Contacts of the strand formed by residues 152 - 159 (chain B) 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 PHE 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B PHE* 3.9 26.0 - + + -
109B SER 4.3 2.9 - - - -
145B ILE* 3.8 37.9 - - + -
150B ILE* 3.7 28.0 - - + -
151B LEU* 1.3 74.4 - - - +
153B TRP* 1.3 63.4 + - - +
154B ILE 3.6 0.3 + - - -
191B SER* 3.1 4.8 - - - -
192B ILE* 2.8 48.7 + - + +
207B ARG* 3.3 37.7 - - + -
208B TRP* 3.9 7.6 - - - -
209B ILE* 3.6 33.7 - - + -
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Residues in contact with TRP 153 (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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113B ASN 2.9 21.6 + - - -
115B TRP* 3.3 33.3 - + + +
118B SER* 3.3 22.9 - - - +
129B LEU* 4.2 5.8 - - + +
152B PHE* 1.3 72.7 - - - +
154B ILE* 1.3 63.0 + - - +
189B CYS* 3.3 34.5 - - + -
190B ILE 3.3 20.6 - - - -
191B SER* 4.3 0.2 - - - -
200B GLU* 3.7 16.6 - - + -
201B TYR 3.2 23.3 - - - -
202B CYS* 3.7 9.0 - - - -
204B THR* 3.1 20.2 - - - -
206B ILE* 3.3 21.3 - - + +
207B ARG 2.8 22.1 + - - +
208B TRP* 3.8 7.7 - - + +
209B ILE* 3.2 24.6 + - - -
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Residues in contact with ILE 154 (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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115B TRP* 2.9 24.8 + - - -
129B LEU* 4.2 5.4 - - - -
130B LEU* 3.7 35.4 - - + +
132B ILE* 3.8 21.5 - - + -
152B PHE 3.9 4.0 - - - +
153B TRP* 1.3 77.2 - - - +
155B GLY* 1.3 58.7 + - - +
156B LEU* 2.9 6.2 + - + -
167B TRP* 3.9 21.1 - - + -
178B LEU* 4.3 6.7 - - + -
190B ILE* 3.1 41.4 + - + +
192B ILE* 3.8 26.5 - - + -
209B ILE* 4.8 1.1 - - + -
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Residues in contact with GLY 155 (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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115B TRP* 4.3 0.7 - - - -
129B LEU* 3.6 22.5 - - - +
130B LEU 2.7 21.6 + - - -
131B LEU* 4.7 0.2 - - - -
154B ILE* 1.3 72.1 - - - +
156B LEU* 1.3 56.6 + - - -
167B TRP* 3.2 12.1 - - - -
168B ILE* 2.9 42.4 + - - +
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Residues in contact with LEU 156 (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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115B TRP* 3.8 6.9 + - - +
154B ILE* 2.9 5.7 + - + +
155B GLY* 1.3 76.0 - - - +
157B ASN* 1.3 62.9 + - - +
165B TRP* 3.9 11.2 - - + -
166B LYS* 3.4 36.1 - - - +
167B TRP* 3.6 34.5 - - + +
173B LEU* 4.3 7.2 - - + -
178B LEU* 3.7 30.5 - - + -
180B ILE* 4.3 8.7 - - + -
189B CYS* 3.8 0.5 - - - -
190B ILE* 3.1 49.5 + - + +
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Residues in contact with ASN 157 (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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115B TRP* 3.5 10.8 - - + -
156B LEU* 1.3 76.7 - - - +
158B PHE* 1.3 66.4 + - - +
159B SER* 3.6 1.9 + - - -
165B TRP* 3.4 8.3 - - - -
166B LYS* 2.9 36.1 + - - +
168B ILE* 6.2 0.2 - - - -
188B SER 3.8 4.0 - - - +
189B CYS* 3.5 24.0 - - - +
502B NAG 1.4 67.6 + - - +
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Residues in contact with PHE 158 (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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157B ASN* 1.3 79.3 + - - +
159B SER* 1.3 72.8 + - - +
160B LEU* 3.6 17.8 + - + +
163B LYS* 3.5 28.3 - - + -
164B ASN* 3.6 26.9 - - - -
165B TRP* 3.6 20.1 - + + -
184B ALA* 3.5 35.9 - - + -
185B LYS* 3.4 32.5 - - - +
186B GLU* 3.8 4.9 - - - -
187B ASN 5.2 3.0 + - - +
188B SER 2.9 23.4 + - - +
502B NAG 4.7 12.0 + - - +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ASN* 3.6 3.4 + - - -
158B PHE* 1.3 73.1 - - - +
160B LEU* 1.3 57.1 + - - +
161B SER* 3.7 5.7 + - - -
162B GLU* 2.6 39.4 + - - -
163B LYS* 2.9 28.9 + - - -
164B ASN 2.9 17.9 + - - -
166B LYS* 3.9 14.6 - - - -
502B NAG 5.9 2.0 - - - -
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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