Contacts of the helix formed by residues 390 - 403 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350B ALA* 3.6 22.2 - - + -
352B ASP* 4.1 11.0 - - - +
353B VAL* 3.6 4.5 - - - -
386B ARG* 3.7 17.9 + - - +
388B LYS* 4.2 4.7 - - + +
389B ILE* 1.3 75.0 - - - +
391B MET* 1.3 60.6 + - - +
392B LYS* 4.0 11.2 + - - +
393B ASP* 2.6 59.2 + - - +
394B PHE* 3.3 8.1 + - - -
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Residues in contact with MET 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ASP* 3.0 36.5 + - - +
353B VAL* 3.4 6.3 - - - +
354B ASN* 3.6 34.8 - - + +
357B ILE* 3.5 37.5 - - + -
358B ILE* 3.7 26.0 - - + -
390B THR* 1.3 71.7 - - - +
392B LYS* 1.3 65.5 + - + +
394B PHE* 2.9 6.0 + - - +
395B GLU* 2.8 52.9 + - + +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ASP* 4.6 12.3 - - - +
390B THR* 4.1 13.0 - - - +
391B MET* 1.3 81.8 - - + +
393B ASP* 1.3 58.2 + - - +
395B GLU* 3.8 21.3 - - - +
396B GLU* 2.9 42.2 + - - +
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ALA* 3.8 23.6 - - - +
380B LEU* 3.5 16.4 - - + +
381B ALA* 4.0 3.8 - - - +
386B ARG* 3.1 33.3 + - - -
389B ILE* 3.5 11.0 - - + -
390B THR* 2.6 41.8 + - - +
392B LYS* 1.3 78.7 - - - +
394B PHE* 1.3 55.1 + - - +
396B GLU* 4.0 9.9 - - - +
397B ALA* 3.0 27.9 + - - +
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LEU* 5.2 2.2 - - + -
344B THR* 4.8 3.8 - - - -
349B LEU* 3.8 27.1 - - + -
353B VAL* 3.9 18.8 - - + -
355B LEU* 4.5 13.9 - - + -
358B ILE* 2.7 37.0 - - + -
373B LEU* 4.3 14.2 - - + +
374B VAL* 4.1 23.8 - - + -
377B ALA* 3.7 15.0 - - + -
389B ILE* 3.4 25.1 - - + -
390B THR 3.3 14.3 + - - -
391B MET* 2.9 4.7 + - - +
393B ASP* 1.3 74.3 - - - +
395B GLU* 1.3 68.1 + - - +
397B ALA* 2.9 15.7 + - - +
398B ILE* 3.0 15.8 + - - +
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ILE* 5.0 1.8 - - + -
361B ARG* 2.5 46.9 + - - +
391B MET* 2.8 46.3 + - + +
392B LYS* 3.8 21.6 - - - +
394B PHE* 1.3 79.6 - - - +
396B GLU* 1.3 62.3 + - + +
398B ILE* 3.3 23.0 + - - +
399B ASP* 3.8 7.3 + - - +
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LEU* 3.7 27.4 - - + +
383B ARG* 5.6 3.9 + - - -
392B LYS* 2.9 30.0 + - - +
393B ASP* 4.0 6.9 - - - +
395B GLU* 1.3 76.0 - - + +
397B ALA* 1.3 62.1 + - - +
399B ASP* 3.2 20.5 + - - +
400B ARG* 3.4 12.6 + - - +
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Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B LEU* 3.5 29.4 - - + +
376B GLU* 4.0 6.3 - - + +
377B ALA 3.8 12.1 - - - +
380B LEU* 4.2 5.6 - - + -
393B ASP 3.0 18.7 + - - +
394B PHE* 2.9 9.3 + - - +
396B GLU* 1.3 73.3 - - - +
398B ILE* 1.3 58.8 + - - +
400B ARG* 2.8 28.2 + - - +
401B VAL* 2.9 17.0 + - - +
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Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ILE* 4.4 10.5 - - + -
361B ARG* 4.1 26.9 - - + +
362B THR* 3.8 20.4 - - + -
365B PHE* 4.6 10.0 - - + -
373B LEU* 3.4 20.2 - - + +
394B PHE 3.0 15.8 + - - +
395B GLU* 3.3 15.3 - - - +
397B ALA* 1.3 76.8 - - - +
399B ASP* 1.3 68.4 + - - +
400B ARG 2.9 1.7 + - - -
401B VAL* 3.4 2.5 + - - +
402B ILE* 3.2 28.0 + - + +
411B LEU* 3.9 28.0 - - + -
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Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B GLU 3.8 7.9 + - - +
396B GLU* 3.2 14.6 + - - +
398B ILE* 1.3 83.2 - - - +
400B ARG* 1.3 60.6 + - - +
402B ILE* 3.8 18.0 - - - +
403B ALA* 3.7 16.8 + - - +
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Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLU* 5.5 8.3 + - - -
175A GLU* 4.0 21.0 + - - -
376B GLU* 3.6 26.8 + - + +
379B LEU* 6.0 2.2 - - - +
380B LEU* 4.2 27.8 - - - +
383B ARG* 4.7 13.5 - - - +
396B GLU* 3.4 7.7 + - - +
397B ALA* 2.8 13.7 + - - +
399B ASP* 1.3 77.1 - - - +
401B VAL* 1.3 68.8 + - - +
402B ILE 3.0 0.9 - - - -
403B ALA* 2.7 19.2 + - - +
404B GLY* 3.3 7.1 + - - -
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 4.1 23.8 - - + -
369B ASP* 4.1 21.8 - - - +
372B ASN* 3.8 20.9 - - + +
373B LEU* 3.6 37.5 - - + +
376B GLU* 3.9 9.8 - - + +
397B ALA 2.9 19.2 + - - +
398B ILE 4.0 2.7 - - - +
400B ARG* 1.3 71.5 - - - +
402B ILE* 1.3 68.0 + - - +
404B GLY* 3.1 9.2 + - - -
405B PRO 3.2 18.2 - - - +
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 4.6 8.1 - - + -
398B ILE 3.2 17.4 + - - +
399B ASP* 3.8 21.1 - - - +
400B ARG 2.9 0.4 + - - -
401B VAL* 1.3 81.0 - - - +
403B ALA* 1.3 59.8 - - + +
404B GLY 2.7 12.3 + - - -
405B PRO* 3.4 9.1 - - - +
410B LEU* 5.5 9.3 + - - +
411B LEU* 3.7 45.3 - - + +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B ASP 3.7 10.3 + - - +
400B ARG* 2.7 13.9 + - - +
402B ILE* 1.3 79.5 - - + +
404B GLY* 1.3 53.4 + - - -
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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