Contacts of the strand formed by residues 234 - 242 (chain A) in PDB entry 1MWT
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 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ILE* 3.5 3.8 - - - +
172A GLY 2.8 38.3 + - - -
173A ILE* 4.8 0.4 - - - +
174A VAL* 3.3 25.7 + - + +
177A ASN* 4.2 8.3 + - - -
211A PHE* 3.3 32.3 - - + -
232A HIS 4.5 0.2 + - - -
233A LEU* 1.3 77.2 + - - +
235A THR* 1.3 74.2 + - - +
236A ASN* 5.4 0.7 - - + -
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Residues in contact with THR 235 (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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169A TYR* 5.1 8.5 - - - -
170A GLU 3.2 4.7 - - - -
171A ILE* 4.3 8.5 - - + -
220A MET* 3.8 32.3 - - + -
225A SER* 6.1 0.7 - - - -
228A ALA* 4.4 19.1 - - + -
233A LEU 5.3 0.2 - - - +
234A THR* 1.3 88.0 - - - +
236A ASN* 1.3 64.0 + - - +
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Residues in contact with ASN 236 (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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169A TYR* 4.4 2.9 - - - -
170A GLU* 2.7 60.3 + - - +
211A PHE* 3.7 29.2 - - + -
234A THR* 5.4 0.7 - - + -
235A THR* 1.3 77.3 - - - +
237A GLU* 1.3 78.0 + - - +
238A THR* 3.4 3.0 + - - -
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Residues in contact with GLU 237 (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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167A THR* 3.3 24.6 + - - +
168A ALA 3.5 7.4 - - - +
169A TYR* 3.8 33.8 + - + -
236A ASN* 1.3 87.3 + - - +
238A THR* 1.3 59.7 + - - +
317B LYS* 4.2 22.3 + - - +
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Residues in contact with THR 238 (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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167A THR* 3.1 7.2 + - - -
168A ALA* 2.7 58.2 + - + +
169A TYR 4.4 0.7 - - - +
170A GLU* 4.1 32.1 + - + +
216A THR* 4.6 5.4 - - + +
236A ASN* 4.2 5.6 - - - +
237A GLU* 1.3 76.2 - - - +
239A GLU* 1.3 74.1 + - - +
240A SER* 5.1 0.9 - - - -
317B LYS* 4.9 3.8 - - - +
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Residues in contact with GLU 239 (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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148A LYS* 3.9 20.8 + - - +
150A GLU* 4.6 9.2 - - - +
165A THR* 4.0 20.8 - - + +
166A GLY 3.5 13.0 - - - +
238A THR* 1.3 86.2 + - - +
240A SER* 1.3 65.3 + - - +
317B LYS* 3.5 33.7 + - - +
318B LYS* 5.8 3.3 - - - -
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Residues in contact with SER 240 (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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165A THR* 4.7 5.2 - - - +
166A GLY 2.9 31.9 + - - +
167A THR 4.1 0.8 + - - -
168A ALA* 3.7 17.3 - - - -
216A THR* 5.6 0.2 - - - -
218A LYS* 5.0 1.0 + - - -
238A THR* 3.8 1.7 + - - -
239A GLU* 1.3 78.2 - - - +
241A ARG* 1.3 70.9 + - - +
242A ASN* 3.8 0.2 - - - +
372A MET* 4.4 4.5 - - - +
373A TYR* 2.8 36.3 + - - -
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Residues in contact with ARG 241 (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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151A ARG* 3.3 33.9 + - - +
152A GLY 3.0 29.3 + - - -
154A ILE* 4.0 6.3 - - - +
163A ALA* 3.5 25.3 + - - +
164A ASN* 3.5 22.7 + - - +
165A THR* 5.0 2.7 + - - +
218A LYS* 4.2 1.9 + - - -
240A SER* 1.3 81.0 + - - +
242A ASN* 1.3 59.6 + - - +
243A TYR* 3.3 24.9 - - + +
256A VAL* 3.8 14.1 - - + -
284A GLU* 2.5 34.7 + - - +
291A LEU* 4.3 1.2 - - - +
369A TYR* 3.7 18.4 - - - -
372A MET* 3.5 20.0 - - + +
373A TYR* 4.4 0.2 + - - -
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Residues in contact with ASN 242 (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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163A ALA* 3.4 5.5 - - - -
164A ASN* 3.0 49.4 + - - +
166A GLY* 3.4 29.6 - - - +
218A LYS* 2.7 28.2 + - - +
241A ARG* 1.3 77.4 - - - +
243A TYR* 1.3 68.0 + - - +
244A PRO* 3.6 20.5 - - - +
369A TYR* 3.3 8.5 + - - -
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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