Contacts of the helix formed by residues 383 - 388 (chain W) in PDB entry 6G0L
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 GLY 383 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379W PHE 5.0 0.6 - - - -
380W GLN* 4.3 2.0 - - - +
381W LEU 3.4 2.4 - - - +
382W THR* 1.3 80.4 + - - +
384W ILE* 1.3 64.0 + - - +
386W TRP* 3.1 17.3 + - - +
387W MET* 3.2 20.4 + - - +
410W GLN* 4.3 23.3 - - - -
595W LEU* 5.9 3.0 - - - +
597W ARG* 4.8 16.4 - - - -
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Residues in contact with ILE 384 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364W LEU* 6.4 2.5 - - + -
376W LEU* 4.1 11.9 - - + -
380W GLN 2.7 27.6 + - - +
381W LEU* 3.4 13.2 + - + +
382W THR 3.1 0.6 - - - -
383W GLY* 1.3 78.8 - - - +
385W ASN* 1.3 58.0 + - - +
386W TRP 3.1 4.7 + - - -
387W MET* 3.5 6.9 + - - +
388W ALA* 3.2 25.3 + - + +
410W GLN* 3.6 21.5 - - - +
413W ALA* 3.3 43.3 - - + +
414W PHE* 4.4 11.2 - - + -
417W TRP* 5.5 6.1 - - + -
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Residues in contact with ASN 385 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361W PHE* 3.3 27.0 - - - -
363W LYS* 3.8 28.9 - - - +
364W LEU* 3.9 17.4 + - + +
381W LEU 3.0 15.1 + - - +
382W THR* 2.8 18.4 + - - +
384W ILE* 1.3 77.0 - - - +
386W TRP* 1.3 58.5 + - + +
388W ALA* 4.8 3.6 - - - +
389W PHE* 2.6 35.5 + - - +
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Residues in contact with TRP 386 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382W THR* 3.1 19.9 + - - -
383W GLY* 3.6 9.0 - - - +
384W ILE 3.1 0.4 - - - -
385W ASN* 1.3 87.9 - - + +
387W MET* 1.3 62.5 + - + +
388W ALA 3.2 1.3 - - - -
389W PHE* 3.3 16.2 - + + +
390W LEU* 2.8 34.1 + - - +
594W ILE 5.5 1.1 - - - -
595W LEU* 3.8 28.9 - - + -
597W ARG* 3.6 25.6 - - - -
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Residues in contact with MET 387 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383W GLY 3.2 20.0 - - - +
384W ILE* 3.8 1.6 - - - +
386W TRP* 1.3 79.6 - - - +
388W ALA* 1.3 53.8 + - - +
390W LEU* 3.7 2.0 - - - +
391W TRP* 2.9 25.6 + - - +
397W GLY* 4.6 19.7 - - - +
398W ILE 5.5 0.2 - - - -
399W LEU* 4.8 22.0 - - + -
410W GLN* 5.5 4.7 - - + +
414W PHE* 2.8 36.8 - - + -
537W ARG 5.9 0.2 - - - +
538W MET* 3.0 46.0 - - + -
595W LEU* 4.6 23.6 - - - -
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Residues in contact with ALA 388 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361W PHE* 4.1 32.4 - - + -
384W ILE* 3.2 18.4 + - + +
385W ASN 4.5 1.6 - - - -
387W MET* 1.3 75.1 - - - +
389W PHE* 1.4 57.6 + - - +
391W TRP* 3.3 19.0 + - + +
392W SER* 3.3 15.6 + - - -
414W PHE* 2.8 16.9 - - + +
417W TRP* 5.1 9.9 - - + +
418W LEU* 6.2 2.9 - - + -
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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