Contacts of the helix formed by residues 394 - 405 (chain A) in PDB entry 5J2N
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 GLN 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A ILE* 1.3 81.9 - - - +
395A LYS* 1.3 67.6 + - - +
396A GLU* 3.2 8.1 + - + +
397A THR* 3.2 23.9 + - - +
398A TRP 3.1 17.2 + - - -
414A TRP* 3.8 3.4 - - - -
416A PHE* 3.3 41.6 - - + +
422A LEU* 4.5 12.6 - - + +
423A VAL 4.6 1.7 + - - +
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Residues in contact with LYS 395 (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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393A ILE 3.7 0.8 + - - -
394A GLN* 1.3 76.0 + - - +
396A GLU* 1.3 63.9 + - + +
398A TRP* 3.4 3.2 + - + +
399A GLU* 2.9 38.2 + - + +
414A TRP* 3.1 69.8 + - + +
415A GLU* 4.4 6.5 - - - +
416A PHE* 4.7 9.0 - - + +
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Residues in contact with GLU 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 GLN* 3.2 7.2 - - + +
395A LYS* 1.3 78.4 - - + +
397A THR* 1.3 61.1 + - - +
399A GLU* 3.8 12.0 - - - +
400A THR* 2.9 36.6 + - - +
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Residues in contact with THR 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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365A VAL* 4.9 2.7 - - + -
393A ILE* 3.9 16.2 - - + +
394A GLN* 3.2 27.4 + - - +
396A GLU* 1.3 77.6 - - - +
398A TRP* 1.3 60.8 + - - +
400A THR* 3.7 6.0 + - - -
401A TRP* 3.3 21.0 + - - +
423A VAL 3.7 20.0 + - - +
424A LYS* 3.9 17.9 - - + +
425A LEU* 4.1 17.1 - - + +
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Residues in contact with TRP 398 (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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365A VAL* 3.8 15.5 - - + -
369A THR* 3.4 17.0 - - - -
393A ILE* 4.1 13.2 - - + +
394A GLN 3.1 11.9 + - - +
395A LYS 3.8 6.5 - - - +
397A THR* 1.3 75.9 - - - +
399A GLU* 1.3 73.5 + - - +
401A TRP* 3.1 26.1 + + - +
402A TRP* 3.0 36.2 + + + +
409A THR* 3.3 46.4 - - + -
410A TRP* 4.1 3.7 - - - +
411A ILE* 3.6 44.4 + - + +
414A TRP* 4.0 29.4 - + + +
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Residues in contact with GLU 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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395A LYS* 2.9 28.5 + - + +
396A GLU* 3.8 13.9 - - - +
398A TRP* 1.3 83.0 - - + +
400A THR* 1.3 58.2 + - - +
402A TRP* 3.3 30.6 + - - -
403A THR* 2.6 37.1 + - - +
360B ALA* 3.6 27.0 - - - +
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Residues in contact with THR 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 GLU* 2.9 20.9 + - - +
397A THR* 3.9 6.9 - - - -
399A GLU* 1.3 76.9 - - - +
401A TRP* 1.3 64.0 + - - +
403A THR* 3.4 6.5 + - - -
404A GLU* 3.3 37.7 + - - +
425A LEU* 4.3 6.5 - - + -
428A GLN* 3.9 28.9 + - - +
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Residues in contact with TRP 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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363A ASN* 3.3 21.5 - - - -
365A VAL* 3.5 32.9 - - + +
366A LYS* 3.8 22.2 - - + +
369A THR* 5.2 1.0 + - - -
397A THR 3.3 14.8 + - - +
398A TRP* 3.1 20.7 + + - +
400A THR* 1.3 79.3 - - - +
402A TRP* 1.3 64.3 + - - +
403A THR 3.2 0.5 + - - -
404A GLU* 3.3 8.0 + - + +
405A TYR* 2.9 79.3 + + + +
409A THR* 4.1 8.2 + - + +
425A LEU* 3.9 17.0 - - + -
508A ALA 3.2 23.1 - - - -
509A GLN* 3.4 28.5 - - + -
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Residues in contact with TRP 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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398A TRP* 3.0 47.5 + - + +
399A GLU* 3.3 42.6 + - - +
401A TRP* 1.3 82.0 - - - +
403A THR* 1.3 66.7 + - - +
405A TYR* 4.2 4.0 - - - -
409A THR* 3.9 26.5 - - + +
331B LYS* 2.8 33.3 + - - +
333B GLY* 6.1 1.6 - - - -
334B GLN* 5.8 9.0 - - - -
359B GLY 5.2 4.5 - - - -
360B ALA* 4.5 9.4 - - - -
362B THR* 3.6 38.6 - - + -
364B ASP* 3.1 39.3 - - - -
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Residues in contact with THR 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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399A GLU* 2.6 25.8 + - - +
400A THR* 3.6 7.8 - - - -
401A TRP 3.1 1.0 - - - -
402A TRP* 1.3 88.8 + - - +
404A GLU* 1.3 63.4 + - + +
405A TYR 4.4 2.1 - - - +
331B LYS* 5.0 3.1 - - - -
333B GLY* 5.2 7.4 - - - -
334B GLN* 5.4 10.6 + - - +
424B LYS* 4.9 5.5 + - - -
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Residues in contact with GLU 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 THR* 3.3 27.2 - - - +
401A TRP* 3.4 5.4 - - + +
403A THR* 1.3 79.1 - - + +
405A TYR* 1.3 67.2 + - - +
406A TRP* 3.3 8.8 + - - -
425A LEU* 3.7 12.1 - - - +
428A GLN* 5.2 7.8 - - - +
429A LEU 5.3 5.2 + - - +
507A GLN* 5.6 3.2 + - - +
509A GLN* 2.4 42.3 + - - +
424B LYS* 3.8 15.2 + - - +
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Residues in contact with TYR 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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366A LYS* 3.3 33.3 + - + -
401A TRP* 2.9 62.4 + + + +
402A TRP* 4.0 4.4 - - - +
403A THR 3.5 1.4 - - - +
404A GLU* 1.3 77.8 - - - +
406A TRP* 1.3 93.2 + + - +
407A GLN* 3.1 53.6 + - + +
409A THR* 4.1 11.2 - - + -
507A GLN 5.7 0.7 - - - -
508A ALA* 4.6 3.4 - - + -
331B LYS* 3.1 27.0 + - - -
418B ASN* 5.0 2.4 + - - -
424B LYS* 5.2 0.6 + - - -
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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