Contacts of the helix formed by residues 148 - 160 (chain A) in PDB entry 2MGZ
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 ASN 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG* 4.6 1.8 - - - -
125A PRO* 5.4 1.0 - - - +
146A MET* 3.3 11.5 - - - +
147A GLN* 1.3 112.4 + - - +
149A PRO* 1.4 70.9 - - - +
150A ASP* 3.4 16.4 + - - +
151A ASP* 3.3 24.1 + - + +
152A ALA 3.2 15.2 + - - -
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 5.3 6.3 - - - +
98A GLY* 3.1 34.8 - - - +
99A PRO 3.6 17.0 - - - +
100A ARG* 3.9 11.4 - - + +
147A GLN 4.8 0.9 - - - +
148A ASN* 1.4 86.7 - - + +
150A ASP* 1.3 64.7 + - + +
152A ALA* 3.2 21.0 + - + +
153A ASP* 3.4 15.6 + - - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLY 5.7 7.0 - - - +
148A ASN* 3.7 19.8 + - - +
149A PRO* 1.3 84.9 - - + +
151A ASP* 1.3 68.1 + - - +
153A ASP* 4.6 5.5 - - - +
154A ARG* 3.6 20.8 + - - +
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 3.2 38.3 - - - +
124A GLY* 4.8 8.3 - - - -
125A PRO* 5.8 2.5 - - + +
146A MET* 4.0 5.8 - - + +
148A ASN* 3.3 27.4 + - + +
149A PRO 3.3 0.6 - - - -
150A ASP* 1.3 87.9 - - - +
152A ALA* 1.3 58.2 + - - +
154A ARG* 2.8 40.3 + - - +
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO 4.7 3.1 - - - +
100A ARG 4.6 4.9 - - - +
102A LEU* 3.8 26.8 - - + +
146A MET* 3.5 30.1 - - + -
148A ASN 3.2 8.9 + - - +
149A PRO* 3.2 15.0 + - + +
151A ASP* 1.3 73.9 - - - +
153A ASP* 1.3 57.2 + - - +
154A ARG 3.1 3.6 - - - -
155A ALA* 2.9 30.0 + - - +
156A ARG 3.5 2.9 + - - -
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Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 4.6 3.0 - - - +
149A PRO 3.4 10.1 + - - +
150A ASP* 4.6 5.1 + - - +
152A ALA* 1.3 77.6 - - - +
154A ARG* 1.3 55.4 + - - +
155A ALA 3.3 0.2 - - - -
156A ARG* 2.8 50.5 + - - +
157A ALA* 3.0 29.6 + - - +
173A LEU* 4.5 16.7 - - + +
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS 5.3 1.6 + - - -
123A VAL* 3.2 40.3 + - + +
150A ASP 3.6 16.5 + - - +
151A ASP* 2.8 47.7 + - - +
152A ALA 2.9 0.4 + - - -
153A ASP* 1.3 77.2 - - - +
155A ALA* 1.3 58.5 + - - +
157A ALA* 3.9 13.4 - - - +
158A GLU* 3.9 8.1 + - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 3.4 36.1 - - + -
123A VAL* 3.7 21.4 - - + +
152A ALA 2.9 7.5 + - - +
154A ARG* 1.3 76.0 - - - +
156A ARG* 1.3 58.8 + - - +
158A GLU* 3.0 6.7 + - - -
159A PHE* 2.9 48.7 + - + -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 4.6 7.2 - - + -
120A PHE* 4.7 0.4 - - - -
152A ALA 3.5 3.1 + - - +
153A ASP* 2.8 53.8 + - - +
155A ALA* 1.3 76.5 - - - +
157A ALA* 1.3 81.8 + - - +
160A ASN* 3.0 48.8 + - - +
171A VAL* 3.5 47.4 - - + +
172A ASN* 4.2 12.8 - - - +
173A LEU* 5.2 2.2 - - + +
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASP* 3.0 18.5 + - - +
154A ARG* 3.9 9.2 - - - +
155A ALA 3.3 0.2 - - - -
156A ARG* 1.3 96.8 - - - +
158A GLU* 1.3 56.5 + - - +
160A ASN 4.9 3.5 - - - +
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 2.8 36.0 + - - +
123A VAL* 5.8 2.1 - - - +
154A ARG 3.9 7.8 + - - +
155A ALA* 3.0 9.3 + - - +
157A ALA* 1.3 77.7 - - - +
159A PHE* 1.3 81.7 + - + +
160A ASN 3.3 8.4 + - - +
162A THR* 3.7 14.8 - - + +
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Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A MET* 3.4 63.9 - - + -
120A PHE* 3.8 22.0 - + - -
122A LYS* 3.8 14.8 - - + -
155A ALA* 2.9 37.5 + - + +
158A GLU* 1.3 93.0 - - + +
160A ASN* 1.3 56.7 + - - +
162A THR* 3.6 8.5 - - + +
164A ILE* 5.1 11.7 - - + -
169A VAL* 3.1 36.9 - - + +
170A GLU 3.5 1.2 + - - -
171A VAL* 3.7 16.9 - - + +
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Residues in contact with ASN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG* 3.0 34.4 + - - +
157A ALA 5.0 3.1 - - - +
158A GLU 3.3 6.4 + - - +
159A PHE* 1.3 76.6 - - - +
161A GLY* 1.3 65.3 + - - +
168A ARG* 6.0 0.8 - - - +
169A VAL 4.1 0.2 - - - -
170A GLU* 3.4 16.8 - - - +
171A VAL 2.9 42.3 + - - +
172A ASN* 5.4 0.8 - - - +
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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