Contacts of the helix formed by residues 390 - 400 (chain r) 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 r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386r ILE* 3.1 40.7 + - + +
387r ALA 3.4 3.8 - - - -
389r ASP* 1.3 100.5 - - + +
391r ILE* 1.3 62.4 - - - +
392r ASP 3.3 2.5 - - - -
393r GLU* 3.1 36.2 + - - +
394r ILE* 3.1 11.8 + - + +
415r PHE* 4.1 21.2 - + + -
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Residues in contact with ILE 391 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387r ALA* 3.0 19.5 + - + +
388r LEU* 3.6 20.5 + - + +
389r ASP 3.7 0.6 - - - -
390r HIS* 1.3 75.7 - - - +
392r ASP* 1.3 61.4 + - - +
394r ILE* 3.2 12.5 + - + -
395r ILE* 3.0 46.9 + - + +
428r MET* 5.5 1.8 - - + -
433r LEU* 3.7 34.5 - - + -
395t ILE* 4.8 2.9 - - + -
399t ARG* 3.1 48.0 - - - +
430t LEU* 4.6 9.0 - - + -
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Residues in contact with ASP 392 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390r HIS 3.3 0.8 - - - -
391r ILE* 1.3 81.1 - - - +
393r GLU* 1.3 63.5 + - + +
395r ILE* 3.6 7.5 + - - +
396r SER* 3.3 20.6 + - - -
395t ILE* 6.3 0.7 - - - -
399t ARG* 4.1 17.7 - - - +
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Residues in contact with GLU 393 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390r HIS* 3.1 32.5 + - + +
392r ASP* 1.3 76.4 - - + +
394r ILE* 1.3 59.1 + - - +
396r SER* 2.5 22.6 + - - -
397r THR* 2.8 22.1 + - - +
415r PHE* 3.8 20.3 - - + -
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Residues in contact with ILE 394 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386r ILE* 5.0 0.9 - - + +
387r ALA* 3.6 31.9 - - + +
390r HIS* 3.1 15.8 + - + +
391r ILE* 3.2 13.9 + - + +
393r GLU* 1.3 75.1 - - - +
395r ILE* 1.3 63.2 + - - +
397r THR* 3.4 8.7 + - - -
398r ILE* 3.1 42.2 + - + +
411r LEU* 3.9 11.6 - - + +
415r PHE* 3.8 33.7 - - + -
417r LEU* 5.1 1.6 - - + -
425r ILE* 3.9 21.8 - - + -
430t LEU* 4.2 9.2 - - + -
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Residues in contact with ILE 395 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391r ILE* 3.0 35.5 + - + +
392r ASP* 3.8 6.7 - - - +
394r ILE* 1.3 74.4 - - - +
396r SER* 1.3 51.6 + - - +
398r ILE* 3.1 8.4 + - + +
399r ARG* 2.8 59.3 + - - +
433r LEU* 5.2 0.4 - - + -
391t ILE* 4.8 2.0 - - + -
392t ASP* 4.9 9.9 - - - +
395t ILE* 3.8 35.9 - - + -
430t LEU* 3.7 30.7 - - + -
433t LEU* 4.0 12.3 - - + -
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Residues in contact with SER 396 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392r ASP 3.3 9.1 + - - -
393r GLU* 2.5 29.6 + - - -
395r ILE* 1.3 76.5 - - - +
397r THR* 1.3 51.4 + - - +
399r ARG* 3.1 9.5 + - - +
400r GLU* 2.9 43.8 + - - +
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Residues in contact with THR 397 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393r GLU* 2.8 19.8 + - - +
394r ILE 3.4 9.6 - - - -
396r SER* 1.3 73.6 + - - +
398r ILE* 1.3 54.9 + - - +
400r GLU* 3.5 19.3 + - - +
401r SER* 2.6 32.1 + - - +
407r ALA 4.8 0.2 - - - +
410r SER* 3.6 34.4 - - - +
411r LEU* 3.9 21.5 - - + +
414r ARG* 5.1 3.8 - - + +
415r PHE* 3.8 15.1 - - + -
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Residues in contact with ILE 398 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394r ILE* 3.1 38.2 + - + +
395r ILE* 3.1 8.7 + - - +
397r THR* 1.3 73.5 - - - +
399r ARG* 1.3 63.3 + - - +
401r SER* 3.3 25.2 + - - +
407r ALA* 4.5 3.4 - - + -
411r LEU* 4.1 18.4 - - + -
425r ILE* 4.6 1.1 - - + -
426r LEU* 4.0 19.1 - - + -
430t LEU* 3.2 49.8 - - + +
433t LEU* 3.8 11.0 - - + -
434t THR* 3.5 20.1 - - + +
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Residues in contact with ARG 399 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395r ILE* 2.8 34.1 + - + +
396r SER* 3.6 8.5 - - - +
398r ILE* 1.3 72.9 - - - +
400r GLU* 1.3 59.7 + - - +
401r SER 3.1 12.8 + - - +
388t LEU 4.8 4.4 + - - -
389t ASP 5.7 1.8 + - - -
391t ILE* 3.0 31.4 - - + +
392t ASP* 2.6 36.4 + - - -
433t LEU* 3.3 31.0 - - + +
434t THR 4.7 0.2 - - - -
435t GLY* 4.4 5.4 + - - -
438t ARG* 5.5 11.5 + - - +
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Residues in contact with GLU 400 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396r SER* 2.9 21.6 + - - +
397r THR* 3.5 25.7 + - - +
399r ARG* 1.3 73.5 - - - +
401r SER* 1.3 60.3 + - - +
402r ASP* 3.6 11.8 - - - +
410r SER* 5.6 2.3 - - - -
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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