Contacts of the helix formed by residues 350 - 358 (chain A) in PDB entry 6M0X
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 PHE 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A TYR* 3.7 31.2 - + - -
276A GLN* 3.3 39.8 + - + +
277A GLU* 3.8 29.4 - - + -
280A LEU* 4.2 21.8 - - + -
305A ILE* 4.4 17.9 - - + -
308A VAL* 4.3 14.6 - - + -
309A LYS* 4.3 18.4 - - + -
348A HIS* 3.9 2.8 - - - +
349A THR* 1.3 76.4 - - - +
351A GLU* 1.3 64.6 + - - +
352A ALA 3.2 3.1 - - - -
353A TYR* 3.2 23.6 + + + -
354A ARG* 3.2 25.8 + - + -
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Residues in contact with GLU 351 (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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276A GLN* 3.6 0.8 + - - -
349A THR* 3.0 6.0 + - - +
350A PHE* 1.3 77.4 - - - +
352A ALA* 1.3 64.3 + - - +
354A ARG* 3.1 29.5 + - - +
355A LYS* 3.3 26.6 + - - +
419A ILE* 4.0 30.9 - - + +
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Residues in contact with ALA 352 (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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271A ALA* 3.6 30.7 - - + +
276A GLN* 3.0 25.5 + - - +
351A GLU* 1.3 77.4 - - - +
353A TYR* 1.3 63.3 + - - +
355A LYS* 3.3 5.9 + - - +
356A MET* 3.0 31.8 + - - +
419A ILE* 4.7 14.7 - - + +
420A PHE* 5.7 2.0 - - + -
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Residues in contact with TYR 353 (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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273A TYR* 3.8 33.0 - + - -
276A GLN* 3.2 8.4 + - - +
309A LYS* 3.4 50.1 - - + +
310A ASN* 6.3 0.2 - - - -
350A PHE* 3.2 22.2 + + + +
352A ALA* 1.3 74.6 - - - +
354A ARG* 1.3 64.2 + - + +
356A MET* 3.0 9.0 + - + +
357A LYS* 2.7 39.1 + - + +
364A ILE* 4.7 13.0 - - + +
365A GLU* 4.0 24.9 + - - +
372A LEU* 4.0 22.2 - - + -
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Residues in contact with ARG 354 (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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308A VAL 3.8 18.2 - - - +
309A LYS 4.4 7.9 - - - +
311A GLU 3.8 14.4 - - - +
312A LYS* 3.3 21.9 + - - +
313A ALA* 4.9 0.8 - - - +
314A MET* 3.1 35.4 + - - +
349A THR* 2.4 56.3 + - - -
350A PHE* 3.2 9.5 + - + +
351A GLU* 3.1 29.4 - - - +
353A TYR* 1.3 81.6 - - + +
355A LYS* 1.3 61.2 + - - +
357A LYS* 3.3 13.8 + - - +
358A THR* 3.4 15.6 + - - +
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Residues in contact with LYS 355 (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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351A GLU* 3.3 15.1 + - - +
352A ALA* 3.3 8.2 + - - +
353A TYR 3.1 0.4 - - - -
354A ARG* 1.3 80.3 - - - +
356A MET* 1.3 57.5 + - + +
358A THR* 2.2 41.1 + - + +
359A LEU 4.0 0.3 + - - -
412A PHE* 3.3 30.0 - - + -
416A ASN* 3.4 28.4 + - - +
419A ILE* 3.9 17.2 - - + +
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Residues in contact with MET 356 (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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271A ALA 4.7 13.9 - - - +
276A GLN* 6.0 0.2 - - - -
352A ALA* 3.1 18.6 - - - +
353A TYR* 3.0 9.2 + - + +
355A LYS* 1.3 76.7 - - + +
357A LYS* 1.3 61.1 + - - +
359A LEU* 3.4 32.2 + - + +
364A ILE* 3.7 22.3 + - + +
372A LEU* 3.8 20.9 - - + -
375A LEU* 3.5 37.7 - - + -
376A ALA* 5.2 4.3 - - - +
379A LEU* 4.1 15.5 - - + -
409A LEU* 5.5 0.2 - - + -
412A PHE* 4.0 16.4 - - + -
420A PHE* 4.6 13.9 - - + -
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Residues in contact with LYS 357 (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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309A LYS 5.7 2.0 - - - +
353A TYR* 2.7 32.0 + - + +
354A ARG* 3.6 9.9 - - - +
355A LYS 3.2 0.4 - - - -
356A MET* 1.3 72.2 - - - +
358A THR* 1.3 61.4 + - + +
359A LEU 3.2 7.9 + - - +
362A LEU 5.2 0.7 - - - +
363A ASP* 5.3 4.9 - - - +
364A ILE* 4.4 10.6 + - + +
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Residues in contact with THR 358 (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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354A ARG 3.4 16.2 - - - +
355A LYS* 2.2 38.3 + - + +
357A LYS* 1.3 76.9 - - + +
359A LEU* 1.3 65.6 + - - +
360A GLU* 3.4 17.3 + - - +
412A PHE* 3.9 9.2 - - - -
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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