Contacts of the helix formed by residues 390 - 400 (chain t) in PDB entry 6QX2
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 HIS 390 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468S ARG* 5.7 2.6 + - - -
1V G 4.1 41.6 + + - +
2V A 6.0 1.6 - - - -
2019W T 6.1 0.7 - - - -
386t ILE* 2.9 44.5 + - + +
387t ALA 3.4 3.4 - - - -
389t ASP* 1.3 91.3 + - + +
391t ILE* 1.3 63.0 + - - +
392t ASP 3.3 2.5 - - - -
393t GLU* 3.1 35.4 + - - +
394t ILE* 3.1 13.0 + - + +
415t PHE* 4.2 19.1 - + + -
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Residues in contact with ILE 391 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395r ILE* 4.8 1.1 - - + -
399r ARG* 3.0 49.6 - - - +
430r LEU* 4.6 7.6 - - + -
387t ALA 3.0 19.9 + - - +
388t LEU* 3.6 12.5 + - - +
389t ASP 3.7 0.6 + - - -
390t HIS* 1.3 75.8 - - - +
392t ASP* 1.3 62.3 + - - +
394t ILE* 3.2 12.8 + - + -
395t ILE* 3.0 48.2 + - + +
428t MET* 5.3 3.1 - - + -
433t LEU* 3.6 38.8 - - + -
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Residues in contact with ASP 392 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395r ILE* 4.9 9.5 - - - +
399r ARG* 2.6 29.4 + - - -
390t HIS 3.2 1.0 + - - -
391t ILE* 1.3 79.0 - - - +
393t GLU* 1.3 68.9 + - - +
395t ILE* 3.6 7.1 + - - +
396t SER* 3.0 26.8 + - - -
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Residues in contact with GLU 393 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1V G 5.2 2.1 - - - +
2019W T 5.9 2.4 - - - +
2020W T 3.5 30.4 - - + +
390t HIS* 3.1 32.4 + - + +
392t ASP* 1.3 86.6 + - - +
394t ILE* 1.3 61.6 + - - +
396t SER* 3.3 7.8 + - - -
397t THR* 2.8 33.3 + - - +
415t PHE* 3.8 17.5 - - + -
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Residues in contact with ILE 394 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430r LEU* 4.1 8.3 - - + -
386t ILE* 5.3 0.7 - - + -
387t ALA* 3.6 32.1 - - + +
390t HIS* 3.1 15.6 + - + +
391t ILE* 3.2 13.7 + - + +
393t GLU* 1.3 75.0 - - - +
395t ILE* 1.3 62.9 + - - +
397t THR* 3.4 8.7 + - - -
398t ILE* 3.1 41.7 + - + +
411t LEU* 3.9 12.1 - - + -
415t PHE* 3.8 34.3 - - + -
417t LEU* 5.0 1.8 - - + -
425t ILE* 3.9 22.9 - - + -
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Residues in contact with ILE 395 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391r ILE* 4.8 2.9 - - + -
392r ASP* 6.3 0.7 - - - -
395r ILE* 3.8 36.1 - - + -
430r LEU* 3.5 33.4 - - + -
433r LEU* 4.1 18.5 - - + +
391t ILE* 3.0 38.9 + - + +
392t ASP* 3.8 7.0 - - - +
394t ILE* 1.3 75.9 - - - +
396t SER* 1.3 51.9 + - - +
398t ILE* 3.1 9.4 + - - +
399t ARG* 2.8 49.9 + - + +
433t LEU* 5.0 0.7 - - + -
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Residues in contact with SER 396 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392t ASP 3.0 13.9 + - - -
393t GLU* 3.3 9.7 + - - -
395t ILE* 1.3 77.1 - - - +
397t THR* 1.3 58.2 + - - +
399t ARG* 3.1 14.7 + - - +
400t GLU* 2.9 41.0 + - - +
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Residues in contact with THR 397 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393t GLU 2.8 19.2 + - - -
394t ILE 3.4 8.7 - - - -
396t SER* 1.3 74.6 - - - +
398t ILE* 1.3 54.1 + - - +
400t GLU* 3.5 18.2 - - - +
401t SER* 2.6 32.3 + - - -
407t ALA 4.8 0.4 - - - +
410t SER* 3.6 33.2 - - - +
411t LEU* 3.9 22.4 - - + -
414t ARG* 4.8 6.3 - - + +
415t PHE* 3.7 14.9 - - + -
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Residues in contact with ILE 398 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430r LEU* 3.2 54.1 - - + +
433r LEU* 3.7 15.0 - - + +
434r THR* 3.7 15.4 - - + -
394t ILE* 3.1 38.1 + - + +
395t ILE* 3.1 7.6 + - - +
397t THR* 1.3 74.0 - - - +
399t ARG* 1.3 64.9 + - - +
401t SER* 3.3 23.9 + - - +
407t ALA* 4.6 2.2 - - + -
411t LEU* 4.1 17.7 - - + -
425t ILE* 4.7 1.1 - - + -
426t LEU* 4.0 18.4 - - + -
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Residues in contact with ARG 399 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388r LEU 5.2 1.2 + - - -
391r ILE* 3.1 35.6 - - - +
392r ASP* 4.1 20.4 - - - +
433r LEU* 3.5 31.2 - - + +
435r GLY* 5.3 0.2 - - - -
438r ARG* 3.5 28.7 + - - +
395t ILE* 2.8 26.0 + - + +
396t SER* 3.1 13.1 + - - +
398t ILE* 1.3 73.3 - - - +
400t GLU* 1.3 60.0 + - - +
401t SER 3.1 8.8 + - - +
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Residues in contact with GLU 400 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396t SER* 2.9 20.6 + - - +
397t THR* 3.5 26.4 - - - +
399t ARG* 1.3 74.0 - - - +
401t SER* 1.3 60.0 + - - +
402t ASP* 3.6 12.9 - - - +
406t VAL* 5.5 0.2 - - - +
410t SER* 5.5 3.5 + - - +
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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