Contacts of the helix formed by residues 390 - 402 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350F ALA* 3.5 22.4 - - + -
352F ASP* 4.2 7.4 - - - +
353F VAL* 3.3 9.0 - - - -
386F ARG* 3.4 23.8 + - - +
388F LYS* 4.5 1.3 - - + +
389F ILE* 1.3 71.2 - - - +
391F MET* 1.3 66.4 + - - +
392F LYS* 3.7 18.8 - - + +
393F ASP* 2.5 37.9 + - - +
394F PHE* 3.2 17.5 - - - -
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Residues in contact with MET 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F ASP* 3.3 32.8 + - - +
353F VAL* 3.3 11.0 - - - +
354F ASN 4.2 20.9 - - - +
357F ILE* 3.1 45.3 - - + -
358F ILE* 4.6 12.6 - - + -
390F THR* 1.3 72.1 - - - +
392F LYS* 1.3 65.9 + - - +
394F PHE* 3.1 5.9 + - - +
395F GLU* 2.4 82.7 + - + +
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Residues in contact with LYS 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F ASP* 5.4 1.5 + - - +
384F GLU* 5.0 11.5 + - - -
390F THR* 3.7 13.6 + - - +
391F MET* 1.3 78.4 - - - +
393F ASP* 1.3 62.8 + - - +
395F GLU* 3.3 12.2 + - - +
396F GLU* 3.0 49.5 + - - +
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Residues in contact with ASP 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377F ALA* 3.8 13.7 - - - +
380F LEU* 3.4 33.2 - - + +
381F ALA* 3.6 3.0 + - - -
384F GLU* 5.6 2.4 - - - +
386F ARG* 2.3 36.1 + - - -
389F ILE* 3.7 17.2 - - + -
390F THR* 2.5 29.5 + - - +
391F MET 3.2 0.6 - - - -
392F LYS* 1.3 80.0 - - - +
394F PHE* 1.3 57.5 + - - +
396F GLU* 3.4 4.2 + - - +
397F ALA* 2.8 28.7 + - - +
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Residues in contact with PHE 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F LEU* 5.0 8.7 - - + -
344F THR* 4.9 3.4 - - - -
349F LEU* 4.9 12.8 - - + -
353F VAL* 3.8 31.4 - - + -
355F LEU* 5.7 2.5 - - + -
358F ILE* 4.1 30.3 - - + -
373F LEU* 4.3 16.6 - - + +
374F VAL* 4.2 26.2 - - + -
377F ALA* 3.9 18.6 - - + -
389F ILE* 3.6 24.9 - - + -
390F THR 3.2 18.8 - - - -
391F MET* 3.1 8.6 + - - +
393F ASP* 1.3 77.0 - - - +
395F GLU* 1.3 58.5 - - - +
397F ALA* 2.6 27.0 + - - +
398F ILE* 3.1 17.9 + - - +
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Residues in contact with GLU 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357F ILE* 5.5 0.4 - - + -
358F ILE* 6.0 1.1 - - + -
391F MET* 2.4 70.8 + - + +
392F LYS* 3.3 17.1 + - - +
394F PHE* 1.3 77.1 - - - +
396F GLU* 1.3 61.0 + - + +
397F ALA 3.5 0.2 + - - -
398F ILE* 3.7 17.5 + - + +
399F ASP* 3.1 22.6 - - - +
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Residues in contact with GLU 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380F LEU* 3.8 22.3 - - + +
392F LYS* 3.0 43.1 + - - +
393F ASP* 3.8 5.3 - - - +
395F GLU* 1.3 74.8 - - + +
397F ALA* 1.3 63.9 + - - +
398F ILE 3.4 0.2 - - - -
399F ASP* 3.7 16.0 + - - +
400F ARG* 3.6 18.4 + - - +
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Residues in contact with ALA 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F LEU* 3.6 29.8 - - + +
376F GLU* 4.0 8.2 - - + +
377F ALA* 3.9 12.1 - - - +
380F LEU* 4.9 1.3 - - - -
393F ASP 2.8 13.6 + - - +
394F PHE* 2.6 22.3 + - - +
396F GLU* 1.3 70.5 - - - +
398F ILE* 1.3 55.7 + - - +
400F ARG* 2.7 37.9 + - - +
401F VAL* 3.2 8.1 + - - +
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Residues in contact with ILE 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358F ILE* 4.3 13.7 - - + -
361F ARG* 4.1 29.4 - - + +
362F THR* 4.2 15.0 - - + -
365F PHE* 4.1 19.1 - - + -
373F LEU* 3.4 29.4 - - + -
394F PHE 3.1 10.4 + - - +
395F GLU* 3.9 14.8 - - + +
396F GLU 3.4 0.4 - - - -
397F ALA* 1.3 76.1 - - - +
399F ASP* 1.3 69.7 + - - +
401F VAL* 3.3 16.3 + - - +
402F ILE* 3.6 13.6 + - + +
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Residues in contact with ASP 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395F GLU 3.1 20.9 - - - +
396F GLU* 3.7 15.9 - - - +
398F ILE* 1.3 81.3 - - - +
400F ARG* 1.3 62.3 + - - +
401F VAL 3.3 1.0 + - - -
402F ILE* 3.5 27.8 + - + +
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Residues in contact with ARG 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376F GLU* 3.4 36.6 + - + +
379F LEU* 5.7 2.2 - - - +
380F LEU* 4.2 24.8 - - - +
383F ARG* 3.9 20.2 - - - +
396F GLU 3.6 9.8 + - - +
397F ALA* 2.7 25.4 + - - +
399F ASP* 1.3 74.0 - - - +
401F VAL* 1.3 60.7 + - - +
402F ILE 5.0 0.5 - - - -
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Residues in contact with VAL 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365F PHE* 3.9 20.2 - - + -
369F ASP* 4.9 15.0 - - + +
372F ASN* 4.5 18.6 - - - +
373F LEU* 3.4 41.1 - - + +
376F GLU* 5.0 3.6 - - + -
397F ALA 3.6 8.3 - - - +
398F ILE 3.6 5.2 - - - +
399F ASP 3.2 0.6 - - - -
400F ARG* 1.3 79.6 - - - +
402F ILE* 1.3 72.8 + - + +
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Residues in contact with ILE 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365F PHE* 4.4 19.7 - - + -
398F ILE* 3.6 14.3 + - + +
399F ASP* 3.5 26.5 - - + +
400F ARG 5.0 0.7 - - - -
401F VAL* 1.3 82.6 - - + +
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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