Contacts of the helix formed by residues 398 - 409 (chain C) in PDB entry 1G3J
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 MET 398 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363C MET* 3.9 17.7 - - + -
364C GLN* 3.6 27.4 - - - +
392C ALA 4.2 3.1 - - - +
395C GLN* 3.6 36.8 - - + +
396C GLU* 3.3 3.1 - - - +
397C GLY* 1.3 76.2 - - - +
399C GLU* 1.3 63.9 + - - +
400C GLY 3.3 2.9 - - - -
401C LEU* 3.1 20.3 + - + +
402C LEU* 2.9 40.6 + - + +
427C LEU* 3.8 37.9 - - + -
434C ASN* 4.3 12.6 - - - +
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Residues in contact with GLU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C GLY* 3.4 4.3 - - - -
398C MET* 1.3 77.4 - - - +
400C GLY* 1.3 63.0 + - - +
402C LEU* 3.5 2.1 + - - +
403C GLY* 3.1 20.6 + - - -
437C MET* 4.0 32.2 - - + +
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Residues in contact with GLY 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C GLY 5.9 1.6 - - - -
397C GLY 4.9 2.2 + - - -
398C MET 3.3 0.6 - - - -
399C GLU* 1.3 79.4 - - - +
401C LEU* 1.3 61.0 + - - +
403C GLY* 3.5 1.4 + - - -
404C THR* 2.8 29.8 + - - -
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Residues in contact with LEU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C MET* 3.8 30.1 - - + +
364C GLN* 5.2 5.8 - - + +
367C GLY* 3.6 30.7 - - - -
370C LEU* 3.7 16.4 - - + -
385C LEU* 3.9 13.2 - - + -
397C GLY 5.6 0.4 + - - -
398C MET* 3.1 39.9 + - + +
400C GLY* 1.3 74.6 - - - +
402C LEU* 1.3 59.1 + - + +
404C THR* 3.2 6.0 + - - -
405C LEU* 2.9 45.2 + - + +
423C ILE* 5.3 0.7 - - + -
427C LEU* 4.1 11.0 - - + -
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Residues in contact with LEU 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C MET* 2.9 27.2 + - + +
399C GLU 3.9 3.4 - - - +
401C LEU* 1.3 75.7 - - - +
403C GLY* 1.3 61.9 + - - +
405C LEU* 3.6 3.7 + - - +
406C VAL* 3.2 31.2 + - - +
424C LEU* 3.8 22.6 - - + +
427C LEU* 3.8 30.1 - - + -
428C THR* 5.4 0.2 - - + -
434C ASN* 3.6 38.1 - - + +
437C MET* 3.9 26.5 - - + -
438C VAL* 3.9 14.4 - - + +
441C VAL* 5.2 1.6 - - - -
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Residues in contact with GLY 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C GLU 3.1 15.2 + - - -
400C GLY* 4.0 1.8 - - - -
401C LEU 3.3 0.2 - - - -
402C LEU* 1.3 78.0 - - - +
404C THR* 1.3 61.7 + - - +
406C VAL* 3.6 2.4 + - - +
407C GLN* 3.2 30.8 + - - +
437C MET* 4.8 6.0 - - - +
441C VAL* 4.6 18.0 - - - +
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Residues in contact with THR 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C GLY 4.4 7.4 + - - +
370C LEU* 3.5 37.9 - - + -
371C THR* 4.2 19.6 - - + +
400C GLY 2.8 16.3 + - - -
401C LEU* 3.6 7.4 - - - -
403C GLY* 1.3 77.5 - - - +
405C LEU* 1.3 58.0 + - - +
407C GLN* 3.2 15.4 + - + +
408C LEU* 2.9 37.3 + - + +
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C LEU* 4.1 11.2 - - + -
382C LEU* 4.0 17.0 - - + -
401C LEU* 2.9 41.6 + - + +
402C LEU* 3.9 1.1 - - - +
404C THR* 1.3 73.6 - - - +
406C VAL* 1.3 65.1 + - - +
408C LEU* 3.2 16.0 + - + +
409C LEU* 3.3 15.6 + - - +
420C ALA* 3.6 13.7 - - + +
423C ILE* 3.5 47.8 - - + -
424C LEU* 3.8 30.3 - - + -
427C LEU* 4.1 7.2 - - + -
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Residues in contact with VAL 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C LEU 3.2 18.5 + - - +
403C GLY 3.8 4.7 - - - +
404C THR 3.3 0.2 - - - -
405C LEU* 1.3 75.3 - - - +
407C GLN* 1.3 65.5 + - + +
409C LEU* 3.1 27.5 + - + +
410C GLY 4.1 0.9 + - - -
424C LEU* 4.2 11.2 - - + -
438C VAL* 4.1 22.9 - - + -
441C VAL* 3.9 37.5 - - + +
442C GLY 4.4 0.4 - - - +
443C GLY* 4.1 7.0 - - - -
446C ALA* 3.8 24.7 - - + +
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Residues in contact with GLN 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C THR* 5.4 5.7 - - - +
403C GLY 3.2 17.4 + - - +
404C THR* 3.2 16.3 + - - +
406C VAL* 1.3 81.3 - - + +
408C LEU* 1.3 59.4 + - + +
410C GLY* 2.9 23.9 + - - -
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Residues in contact with LEU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C LEU* 4.1 38.4 - - + +
371C THR* 5.8 2.7 - - + -
378C VAL* 5.3 2.5 - - + -
382C LEU* 4.1 32.3 - - + -
404C THR* 2.9 24.2 + - + +
405C LEU* 3.2 13.6 + - + +
407C GLN* 1.3 72.4 - - + +
409C LEU* 1.3 63.1 + - - +
410C GLY 3.0 2.5 - - - -
411C SER* 3.1 25.4 + - - -
416C VAL* 3.7 21.5 - - + +
417C VAL* 3.8 4.9 - - - +
420C ALA* 4.1 7.0 - - + -
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Residues in contact with LEU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C LEU 3.3 7.5 + - - +
406C VAL* 3.1 21.4 + - + +
407C GLN 3.0 0.6 - - - -
408C LEU* 1.3 77.0 - - - +
410C GLY* 1.3 56.8 + - - +
411C SER 3.2 1.3 + - - -
417C VAL* 3.5 14.3 - - + +
420C ALA* 3.9 6.1 - - + -
421C ALA* 3.8 37.9 - - + +
424C LEU* 3.6 20.6 - - + -
443C GLY 4.9 0.4 - - - +
446C ALA* 3.8 24.7 - - + +
447C LEU* 3.7 22.0 - - + -
450C THR* 3.5 24.4 + - + +
453C ARG* 3.1 18.5 + - - -
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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