Contacts of the helix formed by residues 391 - 398 (chain A) in PDB entry 2CXO
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 PHE 391 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU* 3.9 13.0 - - + -
380A TRP* 3.5 31.6 - + - -
382A GLU* 3.8 39.7 - - + -
387A GLY* 2.9 20.7 + - - -
390A ALA* 1.3 84.6 - - + +
392A TYR* 1.3 90.6 + + - +
393A GLN 3.1 3.1 - - - +
394A LEU* 3.0 17.3 + - - +
395A ILE* 3.4 12.5 + - + +
353B GLN* 3.8 25.6 - - + +
357B MET* 3.7 31.8 - - + +
358B GLU 4.9 0.9 - - - +
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Residues in contact with TYR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.5 27.5 - - + +
341A TYR* 2.9 33.4 + - - -
382A GLU 5.3 0.6 + - - -
384A GLY* 4.7 3.5 - - - -
387A GLY* 3.1 27.9 + - - -
388A GLN* 3.4 39.6 + - + +
390A ALA 3.9 0.4 - - - -
391A PHE* 1.3 96.8 - + - +
393A GLN* 1.3 66.7 + - - +
394A LEU 3.1 0.2 - - - -
395A ILE* 3.1 13.1 + - + -
396A HIS* 2.9 38.9 + - + -
406A PHE* 3.5 11.1 - + - -
432A GLN* 3.2 27.4 - - + +
436A LEU* 5.8 2.0 - - + -
514B GLY 5.1 0.4 - - - -
515B VAL* 5.6 1.6 - - + -
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Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLN 4.9 0.8 + - - -
390A ALA 5.3 0.4 - - - -
391A PHE 3.1 0.2 - - - -
392A TYR* 1.3 76.9 - - - +
394A LEU* 1.3 57.3 + - - +
396A HIS* 3.9 0.9 - - - +
397A GLN* 2.9 45.2 + - - +
357B MET 4.1 0.4 - - - +
358B GLU* 3.5 46.0 + - + +
361B GLY 3.0 23.7 - - - +
362B LYS* 3.4 13.4 - - - +
512B GLN* 3.2 20.8 + - - +
514B GLY* 2.8 39.1 - - - +
515B VAL* 3.9 9.2 - - + +
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Residues in contact with LEU 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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391A PHE 3.0 10.5 + - - +
393A GLN* 1.3 78.2 - - - +
395A ILE* 1.3 61.8 + - - +
398A GLY* 2.7 32.1 + - - -
400A LYS* 4.3 14.9 - - + +
402A ILE* 3.7 26.1 - - + +
472A ARG* 5.0 0.2 + - - -
357B MET* 3.7 34.7 + - + +
361B GLY* 3.7 26.7 - - - -
376B GLY 3.5 25.1 - - - +
377B PRO 3.6 17.5 - - - +
378B ILE* 4.2 7.0 - - + -
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.5 3.4 - - + -
380A TRP* 4.3 9.9 - - + -
391A PHE* 3.8 37.2 - - + +
392A TYR* 3.1 25.3 + - + +
394A LEU* 1.3 78.0 - - + +
396A HIS* 1.3 51.7 + - + +
400A LYS 4.8 3.8 - - - +
402A ILE* 4.1 29.8 - - + +
404A CYS* 4.2 30.7 - - - -
406A PHE* 6.2 0.2 - - + -
436A LEU* 3.7 23.8 - - + -
472A ARG* 2.8 34.1 + - + +
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Residues in contact with HIS 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 TYR* 2.9 36.2 + + + +
393A GLN 3.9 2.0 - - - +
395A ILE* 1.3 78.4 - - + +
397A GLN* 1.3 62.0 + - + +
432A GLN* 2.8 28.9 + - - -
435A ALA* 3.9 23.3 + - + +
436A LEU* 3.5 34.3 - - + +
468A PHE* 3.9 24.5 - + + +
469A GLU 5.0 5.5 + - - -
470A GLY 5.2 0.5 + - - -
472A ARG* 3.2 24.5 + - - +
514B GLY 3.6 25.4 - - - +
515B VAL* 5.5 0.9 - - - -
518B GLY 5.1 4.1 + - - -
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Residues in contact with GLN 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 GLN* 2.9 24.1 + - - +
396A HIS* 1.3 80.3 - - - +
398A GLY* 1.3 63.3 + - - +
465A HIS 3.1 19.2 + - - +
467A VAL 3.0 23.2 - - - +
468A PHE* 4.0 15.4 - - + -
472A ARG* 4.3 1.8 - - - +
361B GLY 3.6 3.8 - - - -
362B LYS* 3.2 27.9 - - - +
363B TYR* 3.2 29.9 - - + -
513B TRP* 3.7 5.3 - - - +
514B GLY* 3.1 37.9 - - - +
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Residues in contact with GLY 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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394A LEU* 2.7 30.6 + - - -
396A HIS 3.8 0.4 - - - -
397A GLN* 1.3 77.1 - - - +
399A THR* 1.3 65.2 + - - +
400A LYS 3.4 2.7 - - - -
472A ARG* 3.3 17.6 + - - +
361B GLY* 3.8 18.6 - - - -
362B LYS 4.0 2.0 - - - -
363B TYR* 4.3 5.4 - - - +
370B ARG* 4.9 4.0 + - - -
375B THR* 4.7 0.4 - - - -
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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