Contacts of the helix formed by residues 390 - 400 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386C ILE* 2.9 45.2 + - + +
387C ALA 3.4 3.8 - - - -
389C ASP* 1.3 90.4 + - + +
391C ILE* 1.3 62.5 + - - +
392C ASP* 3.3 3.4 - - - -
393C GLU* 3.1 38.7 + - - +
394C ILE* 3.1 11.9 + - + +
415C PHE* 4.1 17.3 - + + -
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Residues in contact with ILE 391 (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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395A ILE* 5.3 0.9 - - + -
399A ARG* 3.1 45.5 - - - +
430A LEU* 4.5 11.0 - - + -
387C ALA 3.0 18.1 + - - +
388C LEU* 3.7 12.8 - - - +
389C ASP 3.7 0.8 + - - -
390C HIS* 1.3 75.9 - - - +
392C ASP* 1.3 63.9 - - - +
394C ILE* 3.2 9.7 + - + -
395C ILE* 3.0 49.6 + - + +
428C MET* 4.9 2.7 - - + -
433C LEU* 3.6 39.7 - - + -
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Residues in contact with ASP 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 5.9 2.8 - - - +
399A ARG* 3.0 27.8 + - - -
390C HIS 3.2 1.0 + - - -
391C ILE* 1.3 78.0 - - - +
393C GLU* 1.3 63.0 + - + +
395C ILE* 3.6 7.7 + - - +
396C SER* 3.1 26.7 + - - -
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Residues in contact with GLU 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C HIS* 3.1 33.7 + - + +
392C ASP* 1.3 74.6 - - + +
394C ILE* 1.3 61.1 + - - +
396C SER* 3.3 8.1 + - - -
397C THR* 2.8 32.6 + - - +
414C ARG* 5.3 4.7 - - - +
415C PHE* 3.8 19.7 - - + -
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Residues in contact with ILE 394 (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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430A LEU* 4.5 2.9 - - + -
386C ILE* 5.0 1.1 - - + +
387C ALA* 3.6 31.6 - - + +
390C HIS* 3.1 15.1 + - + +
391C ILE* 3.2 18.6 + - + +
393C GLU* 1.3 75.2 - - - +
395C ILE* 1.3 62.6 + - - +
397C THR* 3.4 8.1 - - - -
398C ILE* 3.1 41.8 + - + +
411C LEU* 3.9 11.6 - - + +
415C PHE* 3.7 33.7 - - + -
417C LEU* 5.1 1.3 - - + -
425C ILE* 4.0 22.4 - - + -
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Residues in contact with ILE 395 (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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391A ILE* 5.5 1.8 - - + -
395A ILE* 4.3 29.6 - - + -
430A LEU* 3.7 32.3 - - + -
433A LEU* 4.3 11.8 - - + +
391C ILE* 3.0 35.3 + - + +
392C ASP* 3.8 7.4 - - - +
393C GLU 3.3 0.2 - - - -
394C ILE* 1.3 74.9 - - - +
396C SER* 1.3 52.2 + - - +
398C ILE* 3.1 9.1 + - + +
399C ARG* 2.8 62.8 + - + +
433C LEU* 5.0 0.4 - - + -
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Residues in contact with SER 396 (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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392C ASP 3.1 13.7 + - - -
393C GLU* 3.3 9.4 + - - -
395C ILE* 1.3 77.1 - - - +
397C THR* 1.3 56.9 + - - +
399C ARG* 3.1 13.6 + - - +
400C GLU* 2.9 40.6 + - - +
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Residues in contact with THR 397 (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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393C GLU* 2.8 18.9 + - - +
394C ILE 3.4 9.0 - - - -
396C SER* 1.3 74.6 - - - +
398C ILE* 1.3 54.0 + - - +
400C GLU* 3.5 18.6 + - - +
401C SER* 2.6 31.9 + - - +
407C ALA 4.8 0.2 - - - +
410C SER* 3.6 34.0 - - - +
411C LEU* 3.9 22.4 - - + +
414C ARG* 4.7 6.5 - - + +
415C PHE* 3.8 14.7 - - + -
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Residues in contact with ILE 398 (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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430A LEU* 3.5 41.7 - - + +
433A LEU* 4.4 8.5 - - + -
434A THR* 3.5 20.7 - - + +
394C ILE* 3.1 38.3 + - + +
395C ILE* 3.1 8.7 + - + +
397C THR* 1.3 73.4 - - - +
399C ARG* 1.3 64.3 + - - +
401C SER* 3.3 25.1 + - - +
407C ALA* 4.5 3.1 - - + -
411C LEU* 4.1 17.0 - - + -
425C ILE* 4.7 2.5 - - + -
426C LEU* 4.0 27.6 - - + -
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Residues in contact with ARG 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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391A ILE* 3.5 32.7 - - - +
392A ASP* 4.9 13.8 - - - +
433A LEU* 3.8 32.6 - - + +
435A GLY* 4.5 6.4 + - - -
395C ILE* 2.8 37.3 + - + +
396C SER* 3.1 10.3 + - - +
398C ILE* 1.3 72.9 - - - +
400C GLU* 1.3 59.8 - - - +
401C SER 3.1 12.9 + - - +
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Residues in contact with GLU 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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396C SER* 2.9 21.8 + - - +
397C THR* 3.5 25.7 + - - +
399C ARG* 1.3 73.8 - - - +
401C SER* 1.3 59.7 + - - +
402C ASP* 3.6 12.2 - - - +
410C SER* 5.6 2.6 - - - +
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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