Contacts of the strand formed by residues 152 - 159 (chain F) in PDB entry 5MGT
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 PHE 152 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108F PHE* 3.9 23.6 - + + -
109F SER 4.0 13.9 - - - -
145F ILE* 3.9 40.2 - - + -
146F ARG* 5.0 6.1 - - - -
147F ASP* 6.3 0.4 - - + -
150F ILE* 3.8 24.9 - - + -
151F LEU* 1.3 75.6 - - - +
153F TRP* 1.3 64.3 + - - +
154F ILE* 3.6 3.1 + - - +
191F SER* 3.1 4.2 - - - -
192F ILE* 2.9 39.0 + - + +
207F ARG* 3.3 30.5 - - + -
208F TRP* 3.8 7.2 - - - -
209F ILE* 3.6 34.1 - - + -
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Residues in contact with TRP 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ASN 2.9 21.4 + - - -
115F TRP* 3.4 33.3 - + + +
118F SER* 3.3 23.6 - - - -
129F LEU* 4.0 7.1 - - + +
152F PHE* 1.3 73.8 - - - +
154F ILE* 1.3 61.5 + - - +
189F CYS* 3.5 31.6 - - + -
190F ILE 3.6 15.9 - - - -
191F SER* 4.3 0.9 - - - -
200F GLU* 3.9 18.4 - - + -
201F TYR 3.4 20.0 - - - -
202F CYS 3.7 11.7 - - - -
204F THR* 3.2 20.2 - - - -
206F ILE* 3.4 25.0 - - + +
207F ARG 2.9 22.5 + - - +
208F TRP* 3.7 7.8 - - + +
209F ILE 3.3 23.4 + - - +
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Residues in contact with ILE 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F TRP* 3.0 19.6 + - - -
129F LEU* 4.1 5.8 - - - -
130F LEU* 3.6 35.9 - - + +
132F ILE* 3.9 16.8 - - + -
152F PHE 3.9 8.7 - - - +
153F TRP* 1.3 78.5 - - - +
155F GLY* 1.3 57.3 + - - +
156F LEU* 2.9 16.0 + - + -
167F TRP* 3.9 24.7 - - + -
178F LEU* 4.9 2.9 - - + -
190F ILE* 3.0 41.4 + - + +
192F ILE* 3.9 23.1 - - + -
209F ILE* 4.9 1.6 - - + -
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Residues in contact with GLY 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F TRP* 4.5 0.2 - - - -
129F LEU* 3.6 23.9 - - - +
130F LEU 2.7 20.3 + - - -
131F LEU* 3.9 1.3 - - - +
154F ILE* 1.3 67.5 - - - +
156F LEU* 1.3 58.3 + - - -
167F TRP* 3.3 13.5 - - - -
168F ILE* 2.9 42.9 + - - -
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F TRP* 4.0 5.7 + - - -
154F ILE* 2.9 17.6 + - + +
155F GLY* 1.3 75.6 - - - -
157F ASN* 1.3 63.7 + - - +
165F TRP* 3.9 10.8 - - + +
166F LYS 3.4 36.8 - - - +
167F TRP* 3.6 34.5 - - + +
168F ILE* 5.4 0.2 - - - -
173F LEU* 4.5 10.1 - - + -
178F LEU* 3.5 32.5 - - + -
180F ILE* 4.7 0.4 - - + -
189F CYS* 3.7 0.5 - - - -
190F ILE* 3.0 47.6 + - + +
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Residues in contact with ASN 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F TRP* 3.6 12.8 - - + -
156F LEU* 1.3 77.0 - - - +
158F PHE* 1.3 66.8 + - - +
159F SER* 3.6 1.0 + - - -
165F TRP* 3.3 10.9 - - - -
166F LYS* 2.7 43.1 + - - +
168F ILE* 6.1 0.4 - - - -
188F SER 3.6 4.3 - - - +
189F CYS* 3.6 20.9 - - - +
502F NAG 1.5 67.0 + - - +
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Residues in contact with PHE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ASN* 1.3 82.4 + - - +
159F SER* 1.3 71.4 + - - +
160F LEU* 3.8 18.2 + - + -
163F LYS* 3.5 28.3 - - + -
164F ASN* 3.7 25.1 - - - -
165F TRP* 3.5 22.8 - + + -
184F ALA* 3.6 30.1 - - + -
185F LYS* 3.4 39.9 - - - +
186F GLU* 3.9 5.3 - - - -
187F ASN 5.4 3.1 + - - -
188F SER 3.0 16.7 + - - +
502F NAG 5.1 5.2 + - - +
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Residues in contact with SER 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ASN* 3.6 1.2 + - - -
158F PHE* 1.3 74.5 - - - +
160F LEU* 1.3 56.5 + - - +
161F SER* 3.3 19.6 + - - -
162F GLU* 3.6 10.0 + - - +
163F LYS* 2.9 24.3 + - - -
164F ASN 2.8 23.2 + - - -
166F LYS* 4.3 20.7 - - - -
172F PHE* 4.2 15.8 - - - -
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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