Contacts of the helix formed by residues 389 - 393 (chain A) in PDB entry 3U7U
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 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ILE* 3.6 34.5 - - + -
382A TRP* 3.5 41.3 - + - -
388A ASP* 1.3 71.1 - - - +
390A SER* 1.3 57.7 + - - +
391A VAL* 3.1 3.8 - - - +
392A PHE* 2.9 31.5 + + + +
411A ILE* 3.7 28.7 - - + -
414A GLN* 5.1 1.6 - - + -
417A ILE* 3.9 21.5 - - + -
420A LEU* 2.8 44.3 + - + +
421A GLN 3.8 4.6 - - - +
422A PHE* 3.6 33.1 - + + -
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Residues in contact with SER 390 (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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368A ARG* 3.5 25.1 + - - -
386A MET* 6.0 0.9 - - - +
388A ASP* 2.7 25.9 + - - -
389A PHE* 1.3 71.4 - - - +
391A VAL* 1.4 58.3 + - - +
392A PHE 3.0 5.2 - - - -
393A SER* 2.9 30.6 + - - -
420A LEU 4.2 0.2 + - - -
421A GLN* 4.0 24.5 - - - -
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Residues in contact with VAL 391 (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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364A LEU* 3.4 31.2 - - + +
365A ASN* 3.6 23.1 - - - +
367A PHE* 3.1 30.8 - - + +
368A ARG* 3.1 21.2 + - + +
382A TRP* 3.7 33.7 - - + -
386A MET* 4.1 19.7 - - + -
389A PHE 4.5 0.7 - - - -
390A SER* 1.4 78.1 + - - +
392A PHE* 1.4 70.7 + - + +
393A SER 3.3 1.2 + - - -
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Residues in contact with PHE 392 (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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341A LEU* 3.7 21.1 - - + -
343A PHE* 3.9 30.1 - + - -
367A PHE* 3.7 31.0 - + + -
370A VAL* 5.1 4.7 - - + -
373A ILE* 4.4 7.2 - - + -
377A LEU* 4.2 10.1 - - + -
379A ILE* 4.9 3.8 - - + -
382A TRP* 4.1 15.3 - + - -
389A PHE* 2.9 27.2 + + + +
391A VAL* 1.4 91.8 - - + +
393A SER* 1.4 57.6 + - - +
394A ASN 3.2 7.0 + - - -
395A LEU* 3.3 35.7 + - + +
421A GLN 4.7 1.1 - - - -
422A PHE* 3.7 30.6 - + + -
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Residues in contact with SER 393 (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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368A ARG* 4.5 10.8 - - - -
390A SER* 2.9 24.5 + - - -
391A VAL 3.3 2.4 + - - -
392A PHE* 1.4 75.7 - - - +
394A ASN* 1.3 65.1 + - - +
395A LEU 3.6 0.2 - - - -
421A GLN 4.2 9.4 + - - -
423A GLN* 2.9 32.5 + - - +
424A SER* 2.9 27.2 + - - -
494A GLN* 5.2 1.2 + - - -
505A ARG* 3.3 7.4 + - - -
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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