Contacts of the strand formed by residues 141 - 147 (chain A) in PDB entry 3MIZ
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 THR 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A TRP* 3.4 33.6 - - + -
120A VAL* 3.3 14.2 - - + +
122A TYR* 4.2 14.1 - - + -
139A ILE 2.8 19.3 + - - -
140A PRO* 1.3 73.3 + - - +
142A VAL* 1.3 77.2 + - - +
154A LEU* 3.9 34.2 - - + +
155A PRO* 3.4 24.1 - - - +
310A LEU* 4.1 0.4 - - - -
313A LEU* 3.9 6.6 - - - +
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Residues in contact with VAL 142 (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 VAL 3.0 5.9 + - - -
121A LEU* 3.4 17.6 - - + +
122A TYR 3.0 21.7 + - - -
141A THR* 1.3 80.1 - - - +
143A MSE 1.3 74.4 + - - +
144A ILE* 3.9 2.5 + - + -
155A PRO* 3.8 19.3 - - + +
157A ILE* 4.9 0.4 - - + -
306A GLY* 4.0 17.0 - - - +
309A TRP* 3.8 29.8 - - + +
310A LEU* 3.6 33.0 - - + +
313A LEU* 4.3 4.9 - - + -
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Residues in contact with MSE 143 (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 TYR* 3.4 27.1 - - + -
130A VAL* 3.0 27.4 - - + +
132A PRO* 4.2 5.2 - - + -
142A VAL* 1.3 75.8 - - - +
144A ILE* 1.3 64.1 + - - +
145A ASN 4.3 0.2 - - - -
146A CYS* 3.5 33.2 - - + +
147A ARG 3.6 13.9 - - - +
148A PRO* 3.6 30.5 - - - -
154A LEU* 4.0 27.6 - - + -
155A PRO 3.0 16.4 + - - +
156A SER* 3.3 2.8 - - - -
157A ILE* 3.0 26.2 + - - +
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Residues in contact with ILE 144 (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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78A ILE* 3.9 17.7 - - + -
82A ILE* 3.8 21.8 - - + -
121A LEU* 3.7 33.9 - - + -
122A TYR 2.8 10.0 + - - +
123A VAL* 3.4 15.1 - - + +
124A THR 3.4 17.7 + - - -
142A VAL* 4.3 5.4 - - + +
143A MSE 1.3 80.7 - - - +
145A ASN* 1.3 70.5 - - - +
146A CYS* 3.2 4.6 + - - -
157A ILE* 3.5 14.8 - - + +
302A LEU* 3.8 32.3 - - + +
303A GLY* 4.6 0.4 - - - -
306A GLY* 3.9 12.1 - - - -
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Residues in contact with ASN 145 (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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78A ILE* 4.0 11.0 - - + +
124A THR* 2.9 32.5 + - - +
125A MSE 3.5 13.2 - - - +
126A TYR 3.6 5.2 - - - -
127A ARG* 3.1 27.8 - - - +
144A ILE* 1.3 76.9 - - + +
146A CYS* 1.3 59.0 + - - +
157A ILE 2.9 14.3 + - - -
158A GLU* 4.0 5.4 - - - -
159A PRO* 3.2 35.0 - - - +
299A TYR* 3.6 25.4 + - - -
302A LEU* 4.5 1.8 - - + +
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Residues in contact with CYS 146 (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 TYR* 3.7 26.0 - - - -
124A THR* 3.3 29.2 - - + +
128A ARG* 3.1 17.3 - - + +
130A VAL* 4.8 1.3 - - + -
143A MSE 3.5 31.0 - - + +
144A ILE 3.7 6.3 - - - -
145A ASN* 1.3 81.0 - - - +
147A ARG* 1.3 61.1 + - - +
156A SER* 3.3 19.8 - - - -
158A GLU* 3.5 13.9 - - - +
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Residues in contact with ARG 147 (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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127A ARG* 4.2 9.8 - - - +
128A ARG 2.9 5.8 + - - +
129A ILE* 3.0 28.1 - - + +
130A VAL 2.8 23.7 + - - +
143A MSE 3.6 4.7 - - - -
146A CYS* 1.3 75.8 - - - +
148A PRO* 1.3 84.2 - - + +
156A SER* 4.2 4.7 - - - +
158A GLU* 3.6 28.9 + - - +
190A LEU* 3.6 19.6 - - - +
194A LEU* 5.3 1.8 - - - +
323A SER* 5.7 4.9 - - - +
160B ASP* 4.2 19.9 + - - -
162B TYR* 4.3 15.6 - - - -
163B GLN* 4.3 7.2 - - - +
166B ARG* 2.9 33.2 - - - +
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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