Contacts of the helix formed by residues 390 - 402 (chain A) in PDB entry 2CEA
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 THR 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A ALA* 3.9 12.8 - - + -
352A ASP* 3.7 15.9 - - - +
353A VAL* 3.6 4.9 - - - -
386A ARG* 3.9 19.7 + - - +
388A LYS* 3.9 6.3 - - + +
389A ILE* 1.3 78.6 - - - +
391A MET* 1.3 64.3 + - - +
392A LYS* 3.4 15.6 + - - +
393A ASP* 3.1 31.2 + - - +
394A PHE* 3.4 10.7 + - - -
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Residues in contact with MET 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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352A ASP* 3.0 32.8 + - + +
353A VAL* 3.7 4.7 - - - +
354A ASN* 3.3 38.8 - - + +
357A ILE* 3.6 35.9 - - + -
358A ILE* 3.9 18.4 - - + -
361A ARG* 4.7 0.2 - - - +
390A THR* 1.3 73.4 - - - +
392A LYS* 1.3 60.9 + - - +
394A PHE* 3.2 4.3 + - - +
395A GLU* 2.9 58.8 + - + +
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Residues in contact with LYS 392 (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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352A ASP* 5.2 0.6 + - - -
390A THR* 3.3 8.7 + - - +
391A MET* 1.3 78.7 - - - +
393A ASP* 1.3 58.9 + - - +
395A GLU* 3.6 17.6 - - - +
396A GLU* 2.9 45.4 + - + +
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Residues in contact with ASP 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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377A ALA* 4.0 11.2 - - - +
380A LEU* 3.4 26.9 - - + +
381A ALA* 3.7 12.0 - - - +
386A ARG* 2.8 45.3 + - - -
389A ILE* 3.8 12.8 - - + -
390A THR* 3.1 25.6 + - - +
391A MET 3.1 0.6 - - - -
392A LYS* 1.3 80.7 - - - +
394A PHE* 1.3 57.8 + - - +
396A GLU* 3.4 2.6 + - - +
397A ALA* 2.9 29.0 + - - +
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Residues in contact with PHE 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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340A LEU* 4.9 1.6 - - + -
344A THR* 4.2 17.3 - - - -
349A LEU* 4.3 13.2 - - + -
353A VAL* 4.3 13.2 - - + -
355A LEU* 4.7 8.3 - - + -
358A ILE* 3.1 38.4 - - + -
373A LEU* 3.8 18.2 - - + +
374A VAL* 3.9 32.8 - - + -
377A ALA* 4.0 8.5 - - + -
389A ILE* 3.5 26.7 - - + -
390A THR 3.5 13.0 - - - -
391A MET* 3.2 6.6 + - - +
393A ASP* 1.3 76.0 - - - +
395A GLU* 1.3 67.3 + - - +
397A ALA* 3.1 14.7 + - - +
398A ILE* 3.1 20.7 + - - +
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Residues in contact with GLU 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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358A ILE* 5.8 0.4 - - + -
361A ARG* 2.6 39.6 + - - +
391A MET* 2.9 47.1 + - + +
392A LYS* 3.6 27.9 + - - +
394A PHE* 1.3 77.4 - - - +
396A GLU* 1.3 63.3 + - + +
398A ILE* 3.3 16.4 + - + +
399A ASP* 3.0 16.1 - - - +
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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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380A LEU* 3.6 27.9 - - + +
384A GLU* 6.1 0.7 - - - -
392A LYS* 2.9 39.2 + - + +
393A ASP* 5.0 2.1 - - - +
395A GLU* 1.3 73.6 - - + +
397A ALA* 1.3 64.0 + - - +
398A ILE 3.3 0.5 + - - -
399A ASP* 3.4 22.8 + - - +
400A ARG* 3.6 10.3 + - - +
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Residues in contact with ALA 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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373A LEU* 3.3 35.2 - - + +
376A GLU* 4.0 5.8 - - + +
377A ALA* 3.8 12.3 - - - +
380A LEU* 4.7 1.5 - - + +
393A ASP 2.9 18.8 + - - +
394A PHE* 3.1 2.6 + - - +
396A GLU* 1.3 78.5 - - - +
398A ILE* 1.3 54.1 + - - +
400A ARG* 2.6 40.8 + - - +
401A VAL* 3.1 9.8 + - - +
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Residues in contact with ILE 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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358A ILE* 4.2 21.3 - - + -
361A ARG* 4.2 42.6 - - + +
362A THR* 4.1 8.1 - - + -
365A PHE* 4.6 3.9 - - + -
373A LEU* 3.6 24.0 - - + -
394A PHE 3.1 20.6 + - - +
395A GLU* 3.7 15.7 - - - +
396A GLU 3.2 0.6 - - - -
397A ALA* 1.3 76.3 - - - +
399A ASP* 1.3 67.3 + - - +
400A ARG 3.2 0.5 + - - -
401A VAL* 3.4 5.2 + - - +
402A ILE* 3.2 39.6 + - + +
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Residues in contact with ASP 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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361A ARG* 5.8 0.9 + - - -
395A GLU 3.0 16.7 - - - +
396A GLU* 3.5 14.5 - - - +
398A ILE* 1.3 74.4 - - - +
400A ARG* 1.3 63.8 + - + +
402A ILE* 3.2 25.4 + - - +
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Residues in contact with ARG 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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376A GLU* 3.7 36.3 + - + +
380A LEU* 4.6 13.4 - - - +
383A ARG* 3.6 35.0 - - - +
396A GLU* 3.7 13.0 - - - +
397A ALA* 2.6 27.3 + - - +
399A ASP* 1.3 70.5 - - + +
401A VAL* 1.3 58.7 + - - +
402A ILE 3.0 9.5 + - - -
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Residues in contact with VAL 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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365A PHE* 4.1 17.3 - - + -
369A ASP* 3.8 28.7 - - + +
372A ASN* 4.0 15.7 - - + +
373A LEU* 3.5 33.9 - - + +
376A GLU* 4.3 13.5 - - + -
397A ALA 3.1 13.8 + - - +
398A ILE* 3.4 2.6 + - - +
400A ARG* 1.3 73.4 - - - +
402A ILE* 1.3 61.1 + - - +
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Residues in contact with ILE 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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361A ARG 5.7 1.6 - - - +
365A PHE* 4.1 20.4 - - + -
398A ILE* 3.2 32.0 + - + +
399A ASP* 3.5 22.7 - - - +
400A ARG 3.0 6.2 - - - +
401A VAL* 1.3 83.4 - - - +
411A LEU* 6.2 5.2 - - + -
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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