Contacts of the helix formed by residues 390 - 394 (chain B) in PDB entry 1M6B
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 390 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ILE* 3.5 41.1 - - + -
383B TRP* 3.4 42.4 - + + -
389B ASN* 1.3 72.5 - - - +
391B SER* 1.3 51.8 + - - +
392B VAL* 3.1 3.6 - - - -
393B PHE* 2.7 37.0 + - + +
394B SER 3.9 1.2 + - - -
413B ILE* 3.5 33.2 - - + -
416B ASN* 4.2 4.3 - - - -
419B VAL* 4.1 22.0 - - + -
421B SER 4.5 0.2 - - - -
422B LEU* 2.9 37.7 + - + +
423B GLY 4.4 2.3 - - - +
424B PHE* 4.0 27.6 - + + -
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Residues in contact with SER 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ARG* 2.8 24.2 + - - -
389B ASN* 3.1 28.7 + - - +
390B PHE* 1.3 76.5 - - - +
392B VAL* 1.3 55.5 + - - +
393B PHE 2.9 0.2 - - - -
394B SER* 2.8 36.2 + - - -
423B GLY* 4.2 13.2 - - - -
497B GLN* 6.3 0.9 - - - -
1D NAG 4.7 5.4 - - - -
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LEU 3.8 27.1 - - - +
366B ASN* 3.6 13.5 - - - +
368B PHE* 3.3 5.9 - - + +
369B ARG* 3.2 62.4 + - + +
383B TRP* 3.6 35.7 - - + -
387B MET* 4.3 15.3 - - + -
390B PHE 2.9 2.5 + - - +
391B SER* 1.3 76.1 + - - +
393B PHE* 1.3 69.7 + - + +
394B SER 3.3 1.1 - - - -
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Residues in contact with PHE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 3.7 32.1 - - + -
344B PHE* 4.0 15.0 - + - -
368B PHE* 3.6 33.2 - + + -
371B VAL* 4.7 6.7 - - + -
374B ILE* 4.4 6.3 - - + -
378B LEU* 4.1 10.8 - - + -
380B ILE* 4.7 2.7 - - + -
383B TRP* 3.9 24.5 - + - -
390B PHE* 2.7 22.3 + - + +
392B VAL* 1.3 82.9 - - + +
394B SER* 1.3 63.6 + - - +
395B ASN 3.2 2.7 - - - -
396B LEU* 3.0 38.2 + - + +
423B GLY 4.7 0.7 - - - -
424B PHE* 3.7 36.0 - + + -
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Residues in contact with SER 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ARG* 5.1 7.0 + - - -
390B PHE 3.9 0.6 + - - -
391B SER* 2.8 25.4 + - - -
392B VAL 3.3 1.3 - - - -
393B PHE* 1.3 76.4 - - - +
395B ASN* 1.3 62.3 + - - +
423B GLY 4.1 13.5 + - - -
425B ARG* 3.3 41.4 + - - +
426B SER* 2.9 29.9 + - - -
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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