Contacts of the helix formed by residues 416 - 432 (chain A) in PDB entry 2JIF
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 ALA 416 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 4.8 3.8 + - - +
411A THR 3.3 15.3 - - - +
412A ILE* 3.2 18.8 + - + +
415A GLY* 1.3 77.8 - - - +
417A SER* 1.3 66.5 + - - +
418A ASN 3.3 0.4 - - - -
419A ILE* 2.9 20.9 + - + +
420A GLN* 3.1 6.6 + - - +
1433A FAD 3.3 42.1 + - - +
387C GLU 5.7 0.4 - - - +
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Residues in contact with SER 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LYS* 4.6 1.3 + - - +
372A TYR* 3.8 16.2 - - - -
375A SER* 4.2 3.5 + - - -
376A GLU* 2.7 29.8 + - - +
411A THR* 3.0 27.4 + - - +
416A ALA* 1.3 72.2 - - - +
418A ASN* 1.3 66.3 + - - +
420A GLN* 3.0 13.5 + - - +
421A LEU* 3.0 27.2 + - - +
387C GLU* 5.1 5.8 - - - -
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Residues in contact with ASN 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA 3.3 0.6 - - - -
417A SER* 1.3 79.2 - - - +
419A ILE* 1.3 58.0 + - - +
421A LEU* 3.2 6.2 + - - +
422A ASN* 2.9 35.3 + - - +
1433A FAD 3.0 58.1 + - + +
334B HIS* 3.5 19.1 + - + -
332C LEU* 4.0 20.6 - - - +
335C GLN* 3.0 30.8 + - - +
388C TRP* 6.0 0.4 - - - -
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER* 3.9 23.3 - - - +
294A ARG* 4.3 7.6 - - - +
415A GLY* 4.4 1.1 - - - -
416A ALA 2.9 21.0 + - - +
418A ASN* 1.3 72.1 - - - +
420A GLN* 1.3 64.5 + - - +
422A ASN* 3.3 10.2 + - + +
423A THR* 3.0 29.2 + - - +
1433A FAD 3.6 47.3 - - + +
1434A COS 3.4 46.0 - - - +
322C PHE* 4.7 6.1 - - + -
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Residues in contact with GLN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 3.2 26.1 + - - +
368A SER* 3.0 37.2 + - - +
371A LYS* 3.7 21.0 - - + +
372A TYR* 4.0 19.7 - - + -
414A GLU 3.0 18.4 + - - -
415A GLY* 3.0 22.3 + - - +
416A ALA 3.1 11.6 + - - +
417A SER* 3.0 10.9 + - - +
419A ILE* 1.3 78.1 - - - +
421A LEU* 1.3 57.0 + - - +
423A THR* 3.3 5.5 + - - -
424A ILE* 2.9 35.6 + - - +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A TYR* 3.7 47.6 - - + +
417A SER* 3.0 16.8 + - - +
418A ASN* 3.6 9.2 - - - +
420A GLN* 1.3 75.6 - - - +
422A ASN* 1.3 57.5 + - - +
424A ILE* 3.3 4.8 + - + -
425A ALA* 2.9 28.6 + - - +
334B HIS* 3.5 46.4 - - + +
337B ALA* 3.4 29.2 - - + +
338B HIS* 4.1 9.4 - - + +
335C GLN* 5.8 2.0 - - - +
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Residues in contact with ASN 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ASN 2.9 17.0 + - - -
419A ILE* 3.5 16.2 - - + +
421A LEU* 1.3 75.6 - - - +
423A THR* 1.3 61.4 - - - +
425A ALA* 3.4 7.2 + - - +
426A LYS* 3.0 32.5 + - + +
1433A FAD 3.3 33.7 + - - -
330B GLN* 3.3 13.6 + - - +
333B GLN* 4.1 8.5 - - - +
334B HIS* 2.7 27.9 + - - -
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Residues in contact with THR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 4.1 11.8 + - - +
364A ILE* 4.0 23.1 - - + +
365A LYS* 5.4 0.2 - - - -
368A SER* 3.4 22.7 - - - +
419A ILE* 3.0 18.6 + - - +
420A GLN* 3.5 7.4 - - - -
422A ASN* 1.3 74.0 - - - +
424A ILE* 1.3 66.1 + - - +
426A LYS* 3.2 17.8 + - - +
427A HIS* 3.2 27.3 + - + +
1434A COS 4.1 20.3 + - - +
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Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS* 4.0 12.7 - - + +
