Contacts of the helix formed by residues 411 - 422 (chain F) in PDB entry 2JG7
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 411 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319D GLU* 4.5 16.4 - - - +
323D LYS* 6.1 4.3 - - - +
409F PHE* 3.3 13.2 - - - -
410F LYS* 1.3 94.0 - - + +
412F GLU* 1.3 63.4 + - - +
413F GLU* 4.0 11.1 + - - +
414F GLU* 3.1 43.0 + - - +
415F ALA 3.3 1.2 + - - -
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Residues in contact with GLU 412 (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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277F PHE* 3.8 21.6 - - + -
410F LYS 4.0 1.0 + - - -
411F THR* 1.3 69.5 - - - +
413F GLU* 1.3 67.8 + - - +
415F ALA* 3.2 2.6 + - - +
416F PHE* 3.0 56.5 + - + -
437F ARG* 2.8 30.5 + - - +
440F ARG* 2.7 47.5 + - - +
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Residues in contact with GLU 413 (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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326D LYS* 4.1 22.7 + - - -
411F THR* 3.3 10.2 + - - +
412F GLU* 1.3 78.8 - - - +
414F GLU* 1.3 57.5 + - - +
416F PHE* 3.6 6.2 + - - +
417F ALA* 3.0 33.8 + - + +
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Residues in contact with GLU 414 (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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409F PHE* 4.0 2.8 - - + -
410F LYS* 3.0 33.1 + - - +
411F THR* 3.1 28.8 + - - +
413F GLU* 1.3 75.5 - - - +
415F ALA* 1.3 61.1 + - - +
417F ALA* 3.2 4.6 + - - +
418F TRP* 2.8 67.8 + - + +
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Residues in contact with ALA 415 (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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275F ILE* 3.6 36.9 - - + +
277F PHE* 4.5 3.8 - - + -
308F MET* 4.0 10.0 - - - +
409F PHE* 3.8 26.0 - - + -
411F THR 3.3 0.8 + - - -
412F GLU 3.2 7.8 + - - +
414F GLU* 1.3 79.1 - - - +
416F PHE* 1.3 58.9 + - - +
418F TRP* 3.2 5.6 + - - +
419F ASN* 2.9 30.5 + - - +
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Residues in contact with PHE 416 (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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275F ILE* 4.4 2.7 - - + -
277F PHE* 3.8 20.2 - + - -
412F GLU* 3.0 48.6 + - + +
413F GLU* 3.8 6.5 - - - +
415F ALA* 1.3 80.3 - - + +
417F ALA* 1.3 62.5 + - - +
419F ASN* 3.3 6.8 + - - +
420F ASN* 3.1 33.8 + - - +
430F ILE* 4.1 7.0 - - + -
437F ARG* 4.3 8.1 - - + -
440F ARG* 4.3 4.7 - - + -
441F TRP* 3.5 60.1 - + + -
445F LYS 3.7 22.4 - - - +
446F GLY* 4.1 4.7 - - - +
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Residues in contact with ALA 417 (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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413F GLU* 3.0 21.6 + - + +
414F GLU* 3.6 4.9 - - - +
416F PHE* 1.3 75.3 - - - +
418F TRP* 1.3 62.9 + - + +
420F ASN* 3.2 8.2 + - - +
421F GLU* 2.8 31.8 + - - +
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Residues in contact with TRP 418 (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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306F ARG* 2.7 25.0 + - - +
308F MET* 3.8 24.5 - - + -
390F HIS* 3.5 60.5 + + + -
407F LEU* 4.2 12.3 - - + -
408F LYS 3.3 28.9 - - - -
409F PHE* 3.6 22.7 - + + -
414F GLU* 2.8 54.4 + - + +
415F ALA* 3.7 3.8 - - - +
417F ALA* 1.3 75.2 - - + +
419F ASN* 1.3 61.0 + - - +
421F GLU* 3.1 26.6 - - - +
422F VAL 4.3 0.2 + - - -
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Residues in contact with ASN 419 (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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273F ALA* 3.5 21.1 + - - +
275F ILE* 4.0 12.1 - - + +
306F ARG* 3.0 25.9 + - - +
308F MET* 3.7 5.0 - - + +
415F ALA 2.9 13.4 + - - +
416F PHE* 3.3 10.1 - - - +
418F TRP* 1.3 77.1 - - - +
420F ASN* 1.3 79.5 + - - +
422F VAL* 3.9 6.1 - - - +
427F SER 4.7 0.3 - - - +
428F SER* 3.5 15.2 - - - -
441F TRP* 3.6 14.9 - - + -
447F SER* 3.4 21.6 + - - +
448F ASP* 4.5 1.7 - - - +
449F CYS* 4.2 10.0 - - - -
471F LYS* 4.6 0.9 + - - -
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Residues in contact with ASN 420 (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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416F PHE* 3.1 21.2 + - - +
417F ALA* 3.8 7.4 - - - +
419F ASN* 1.3 96.6 + - - +
421F GLU* 1.3 59.9 + - - +
422F VAL 3.2 3.8 - - - +
445F LYS 5.3 0.8 + - - -
446F GLY 3.1 23.0 + - - -
447F SER* 3.7 1.0 - - - -
448F ASP* 3.1 39.0 + - - +
471F LYS* 2.9 20.3 + - - +
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Residues in contact with GLU 421 (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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306F ARG* 5.1 0.9 + - - -
390F HIS* 2.8 47.2 + - - +
391F ASP* 4.6 1.8 - - - +
396F HIS* 2.9 36.2 + - + +
417F ALA 2.8 12.7 + - - +
418F TRP* 3.1 31.5 + - - +
420F ASN* 1.3 77.7 - - - +
422F VAL* 1.3 62.8 + - + +
423F GLN* 5.5 1.6 - - - +
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Residues in contact with VAL 422 (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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271F ASN* 4.0 14.6 - - + +
306F ARG* 3.5 44.2 - - - +
396F HIS* 3.9 37.0 - - + +
419F ASN 3.9 5.6 - - - +
420F ASN 3.3 1.0 - - - +
421F GLU* 1.3 81.1 - - + +
423F GLN* 1.3 60.3 + - - +
424F GLN* 3.4 33.7 - - + +
471F LYS* 2.8 25.3 + - - +
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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