Contacts of the helix formed by residues 390 - 396 (chain S) in PDB entry 5GJQ
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 390 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389S ASP* 1.3 71.7 - - - +
391S THR* 1.3 61.3 + - - +
392S TYR* 3.0 8.7 + - - -
393S THR* 3.7 16.0 + - - -
394S LEU* 4.2 7.3 + - - +
213T GLU* 4.8 9.0 - - - +
216T PRO* 4.8 13.5 - - - +
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Residues in contact with THR 391 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327S THR 5.4 0.7 - - - +
330S LYS* 4.2 19.3 - - + +
331S LEU* 4.3 13.9 - - + +
334S VAL* 4.0 12.8 - - + -
360S TYR* 3.0 24.8 + - - +
386S PHE* 3.7 3.5 + - - +
389S ASP* 3.1 29.4 + - + +
390S GLY* 1.3 77.3 - - - +
392S TYR* 1.3 64.2 + - - +
393S THR 3.5 0.2 - - - -
394S LEU* 3.1 16.6 + - - +
395S ILE* 2.9 27.4 + - - +
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Residues in contact with TYR 392 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379S LEU* 5.5 7.2 - - + -
383S GLY* 4.6 13.9 - - - -
386S PHE* 3.6 33.5 + - + +
387S GLN* 4.4 22.4 - - + -
389S ASP 4.4 4.3 - - - +
390S GLY 3.0 2.1 - - - +
391S THR* 1.3 79.0 + - - +
393S THR* 1.3 74.6 + - - +
395S ILE* 2.7 30.2 + - + +
396S ILE* 3.0 38.1 + - + +
216T PRO* 4.3 16.8 - - + -
217T ALA 6.0 1.8 - - - -
222T THR 5.5 2.9 + - - -
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Residues in contact with THR 393 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390S GLY 3.7 3.0 + - - -
391S THR 3.5 0.4 - - - -
392S TYR* 1.3 87.5 - - - +
394S LEU* 1.3 64.9 + - - +
396S ILE* 3.9 8.3 + - - +
397S ARG* 3.3 22.8 + - - +
212T LEU* 4.2 13.1 - - - +
213T GLU* 3.1 43.0 - - - +
216T PRO* 3.9 16.7 - - - +
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Residues in contact with LEU 394 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294S ARG* 6.0 1.1 - - + -
297S ALA* 4.8 8.1 - - + -
298S ILE* 4.3 26.0 - - + +
331S LEU* 3.4 33.4 - - + -
334S VAL* 3.5 21.1 - - + -
335S VAL* 5.8 0.7 - - + -
338S LEU* 4.0 14.1 - - + +
390S GLY 4.3 7.4 - - - +
391S THR* 3.2 18.1 - - - +
392S TYR 3.0 0.4 - - - -
393S THR* 1.3 80.9 + - - +
395S ILE* 1.3 59.2 + - - +
397S ARG* 2.9 63.1 + - - +
398S LEU 4.0 0.5 + - - -
213T GLU* 5.6 0.7 - - + -
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Residues in contact with ILE 395 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334S VAL* 4.1 15.0 - - + -
337S LEU* 6.2 0.4 - - + -
338S LEU* 4.9 1.1 - - - -
360S TYR* 3.4 32.3 - - + -
363S LEU* 3.6 35.2 - - + -
375S PHE* 3.8 9.4 - - + -
379S LEU* 4.9 7.4 - - + -
386S PHE* 4.1 18.4 - - + -
391S THR* 2.9 21.9 + - - +
392S TYR* 2.7 15.5 + - + +
394S LEU* 1.3 72.2 - - - +
396S ILE* 1.3 59.8 + - + +
398S LEU* 2.9 41.4 + - + +
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Residues in contact with ILE 396 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375S PHE* 4.9 6.1 - - - -
379S LEU* 5.7 7.9 - - + -
392S TYR* 3.0 53.5 + - + +
393S THR* 4.3 7.6 - - - +
394S LEU 3.2 0.6 + - - -
395S ILE* 1.3 77.6 - - + +
397S ARG* 1.3 60.5 + - - +
398S LEU 3.2 0.6 + - - -
399S ARG* 4.0 21.1 - - - +
234T GLN* 5.3 5.4 - - - +
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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