Contacts of the helix formed by residues 390 - 400 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386J ILE* 3.1 39.3 + - + +
387J ALA 3.4 3.8 - - - -
389J ASP* 1.3 102.6 - - + +
391J ILE* 1.3 62.6 + - - +
392J ASP* 3.3 2.9 - - - -
393J GLU* 3.1 36.4 + - - +
394J ILE* 3.1 12.6 + - + +
415J PHE* 4.1 21.5 - + + -
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Residues in contact with ILE 391 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387J ALA 3.0 19.4 + - - +
388J LEU* 3.6 19.7 + - + +
389J ASP 3.7 0.6 - - - -
390J HIS* 1.3 75.5 - - - +
392J ASP* 1.3 65.6 + - - +
394J ILE* 3.2 7.8 + - + -
395J ILE* 3.0 46.3 + - + +
428J MET* 5.3 2.0 - - + -
433J LEU* 3.7 37.2 - - + -
395L ILE* 5.3 4.0 - - + -
399L ARG* 4.0 36.6 - - - +
430L LEU* 4.3 16.2 - - + -
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Residues in contact with ASP 392 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390J HIS 3.2 1.0 + - - -
391J ILE* 1.3 83.1 - - + +
393J GLU* 1.3 63.1 + - + +
395J ILE* 3.6 7.7 + - - +
396J SER* 3.3 20.4 + - - -
395L ILE* 6.3 2.2 - - - -
399L ARG* 5.5 8.5 - - - +
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Residues in contact with GLU 393 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390J HIS* 3.1 31.1 + - + +
392J ASP* 1.3 77.3 - - + +
394J ILE* 1.3 58.9 + - - +
396J SER* 2.5 22.6 + - - -
397J THR* 2.8 21.9 + - - +
415J PHE* 3.8 20.5 - - + -
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Residues in contact with ILE 394 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386J ILE* 5.4 0.2 - - + -
387J ALA* 3.6 32.5 - - + +
390J HIS* 3.1 15.8 + - + +
391J ILE* 3.2 18.8 + - + +
393J GLU* 1.3 74.6 - - - +
395J ILE* 1.3 62.1 + - - +
397J THR* 3.4 9.9 + - - -
398J ILE* 3.1 41.6 + - + +
411J LEU* 3.9 10.8 - - + -
415J PHE* 3.8 33.2 - - + -
417J LEU* 5.0 2.0 - - + -
425J ILE* 3.9 23.1 - - + -
430L LEU* 4.7 2.2 - - + -
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Residues in contact with ILE 395 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391J ILE* 3.0 37.4 + - + +
392J ASP* 3.8 7.2 - - - +
393J GLU 3.3 0.2 - - - -
394J ILE* 1.3 75.9 - - - +
396J SER* 1.3 52.4 + - - +
398J ILE* 3.1 9.1 + - + +
399J ARG* 2.8 57.7 + - - +
433J LEU* 5.0 0.4 - - + -
391L ILE* 4.9 7.9 - - + -
392L ASP* 6.0 2.0 - - - +
395L ILE* 4.4 22.9 - - + -
430L LEU* 3.6 32.5 - - + -
433L LEU* 3.8 20.1 - - + +
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Residues in contact with SER 396 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392J ASP 3.3 8.2 + - - -
393J GLU* 2.5 29.8 + - - -
395J ILE* 1.3 77.5 - - - +
397J THR* 1.3 56.1 + - - +
399J ARG* 3.1 8.9 + - - +
400J GLU* 2.9 39.8 + - - +
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Residues in contact with THR 397 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393J GLU* 2.8 18.9 + - - +
394J ILE 3.4 8.3 - - - -
396J SER* 1.3 74.8 + - - +
398J ILE* 1.3 53.7 + - - +
400J GLU* 3.5 19.4 - - - +
401J SER* 2.6 32.1 + - - +
407J ALA 4.9 0.4 - - - +
410J SER* 3.6 34.3 - - - +
411J LEU* 3.9 22.2 - - + -
414J ARG* 5.1 3.5 - - + +
415J PHE* 3.8 14.9 - - + -
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Residues in contact with ILE 398 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394J ILE* 3.1 38.5 + - + +
395J ILE* 3.6 9.2 - - + +
397J THR* 1.3 73.5 - - - +
399J ARG* 1.3 63.9 + - - +
400J GLU 3.5 0.2 - - - -
401J SER* 3.3 25.2 + - - +
407J ALA* 4.5 3.1 - - + -
411J LEU* 4.1 17.0 - - + -
425J ILE* 4.8 2.0 - - + -
426J LEU* 4.0 23.8 - - + -
430L LEU* 3.5 39.0 - - + +
433L LEU* 4.1 4.7 - - + -
434L THR* 3.4 31.2 - - + +
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Residues in contact with ARG 399 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395J ILE* 2.8 39.4 + - + +
396J SER* 3.6 8.7 - - - +
398J ILE* 1.3 73.6 - - - +
400J GLU* 1.3 59.7 + - - +
401J SER 3.1 8.0 + - - +
388L LEU 4.4 7.5 + - - -
391L ILE* 3.3 32.9 - - - +
392L ASP* 3.8 16.4 + - - -
433L LEU* 3.3 25.6 - - + +
435L GLY* 4.7 0.7 - - - -
438L ARG* 2.7 38.4 + - - +
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Residues in contact with GLU 400 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396J SER* 2.9 20.8 + - - +
397J THR* 3.5 26.0 + - - +
399J ARG* 1.3 74.5 - - - +
401J SER* 1.3 61.7 + - - +
402J ASP* 3.6 12.0 - - - +
406J VAL* 5.5 0.3 - - - +
410J SER* 5.5 3.0 - - - +
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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