Contacts of the helix formed by residues 252 - 261 (chain A) in PDB entry 1MRA
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 PRO 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ARG* 3.3 16.4 - - - +
251A GLY* 1.3 85.3 - - - +
253A GLU* 1.3 57.9 + - - +
255A MET* 3.1 10.8 + - + +
256A PHE* 2.9 31.8 + - - +
274A ILE* 3.4 15.5 - - + +
279A GLY* 3.8 27.1 - - - +
282A ARG* 4.1 25.1 - - + +
283A ALA* 4.4 7.4 - - + +
286A LEU* 3.9 12.1 - - + +
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Residues in contact with GLU 253 (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 TYR* 4.4 4.0 - - - +
101A ARG* 2.4 47.3 + - - -
250A LEU 4.1 5.0 - - - +
251A GLY* 4.0 3.8 - - - -
252A PRO* 1.3 83.5 - - - +
254A GLU* 1.4 66.0 + - + +
256A PHE* 3.7 7.6 + - - +
257A LYS* 3.5 36.4 + - - +
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Residues in contact with GLU 254 (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 THR* 4.1 7.8 + - - -
226A GLN* 5.1 4.7 + - - +
229A TYR* 3.5 25.7 + - - +
248A ASN 3.6 8.5 - - - +
249A TRP* 3.7 8.3 + - - -
250A LEU* 2.8 57.7 + - - +
251A GLY 3.1 6.1 + - - +
253A GLU* 1.4 79.7 - - + +
255A MET* 1.3 65.3 + - - +
257A LYS* 3.3 13.5 + - + +
258A ALA* 3.3 18.5 + - - +
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Residues in contact with MET 255 (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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249A TRP* 3.6 43.8 - - + -
251A GLY 3.4 4.2 + - - +
252A PRO* 3.2 15.3 - - + +
254A GLU* 1.3 76.2 - - - +
256A PHE* 1.3 67.1 + - - +
258A ALA* 3.1 3.8 + - - +
259A LEU* 2.9 49.3 + - + +
267A ALA* 5.0 4.9 - - + -
269A PRO* 4.7 2.5 - - - -
274A ILE* 4.4 3.4 - - + -
283A ALA* 3.4 50.7 - - + +
286A LEU* 3.9 5.8 - - + -
287A ALA* 3.9 15.9 - - + +
294A MET* 4.4 6.1 - - - -
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Residues in contact with PHE 256 (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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252A PRO 2.9 15.7 + - - +
253A GLU* 3.7 9.4 - - - +
255A MET* 1.3 76.0 - - - +
257A LYS* 1.3 62.0 + - + +
259A LEU* 3.4 5.0 + - - +
260A SER* 2.8 47.4 + - - -
286A LEU* 4.1 24.2 - - + -
290A PHE* 4.0 26.7 - + - -
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Residues in contact with LYS 257 (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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229A TYR* 3.7 19.2 - - + +
253A GLU* 3.5 26.8 + - - +
254A GLU* 3.3 15.9 + - + +
255A MET 3.2 0.4 - - - -
256A PHE* 1.3 85.1 - - + +
258A ALA* 1.3 62.3 + - - +
260A SER* 3.1 15.2 + - - -
261A ILE* 3.5 17.3 + - - +
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Residues in contact with ALA 258 (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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229A TYR* 3.8 25.8 - - + -
245A MET* 4.7 1.1 - - - -
249A TRP* 3.5 39.9 - - + +
254A GLU 3.3 3.9 + - - +
255A MET 3.1 3.9 + - - +
257A LYS* 1.3 75.9 - - - +
259A LEU* 1.3 67.7 + - - +
260A SER 3.3 0.3 + - - -
261A ILE* 3.3 5.9 + - - +
263A ALA* 3.1 34.4 + - + +
264A CYS* 5.6 0.2 - - - -
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Residues in contact with LEU 259 (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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249A TRP* 4.2 11.2 - - + -
255A MET* 2.9 49.1 + - + +
256A PHE 3.8 3.1 - - - +
258A ALA* 1.3 76.8 - - - +
260A SER* 1.3 65.0 + - - +
261A ILE 3.2 0.3 + - - -
262A GLY* 3.2 11.4 + - - +
263A ALA 4.9 0.9 - - - +
264A CYS* 4.1 20.2 - - - +
267A ALA* 5.3 0.2 - - + -
286A LEU* 4.3 5.8 - - + +
290A PHE* 3.4 56.9 - - + -
292A ILE* 3.9 30.3 - - + -
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Residues in contact with SER 260 (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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256A PHE* 2.8 43.5 + - - -
257A LYS* 3.6 8.1 - - - -
258A ALA 3.1 1.0 - - - -
259A LEU* 1.3 80.4 - - - +
261A ILE* 1.3 61.7 + - - +
262A GLY 3.8 0.2 + - - -
290A PHE* 3.9 14.5 - - - -
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Residues in contact with ILE 261 (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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229A TYR* 3.3 34.1 - - + +
230A GLU* 3.7 20.6 - - + +
233A GLN* 3.3 19.3 - - + +
257A LYS 3.5 10.3 + - - +
258A ALA 3.5 11.7 - - - +
259A LEU 3.1 0.2 - - - -
260A SER* 1.3 82.1 - - - +
262A GLY* 1.3 62.5 + - - +
263A ALA* 4.2 5.6 - - + +
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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