Contacts of the strand formed by residues 297 - 303 (chain A) in PDB entry 1MWR
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 TYR 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A TYR* 2.5 62.7 + + + -
144A ILE* 5.7 4.7 - - + -
146A ASN* 4.4 9.0 - - + +
147A LEU* 3.7 11.4 - - - +
295A ASP 5.6 0.9 - - - -
296A GLY* 1.3 76.4 - - - +
298A ARG* 1.3 74.0 + - - +
299A VAL* 4.7 0.7 - - + -
314A ILE* 4.0 13.6 - - + +
316A LYS* 2.8 65.5 + - + +
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Residues in contact with ARG 298 (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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143A HIS 3.7 0.2 - - - +
144A ILE* 3.4 6.6 - - - +
145A GLU* 3.3 37.7 + - + +
147A LEU* 3.7 38.2 - - + +
297A TYR* 1.3 80.5 - - - +
299A VAL* 1.3 67.7 + - - +
300A THR* 3.8 25.4 - - + -
309A ILE* 4.8 15.0 - - - +
312A THR* 4.1 11.0 + - + -
314A ILE 3.2 12.8 - - - +
315A GLU* 2.4 35.2 + - - +
148B LYS* 4.0 23.0 - - - +
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Residues in contact with VAL 299 (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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73A LEU* 3.7 26.5 - - + -
105A TYR* 4.0 36.6 - - + -
108A ILE* 5.6 0.4 - - + -
142A ILE* 3.7 15.0 - - + -
143A HIS 3.2 4.9 - - - +
144A ILE* 4.4 9.2 - - + -
297A TYR* 4.7 2.5 - - + -
298A ARG* 1.3 77.2 - - - +
300A THR* 1.3 67.9 + - - +
312A THR 3.7 0.2 - - - -
313A LEU* 2.8 37.0 + - + -
314A ILE* 2.8 32.3 + - + +
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Residues in contact with THR 300 (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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142A ILE* 3.2 10.0 - - - +
143A HIS* 2.9 34.1 + - - +
298A ARG* 3.8 22.2 - - + -
299A VAL* 1.3 82.5 - - - +
301A ILE* 1.3 63.7 + - - +
302A VAL* 3.5 6.4 - - - +
309A ILE* 4.0 13.5 - - + -
311A HIS 3.2 15.5 - - - +
312A THR* 3.6 18.2 - - - +
313A LEU* 4.2 3.6 - - - +
1207A CL 3.0 25.0 - - + +
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Residues in contact with ILE 301 (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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133A ILE* 3.8 20.6 - - + -
134A PRO 3.8 8.3 - - - +
135A GLY 3.9 2.9 - - - -
136A MSE 3.6 28.3 - - + +
140A GLN* 3.0 40.6 - - + +
141A SER 3.6 3.6 - - - +
142A ILE* 3.4 20.0 - - + -
300A THR* 1.3 73.4 - - - +
302A VAL* 1.3 54.3 + - - +
309A ILE* 3.7 1.2 - - - -
310A ALA* 2.8 37.5 + - + -
311A HIS* 2.9 21.3 + - + +
313A LEU* 3.9 14.4 - - + -
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Residues in contact with VAL 302 (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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140A GLN* 3.1 26.6 - - - -
141A SER* 3.1 11.8 + - - -
143A HIS* 3.5 41.3 - - + +
145A GLU* 4.1 0.4 - - - +
300A THR* 3.5 21.3 - - - +
301A ILE* 1.3 76.5 - - - +
303A ASP* 1.3 77.2 + - - +
304A ASP* 3.6 1.6 + - - +
307A ASN* 3.4 25.6 - - + -
308A THR 3.6 7.9 - - - +
309A ILE* 4.3 8.1 - - + -
1207A CL 3.7 9.6 - - + -
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Residues in contact with ASP 303 (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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139A ASP 3.6 8.7 - - - +
140A GLN* 4.1 13.1 + - - +
302A VAL* 1.3 89.9 - - - +
304A ASP* 1.3 64.3 + - - +
306A SER* 3.6 15.9 - - - +
307A ASN* 3.4 10.0 + - - +
308A THR* 2.8 25.7 + - - +
309A ILE 4.6 0.2 - - - -
310A ALA* 3.9 14.5 - - - +
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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