Contacts of the helix formed by residues 395 - 407 (chain A) in PDB entry 3OJW
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 GLU 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A ALA 4.0 1.9 - - - +
394A SER* 1.3 78.2 + - - +
396A PRO* 1.3 77.0 - - - +
397A SER* 3.1 36.9 + - - +
398A GLU* 3.0 19.2 + - + +
399A GLN* 2.9 20.4 + - - +
436A SER* 2.9 24.4 + - - +
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Residues in contact with PRO 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A SER 3.4 9.8 - - - +
395A GLU* 1.3 95.3 - - - +
397A SER* 1.3 58.0 + - - +
399A GLN* 3.0 13.2 + - + +
400A GLU* 2.8 49.6 + - + +
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A GLU* 3.1 24.4 + - - +
396A PRO* 1.3 77.4 - - - +
398A GLU* 1.3 63.6 + - - +
400A GLU* 3.6 11.1 + - - +
401A HIS* 3.0 27.9 + - - +
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA* 4.4 5.4 - - + -
395A GLU* 3.0 21.1 + - + +
397A SER* 1.3 84.0 + - - +
399A GLN* 1.3 65.3 + - - +
401A HIS* 3.1 4.4 + - - +
402A LEU* 3.0 28.2 + - - +
433A ASP 4.4 1.6 - - - +
434A TYR* 3.5 37.5 - - + +
435A PRO* 3.3 23.6 - - - +
436A SER* 2.6 43.8 + - - +
437A LEU 4.0 0.2 + - - -
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Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ALA 3.3 21.9 - - - +
391A GLN* 5.4 3.5 - - - +
393A ALA* 3.8 22.3 - - - +
395A GLU 2.9 12.0 + - - +
396A PRO* 3.4 12.8 - - + +
398A GLU* 1.3 76.0 - - - +
400A GLU* 1.3 68.0 + - - +
402A LEU* 3.2 6.1 + - - +
403A HIS* 3.1 48.0 + - + +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A PRO* 2.8 36.1 + - - +
397A SER* 3.7 8.2 + - - +
399A GLN* 1.3 80.2 - - + +
401A HIS* 1.3 64.4 + - - +
403A HIS* 3.3 9.2 + - - +
404A LYS* 3.0 23.6 + - - +
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Residues in contact with HIS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A SER 3.0 18.2 + - - +
398A GLU* 3.1 5.6 + - - +
400A GLU* 1.3 75.0 - - - +
402A LEU* 1.3 62.1 + - - +
404A LYS* 3.3 12.4 + - + +
405A MET* 3.0 31.9 + - + +
415A LEU* 3.6 35.5 - - + +
419A TRP* 5.1 12.1 - + - -
434A TYR* 2.5 38.0 + - + +
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A LEU* 4.1 33.3 - - + +
389A LEU* 4.5 1.3 - - + -
390A ALA* 3.9 29.4 - - + +
393A ALA* 4.2 8.7 - - + -
398A GLU 3.0 17.3 + - - +
399A GLN 3.5 6.3 - - - +
401A HIS* 1.3 78.9 - - - +
403A HIS* 1.3 56.8 + - - +
405A MET* 3.3 26.0 + - + +
406A ALA* 3.0 28.5 + - - +
430A ILE* 4.5 4.5 - - + -
434A TYR* 3.8 23.6 - - + -
437A LEU* 4.1 25.8 - - + -
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Residues in contact with HIS 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A TYR* 3.8 41.6 + + - -
390A ALA* 3.2 28.1 - - + +
391A GLN* 5.0 1.8 - - - -
399A GLN* 3.1 43.7 + - + +
400A GLU* 3.3 9.7 + - - +
402A LEU* 1.3 73.6 - - - +
404A LYS* 1.3 61.0 + - - +
406A ALA* 3.1 4.4 + - - +
407A SER* 2.8 32.2 + - - -
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Residues in contact with LYS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLU 3.0 15.9 + - - +
401A HIS* 3.6 13.6 - - + +
403A HIS* 1.3 74.9 - - - +
405A MET* 1.3 61.3 + - - +
407A SER* 2.9 23.6 + - - +
409A SER* 5.3 1.6 - - - +
411A GLU* 4.1 37.7 + - - +
412A GLY* 2.9 23.1 - - - +
415A LEU* 4.1 21.6 - - + +
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Residues in contact with MET 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A THR* 4.0 3.5 - - - +
386A LEU* 4.2 12.8 - - + -
401A HIS* 3.0 17.2 + - - +
402A LEU* 3.5 32.8 - - + +
404A LYS* 1.3 76.3 - - - +
406A ALA* 1.3 60.0 + - - +
407A SER 3.7 2.1 + - - +
412A GLY 4.0 9.0 - - - +
415A LEU* 3.4 31.9 - - + -
416A TYR* 3.4 30.4 - - + +
419A TRP* 3.6 27.6 - - + -
420A VAL* 3.6 15.7 - - - -
430A ILE* 6.0 0.4 - - + -
434A TYR* 3.2 27.1 - - + +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A THR* 3.3 41.6 - - - +
386A LEU* 4.3 1.8 - - + -
387A TYR* 3.7 28.8 - - + +
402A LEU 3.0 16.5 + - - +
403A HIS* 3.1 6.2 + - - +
405A MET* 1.3 77.1 - - - +
407A SER* 1.3 63.3 + - - +
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Residues in contact with SER 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A THR* 5.7 1.4 - - - +
403A HIS 2.8 14.6 + - - -
404A LYS* 2.9 20.2 + - - -
405A MET 3.3 2.4 - - - +
406A ALA* 1.3 82.3 - - - +
408A SER* 1.3 61.4 + - - +
409A SER* 3.1 23.2 + - - -
412A GLY 4.1 1.6 - - - -
413A LYS* 3.9 17.7 + - - +
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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