Contacts of the helix formed by residues 300 - 310 (chain A) in PDB entry 2MX7
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 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A LEU* 4.0 11.6 - - + +
299A VAL* 1.3 98.4 - - + +
301A ASP* 1.3 61.2 + - - +
302A ALA* 3.9 10.3 - - + +
303A TYR* 2.9 38.0 + - + +
304A LYS* 3.3 7.9 + - - +
356A TYR* 3.4 44.0 - - + +
359A LEU* 4.3 4.7 - - + -
385A ILE* 5.4 5.4 - - + -
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL 3.9 1.6 + - - +
300A PRO* 1.3 73.0 - - - +
302A ALA* 1.3 53.8 + - - +
304A LYS* 3.2 27.7 + - + +
305A LYS* 2.8 35.2 + - - +
385A ILE* 5.7 4.4 - - + +
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Residues in contact with ALA 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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300A PRO* 3.0 5.8 - - + +
301A ASP* 1.3 79.6 - - - +
303A TYR* 1.3 56.4 + - - +
305A LYS* 3.4 7.7 - - - +
306A ILE* 3.0 34.9 + - - +
356A TYR* 6.0 0.4 - - + -
359A LEU* 3.6 27.4 - - + -
385A ILE* 3.6 38.3 - - + +
386A PRO* 4.0 5.4 - - + -
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.4 27.6 - - + -
300A PRO* 2.9 25.8 + - + +
302A ALA* 1.3 76.2 - - - +
304A LYS* 1.3 63.5 + - + +
305A LYS 3.1 1.3 - - - -
306A ILE* 2.9 20.4 + - - +
307A LEU* 3.0 25.8 + - + +
311A MET* 3.7 30.3 - - + +
316A ILE* 4.0 6.9 - - + +
352A LYS* 4.5 20.4 + - + +
355A LEU* 3.4 42.2 - - + -
359A LEU* 3.7 6.6 - - + +
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Residues in contact with LYS 304 (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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299A VAL* 4.5 22.6 - - + +
300A PRO 3.3 1.7 + - - +
301A ASP* 3.2 44.2 + - + +
303A TYR* 1.3 78.4 - - + +
305A LYS* 1.3 62.5 + - - +
307A LEU* 3.1 28.7 - - - +
308A GLU* 3.4 14.3 + - - +
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Residues in contact with LYS 305 (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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301A ASP 2.8 23.9 + - - +
302A ALA* 3.4 11.0 - - - +
304A LYS* 1.3 72.8 - - - +
306A ILE* 1.3 58.0 + - + +
308A GLU* 2.9 22.9 + - + +
309A THR* 2.7 50.2 + - - +
386A PRO 5.2 3.8 + - - +
388A LEU* 2.6 45.5 + - + +
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Residues in contact with ILE 306 (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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302A ALA 3.0 9.1 + - - +
303A TYR* 2.9 13.2 + - - +
305A LYS* 1.3 84.8 - - + +
307A LEU* 1.3 53.4 + - - +
309A THR* 3.6 13.2 - - + +
310A THR* 2.7 46.6 + - + -
311A MET* 2.7 40.6 + - + -
321A LEU* 4.6 11.9 - - + -
325A LEU* 6.0 2.0 - - + -
339A TRP* 5.4 4.5 - - + -
355A LEU* 4.3 15.9 - - + -
359A LEU* 3.3 30.7 - - + -
386A PRO* 4.8 6.1 - - + -
388A LEU* 6.3 4.0 - - + -
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Residues in contact with LEU 307 (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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303A TYR* 3.0 42.8 + - + +
304A LYS* 3.1 15.5 - - - +
306A ILE* 1.3 75.1 - - - +
308A GLU* 1.3 65.0 + - + +
311A MET* 2.9 65.5 + - + +
312A THR 3.6 18.4 - - - +
313A PRO* 4.9 2.5 - - + -
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Residues in contact with GLU 308 (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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304A LYS* 3.9 14.7 - - - +
305A LYS* 2.9 20.8 + - + +
307A LEU* 1.3 78.7 - - + +
309A THR* 1.3 65.4 + - - +
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Residues in contact with THR 309 (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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305A LYS* 2.7 50.3 + - - +
306A ILE* 3.4 15.5 - - + +
307A LEU 4.3 0.2 - - - -
308A GLU* 1.3 77.0 - - - +
310A THR* 1.3 67.6 + - + +
320A LYS* 4.0 10.0 + - - +
321A LEU* 5.3 4.0 - - + -
324A ILE* 3.5 41.8 - - + +
325A LEU* 5.4 1.3 - - + -
388A LEU* 5.2 9.8 - - + +
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Residues in contact with THR 310 (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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306A ILE* 2.7 28.9 + - + +
309A THR* 1.3 79.4 - - + +
311A MET* 1.3 65.2 + - + +
312A THR* 4.4 0.2 - - - +
317A ASP* 2.6 47.8 + - - +
320A LYS* 2.9 25.7 - - - +
321A LEU* 2.8 47.9 + - + -
324A ILE* 4.2 0.2 - - - -
339A TRP* 5.2 3.8 - - + -
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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