN 2.9 18.1 + - - +
118C SER 3.3 5.4 + - - +
120C ALA* 1.3 76.5 - - - +
122C CYS* 1.3 56.2 + - - +
124C THR* 3.1 9.9 + - - +
125C LYS* 2.7 63.3 + - - +
208C TRP* 2.9 42.7 + - + -
210C CYS* 3.9 2.4 - - - -
168D ILE 4.7 1.3 + - - -
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Residues in contact with CYS 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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118C SER 3.1 18.2 + - - -
119C LEU 3.7 5.6 - - - +
121C ASP* 1.3 75.4 - - - +
123C SER* 1.3 63.1 - - - +
125C LYS* 3.0 8.5 + - - +
127C SER* 2.8 38.8 + - - +
129C LEU* 3.7 26.7 - - + +
208C TRP* 3.6 8.5 - - - -
210C CYS* 2.1 55.0 - - - -
123D SER* 4.1 0.9 - - - +
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Residues in contact with SER 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 LEU 2.9 15.5 + - - -
120C ALA 3.8 3.1 - - - -
122C CYS* 1.3 75.8 - - - +
124C THR* 1.3 56.2 + - - +
126C GLU* 2.9 16.5 + - - -
127C SER 3.5 6.0 + - - -
119D LEU* 3.5 28.3 - - - +
122D CYS* 4.1 0.2 - - - +
123D SER* 4.0 11.9 + - - -
127D SER 2.7 38.5 + - - +
128D SER* 3.1 17.3 - - - -
129D LEU 3.7 1.2 + - - -
168D ILE* 3.8 1.6 - - - +
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Residues in contact with THR 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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120C ALA 2.7 26.7 + - - -
121C ASP* 3.4 9.2 - - - +
123C SER* 1.3 72.2 - - - +
125C LYS* 1.3 62.8 + - + +
126C GLU* 3.4 9.4 + - - +
128D SER* 4.5 9.4 + - - -
131D LEU* 5.9 2.9 - - + -
168D ILE* 3.1 24.5 + - - +
169D ASN* 3.4 28.4 + - + +
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Residues in contact with LYS 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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98C TRP* 4.6 9.2 - - + -
107C LEU* 3.6 33.7 - - + -
121C ASP* 2.7 48.4 + - - +
122C CYS 3.0 7.1 + - - +
124C THR* 1.3 80.3 - - + +
126C GLU* 1.3 65.2 + - - +
127C SER* 3.5 6.7 + - - +
208C TRP* 5.4 0.4 - - - -
210C CYS* 4.9 3.1 - - - -
212C LYS* 3.0 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