Contacts of the helix formed by residues 347 - 355 (chain A) in PDB entry 3MOS
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 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ARG* 3.6 47.3 - - + +
319A LYS* 3.6 50.0 - - + -
322A GLY* 3.0 25.5 - - - -
343A LYS 3.0 10.2 + - - -
344A ASN 4.1 12.1 - - - -
345A SER 3.3 4.9 - - - -
346A THR* 1.3 81.3 - - - +
348A SER* 1.3 60.0 + - - +
349A GLU* 3.0 23.3 - - - +
350A ILE* 3.1 31.6 + - + +
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Residues in contact with SER 348 (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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321A TYR* 4.6 3.8 - - - -
322A GLY* 4.8 3.1 - - - -
325A LEU* 4.6 15.3 - - - -
337A ALA* 5.1 2.7 - - - -
338A LEU 5.3 0.2 - - - -
339A ASP* 2.6 29.8 + - - +
343A LYS* 3.3 6.8 + - - +
346A THR* 3.1 5.4 + - - -
347A PHE* 1.3 76.1 - - - +
349A GLU* 1.3 64.9 + - - +
350A ILE 3.0 0.4 - - - -
351A PHE* 3.0 19.0 + - - +
352A LYS 3.1 9.2 + - - -
359A PHE* 3.7 15.5 - - - -
387A SER* 3.5 19.5 - - - -
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Residues in contact with GLU 349 (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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343A LYS* 3.2 33.1 + - + +
344A ASN* 3.3 31.3 - - - +
347A PHE* 3.0 23.7 - - - -
348A SER* 1.3 79.3 + - - +
350A ILE* 1.3 70.8 + - + +
352A LYS* 3.5 9.6 - - + +
353A LYS* 2.9 24.9 + - - +
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Residues in contact with ILE 350 (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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319A LYS* 4.2 5.4 - - + +
322A GLY 3.8 7.0 - - - +
323A GLN* 3.8 35.0 - - + +
326A ALA* 3.7 17.9 - - + -
347A PHE* 3.1 40.5 + - + +
348A SER 3.0 1.2 - - - -
349A GLU* 1.3 81.2 - - + +
351A PHE* 1.3 61.2 + - - +
353A LYS* 3.3 8.7 + - + +
354A GLU* 3.2 35.2 + - + +
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Residues in contact with PHE 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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322A GLY 4.4 1.2 + - - +
325A LEU* 3.4 43.1 - - + -
326A ALA* 3.9 10.6 - - - +
329A GLY* 3.9 4.9 - - - -
335A ILE* 3.7 42.2 - - + -
337A ALA* 3.6 21.5 - - + -
347A PHE 4.3 0.6 + - - -
348A SER* 3.0 10.1 + - - +
350A ILE* 1.3 76.7 - - - +
352A LYS* 1.3 57.8 + - - +
354A GLU 3.3 0.5 + - - -
355A HIS* 2.7 68.6 + + + +
358A ARG* 3.5 31.2 - - + -
359A PHE* 4.3 4.7 - + - -
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Residues in contact with LYS 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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343A LYS* 3.8 29.9 - - + +
348A SER 3.1 8.8 + - - +
349A GLU* 3.5 11.2 - - + +
351A PHE* 1.3 75.7 - - - +
353A LYS* 1.3 62.2 + - - +
356A PRO* 3.1 34.9 - - + +
359A PHE* 3.6 49.1 - - + -
361A GLU* 5.8 2.9 - - - -
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Residues in contact with LYS 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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349A GLU 2.9 13.3 + - - +
350A ILE* 3.5 12.8 - - + +
351A PHE 3.2 0.2 - - - -
352A LYS* 1.3 77.7 - - - +
354A GLU* 1.3 67.9 + - + +
356A PRO* 3.8 6.8 - - - +
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Residues in contact with GLU 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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326A ALA* 3.7 17.0 - - + +
330A HIS* 2.8 33.5 + - + +
350A ILE* 3.2 25.9 + - + +
353A LYS* 1.3 88.7 - - + +
355A HIS* 1.3 81.5 + - + +
356A PRO* 3.5 4.9 - - - +
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Residues in contact with HIS 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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326A ALA* 2.9 23.0 + - - -
329A GLY* 3.4 22.6 - - - -
330A HIS* 3.4 33.2 + + - -
351A PHE* 2.7 60.0 + + + +
354A GLU* 1.3 85.3 + - + +
356A PRO* 1.4 65.3 - - - +
357A ASP* 3.2 2.9 - - - -
358A ARG* 2.9 37.7 + - - +
359A PHE* 3.5 7.1 + - - +
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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