Contacts of the strand formed by residues 145 - 150 (chain A) in PDB entry 3MXW
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 ALA 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A MET* 5.6 0.7 - - - +
102A CYS* 4.4 3.3 - - - -
127A GLY 3.4 13.2 - - - +
139A LEU* 3.7 4.1 + - + -
140A HIS* 3.3 34.8 + - + +
143A GLY 3.4 2.6 + - - -
144A ARG* 1.3 82.5 + - - +
146A VAL* 1.3 68.7 + - - +
182A HIS* 3.5 27.1 - - + -
183A CYS 3.2 12.1 - - - +
184A SER* 3.9 4.9 - - - -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A MET* 3.9 28.9 - - + -
102A CYS* 3.9 9.0 - - - -
106A LEU* 3.7 26.2 - - + -
124A VAL* 4.2 8.5 - - + -
126A GLU 3.2 12.1 - - - +
127A GLY* 4.2 2.2 - - - -
140A HIS* 3.7 1.5 - - - -
145A ALA* 1.3 79.8 - - - +
147A ASP* 1.3 65.7 + - - +
148A ILE* 3.8 14.8 + - + -
170A PHE* 4.0 17.7 - - + -
181A ILE 3.6 1.0 - - - +
182A HIS* 4.4 0.2 + - - -
183A CYS* 2.8 41.3 + - + +
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Residues in contact with ASP 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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124A VAL* 3.4 5.9 - - - +
125A THR* 2.8 46.7 + - - +
126A GLU* 2.9 11.9 + - + +
134A HIS* 3.3 10.6 - - - -
140A HIS* 3.5 3.3 - - - -
146A VAL* 1.3 73.2 - - - +
148A ILE* 1.3 56.5 + - - +
180A HIS* 3.4 26.7 - - + -
181A ILE 3.2 3.1 - - - -
182A HIS* 3.3 5.0 + - - -
400A ZN 2.0 37.5 - - - -
98H ARG* 2.6 24.6 + - - +
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Residues in contact with ILE 148 (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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106A LEU* 4.0 9.4 - - + -
109A LEU* 3.5 28.9 - - + -
122A LEU* 3.9 13.2 - - + -
123A ARG 3.1 13.0 - - - +
124A VAL* 4.1 4.7 - - + +
146A VAL* 3.8 23.6 - - + -
147A ASP* 1.3 79.4 - - - +
149A THR* 1.3 69.5 + - - +
158A TYR* 5.3 0.2 - - - -
161A LEU* 3.7 24.0 - - + +
165A ALA* 4.4 3.1 - - + -
180A HIS* 3.5 1.2 - - - -
181A ILE* 2.9 49.1 + - + +
183A CYS* 3.7 17.9 - - - -
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Residues in contact with THR 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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122A LEU* 3.9 4.5 - - - +
123A ARG* 2.9 60.6 + - - +
125A THR* 3.9 10.5 - - + -
148A ILE* 1.3 77.8 - - - +
150A THR* 1.3 71.1 + - - +
153A ARG* 4.1 0.2 - - - +
158A TYR* 3.4 23.6 - - + +
161A LEU* 3.4 18.7 - - - +
179A ALA 3.3 25.8 - - - +
180A HIS* 4.4 1.3 - - - -
97H GLU* 3.8 4.0 - - - +
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Residues in contact with THR 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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113A VAL* 4.6 3.4 - - + -
117A TRP* 3.8 33.9 - - + -
120A VAL* 3.6 9.6 - - + -
121A LYS 3.6 4.3 - - - -
123A ARG* 3.8 1.5 - - - +
149A THR* 1.3 91.4 + - - +
151A SER* 1.3 66.1 + - - +
152A ASP* 2.7 23.9 + - - -
153A ARG* 3.0 11.6 + - - +
154A ASP 3.7 5.7 + - - -
157A LYS* 4.0 14.0 - - + +
158A TYR* 3.7 15.9 - - + -
161A LEU* 4.3 14.1 - - + -
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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