Contacts of the helix formed by residues 388 - 402 (chain A) in PDB entry 5XOU
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 GLY 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A PRO 3.0 12.9 + - - +
386A SER 3.2 3.0 + - - -
387A GLN* 1.3 75.9 - - - +
389A LEU* 1.3 58.6 + - - -
391A PHE* 3.0 25.6 + - - +
392A ARG* 3.5 3.1 + - - +
420A ARG* 6.1 0.4 - - - -
424A LEU* 5.6 2.9 - - - +
564B GLU* 4.0 8.5 - - - -
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Residues in contact with LEU 389 (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 GLN 3.2 2.6 + - - -
388A GLY* 1.3 69.2 - - - -
390A ALA* 1.3 67.4 + - - +
391A PHE 3.0 1.6 - - - -
392A ARG* 3.0 18.3 + - + +
393A GLU* 3.0 11.8 + - - +
520B TRP* 4.7 9.0 - - + -
524B GLU* 3.9 34.1 - - + +
527B LEU* 4.2 19.1 - - + -
528B TRP* 4.1 20.4 - - + -
537B LEU* 3.8 29.2 - - + -
564B GLU* 3.2 48.6 + - + +
566B ILE* 4.9 0.2 - - + -
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLN* 3.5 29.5 + - + +
388A GLY 3.3 0.2 - - - -
389A LEU* 1.3 76.9 - - - +
391A PHE* 1.3 63.8 + - - +
393A GLU* 3.0 19.5 + - - +
394A ALA* 3.1 13.7 + - - +
564B GLU* 5.0 1.4 + - - -
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Residues in contact with PHE 391 (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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349A LEU* 3.7 28.7 - - + -
381A LEU* 5.2 3.6 - - + -
383A ALA* 3.5 36.1 - - + -
384A HIS* 3.0 32.5 - - - +
385A PRO* 3.4 20.2 - - + -
387A GLN* 4.2 3.5 + - + +
388A GLY 3.0 16.1 + - - +
390A ALA* 1.3 78.4 - - - +
392A ARG* 1.3 61.8 + - - +
394A ALA* 3.0 15.4 + - + +
395A LEU* 3.1 44.1 + - + +
421A LEU* 4.7 1.1 - - + -
424A LEU* 3.8 25.1 - - + -
425A LEU* 4.2 8.3 - - + -
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLY 3.5 2.8 + - - +
389A LEU* 3.0 16.6 + - + +
391A PHE* 1.3 78.1 - - - +
393A GLU* 1.3 64.0 + - - +
395A LEU* 3.0 13.6 + - + +
396A ARG* 2.9 21.3 + - - +
424A LEU* 4.3 14.8 - - + +
427A ARG* 3.5 24.4 + - - +
428A GLU* 3.0 36.8 + - + +
676A GLU* 5.7 1.2 + - - -
524B GLU* 2.8 50.2 + - - +
525B GLU* 2.8 33.9 + - - -
528B TRP* 3.6 39.6 - - + +
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Residues in contact with GLU 393 (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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389A LEU 3.0 9.7 + - - +
390A ALA* 3.0 13.4 + - - +
392A ARG* 1.3 74.6 - - - +
394A ALA* 1.3 57.6 + - - +
396A ARG* 3.0 24.8 + - - +
397A LYS* 2.9 47.7 + - - +
528B TRP* 3.0 33.3 - - + -
531B ARG* 2.8 36.8 + - - -
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Residues in contact with ALA 394 (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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381A LEU* 4.2 13.3 - - + +
382A HIS 5.5 1.3 - - - +
383A ALA* 3.7 27.1 - - + -
390A ALA 3.1 8.6 + - - +
391A PHE* 3.0 9.7 + - + +
393A GLU* 1.3 74.4 - - - +
395A LEU* 1.3 64.1 + - - +
397A LYS* 3.1 13.2 + - - +
398A ALA* 2.8 23.7 + - - +
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Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LEU* 3.8 27.8 - - + -
391A PHE* 3.1 47.2 + - + +
392A ARG* 3.0 12.0 + - - +
394A ALA* 1.3 76.0 - - + +
396A ARG* 1.3 63.8 + - - +
398A ALA* 3.1 6.7 + - - +
399A LYS* 2.9 23.4 + - - +
424A LEU* 4.3 11.9 - - + +
425A LEU* 4.0 35.2 - - + -
428A GLU* 3.9 16.6 - - + -
430A LEU* 3.8 17.7 - - + +
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Residues in contact with ARG 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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392A ARG 2.9 11.2 + - - +
393A GLU* 3.0 42.3 + - - +
395A LEU* 1.3 73.9 - - - +
397A LYS* 1.3 86.0 + - - +
399A LYS* 3.0 6.8 + - - +
400A GLU* 3.0 42.9 + - - +
428A GLU* 3.4 28.6 + - - +
528B TRP* 4.0 16.4 - - + +
531B ARG* 3.4 16.5 - - - +
532B ARG* 5.4 8.3 - - - +
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Residues in contact with LYS 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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393A GLU* 2.9 36.0 + - + +
394A ALA* 3.3 14.6 - - - +
396A ARG* 1.3 92.4 - - - +
398A ALA* 1.3 63.0 + - - +
400A GLU* 3.0 20.1 + - - +
401A GLU* 3.0 26.7 + - - +
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Residues in contact with ALA 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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379A HIS* 6.0 0.7 - - + -
381A LEU* 3.7 24.2 - - + -
394A ALA 2.8 15.8 + - - +
395A LEU* 3.4 8.7 - - - +
397A LYS* 1.3 73.0 - - - +
399A LYS* 1.3 62.6 + - - +
401A GLU* 3.2 16.8 + - - +
402A GLY 3.3 0.5 + - - -
403A VAL* 3.1 42.3 + - + +
430A LEU* 4.8 4.9 - - + -
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Residues in contact with LYS 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 LEU 2.9 11.7 + - - +
396A ARG* 3.0 11.0 + - - +
398A ALA* 1.3 77.3 - - - +
400A GLU* 1.3 63.3 + - - +
402A GLY* 3.2 11.8 + - - -
403A VAL 3.8 18.1 + - - -
404A GLN* 5.3 0.8 - - - +
428A GLU* 3.6 24.2 - - - +
429A GLY* 4.4 8.9 + - - -
430A LEU* 3.7 19.7 - - + +
676A GLU* 5.2 6.1 - - - -
678A ASP* 5.5 1.8 + - - -
681A LYS* 4.0 18.0 - - - +
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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 ARG* 3.0 31.2 + - - +
397A LYS* 3.0 12.2 + - - +
399A LYS* 1.3 76.8 - - - +
401A GLU* 1.3 63.1 + - + +
402A GLY* 3.0 2.9 + - - -
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Residues in contact with GLU 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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377A ARG* 3.3 21.8 + - - +
379A HIS* 3.6 28.4 + - + -
397A LYS* 3.0 26.7 + - - +
398A ALA* 3.2 12.2 + - - +
400A GLU* 1.3 77.7 - - + +
402A GLY* 1.3 58.2 + - - +
403A VAL 3.8 0.4 - - - -
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA* 3.4 16.9 - - - +
377A ARG* 4.0 5.6 + - - -
399A LYS* 3.2 7.0 + - - -
400A GLU 3.0 6.7 - - - -
401A GLU* 1.3 81.7 - - - +
403A VAL* 1.3 68.8 + - - +
404A GLN* 3.2 13.9 + - - +
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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