Contacts of the strand formed by residues 146 - 154 (chain C) in PDB entry 5MG3
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 GLU 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C LEU* 4.0 6.9 - - - +
144C GLN* 3.5 13.6 + - - +
145C ASN* 1.3 96.1 - - + +
147C LEU* 1.3 59.8 + - - +
148C GLN* 4.2 9.7 + - + +
166C VAL* 4.4 21.3 - - + +
167C LEU 3.4 3.4 - - - +
168C LYS* 3.7 28.4 - - + +
175C ASN* 5.7 2.4 + - - -
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Residues in contact with LEU 147 (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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63C VAL* 3.8 27.1 - - + -
64C LYS 4.6 3.6 - - - +
65C THR* 5.8 0.9 - - - -
138C TYR* 3.9 39.5 - - + +
139C VAL 5.5 3.4 - - - +
140C LEU* 3.9 36.3 - - + +
146C GLU* 1.3 71.9 - - - +
148C GLN* 1.3 72.1 + - - +
149C VAL* 4.3 2.5 - - + -
166C VAL* 3.3 3.0 - - - -
167C LEU* 2.8 51.1 + - + +
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Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C TYR* 4.6 4.5 - - - -
146C GLU* 4.2 8.9 + - + +
147C LEU* 1.3 82.2 - - - +
149C VAL* 1.3 62.9 + - - +
150C PRO* 3.5 10.0 - - + +
164C THR* 3.9 15.2 - - + +
165C PHE 3.7 3.8 - - - -
166C VAL* 3.9 23.3 - - + +
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ILE* 4.7 3.6 - - + -
63C VAL* 4.2 22.9 - - + -
72C ILE* 4.7 4.5 - - + -
133C VAL* 4.7 0.2 - - + -
138C TYR* 3.5 48.5 - - + +
147C LEU* 4.3 7.2 - - + -
148C GLN* 1.3 70.0 - - - +
150C PRO* 1.4 62.0 - - - +
151C MET* 3.6 24.8 + - - -
163C LYS 3.7 0.5 - - - +
164C THR* 3.4 2.9 - - - +
165C PHE* 2.8 47.5 + - + +
167C LEU* 4.6 2.0 - - + -
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Residues in contact with PRO 150 (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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132C ASN 4.1 2.4 - - - +
133C VAL* 3.9 15.5 - - + +
134C GLU* 5.3 2.9 + - + +
138C TYR* 4.0 12.8 - - - +
148C GLN* 3.5 13.0 - - + +
149C VAL* 1.4 81.5 - - - +
151C MET* 1.4 63.5 + - - +
152C THR* 4.0 12.1 + - + +
162C THR* 3.8 13.0 - - + -
163C LYS 3.7 4.7 - - - +
164C THR* 3.6 20.0 - - + +
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Residues in contact with MET 151 (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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61C ILE* 4.8 1.6 - - + -
72C ILE* 3.8 21.1 - - + -
73C ASN 4.4 4.7 - - - +
74C THR* 4.6 9.4 - - + -
77C GLY* 3.4 34.8 - - - +
131C TYR* 3.6 25.1 - - + -
132C ASN 3.9 1.3 - - - -
133C VAL* 3.8 31.4 - - + +
149C VAL* 3.7 25.4 - - - -
150C PRO* 1.4 71.6 - - - +
152C THR* 1.4 55.6 + - - +
162C THR* 3.5 2.6 - - - -
163C LYS* 2.8 44.3 + - + +
165C PHE* 3.6 17.0 - - + -
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Residues in contact with THR 152 (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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131C TYR* 3.6 3.3 - - - -
132C ASN* 3.0 49.7 + - - +
150C PRO* 4.0 15.3 - - + +
151C MET* 1.4 72.8 - - - +
153C TYR* 1.4 59.5 + - - +
160C THR* 5.7 3.6 - - + -
161C PHE 3.6 4.9 - - - -
162C THR* 3.6 26.0 - - + +
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Residues in contact with TYR 153 (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 PRO* 4.0 21.1 - - + -
129C PRO* 3.5 39.7 - - + +
130C LEU 4.4 16.8 - - - -
131C TYR* 3.4 25.6 - - + -
132C ASN* 5.4 2.7 - - - -
152C THR* 1.4 75.0 - - - +
154C THR* 1.4 75.9 + - - +
155C ASP* 3.5 35.2 + - + -
160C THR* 3.7 2.5 - - - +
161C PHE* 2.8 41.3 + + + +
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Residues in contact with THR 154 (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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153C TYR* 1.4 88.9 + - - +
155C ASP* 1.3 68.5 + - - +
158C GLY* 3.8 10.6 + - - -
159C ASN 2.8 21.2 + - - -
160C THR* 4.2 10.4 + - - +
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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