368A SER* 3.6 18.2 - - - +
369A MET* 3.7 52.9 - - + +
372A TYR* 4.7 3.4 - - + -
420A GLN 2.9 25.9 + - - +
421A LEU* 3.7 15.0 - - + +
423A THR* 1.3 75.4 - - - +
425A ALA* 1.3 61.7 + - - +
427A HIS* 3.2 5.5 + - - +
428A ILE* 3.0 27.9 + - + +
337B ALA* 3.6 25.4 - - + +
340B ALA* 4.5 0.4 - - + -
341B THR* 3.8 10.8 - - - +
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Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU 2.9 17.4 + - - +
422A ASN 3.6 2.2 - - - +
424A ILE* 1.3 77.4 - - - +
426A LYS* 1.3 62.0 + - - +
428A ILE* 3.2 8.2 + - - -
429A ASP 3.0 19.2 + - - -
327B PHE* 3.3 18.6 - - + -
333B GLN* 3.6 49.8 - - + +
336B VAL* 5.8 0.9 - - + -
337B ALA* 4.6 3.1 - - - +
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Residues in contact with LYS 426 (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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422A ASN* 3.0 22.3 + - + +
423A THR* 3.2 11.2 + - - +
425A ALA* 1.3 74.7 - - - +
427A HIS* 1.3 65.2 + - + +
429A ASP* 3.4 9.2 + - - +
430A ALA* 3.2 20.6 + - - +
1434A COS 3.9 31.0 - - + +
327B PHE* 5.4 0.4 - - - -
333B GLN* 5.9 1.3 - - - +
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Residues in contact with HIS 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ILE* 3.7 39.9 - - + +
365A LYS* 3.9 28.0 + - + +
423A THR* 3.2 32.3 + - + +
424A ILE 3.2 8.3 + - - +
426A LYS* 1.3 79.8 - - + +
428A ILE* 1.3 64.8 + - - +
430A ALA* 3.2 10.3 + - - +
431A GLU* 3.1 33.1 + - - +
1434A COS 5.5 2.0 + - - -
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Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS* 4.3 12.8 - - + +
424A ILE* 3.0 29.3 + - + +
425A ALA* 3.2 10.7 + - - +
427A HIS* 1.3 74.5 - - - +
429A ASP* 1.3 63.1 + - - +
431A GLU* 3.1 27.0 + - - +
432A TYR* 3.2 33.0 + - + +
309B PHE* 4.3 11.0 - - + -
313B ILE* 4.1 16.1 - - + +
327B PHE* 4.1 9.6 - - + -
336B VAL* 4.1 15.0 - - + -
337B ALA* 5.5 0.4 - - - -
340B ALA* 3.9 23.1 - - + -
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Residues in contact with ASP 429 (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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425A ALA 3.0 13.3 + - - +
426A LYS* 3.4 13.2 - - - +
427A HIS 3.2 0.2 - - - -
428A ILE* 1.3 77.5 - - - +
430A ALA* 1.3 59.4 + - - +
431A GLU 3.4 0.2 + - - -
432A TYR* 3.2 4.0 + - - +
317B LYS* 2.7 56.2 + - - +
325B ARG* 2.9 38.7 + - - -
327B PHE* 3.6 15.6 - - + -
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Residues in contact with ALA 430 (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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426A LYS 3.2 8.8 + - - +
427A HIS* 3.2 14.9 + - - +
429A ASP* 1.3 78.3 - - - +
431A GLU* 1.3 62.0 + - + +
432A TYR* 3.7 2.9 + - - +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS* 3.1 40.4 + - - +
427A HIS* 3.3 22.6 + - - +
428A ILE* 3.1 18.6 + - - +
430A ALA* 1.3 79.4 - - + +
432A TYR* 1.3 73.9 + - + +
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Residues in contact with TYR 432 (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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428A ILE* 3.2 41.4 + - + +
429A ASP 3.2 2.4 - - - +
430A ALA 3.4 3.1 - - - +
431A GLU* 1.3 93.0 - - + +
306B GLN* 3.7 4.7 + - - -
309B PHE* 3.6 20.8 - + - -
310B ASP* 2.5 56.4 + - + -
313B ILE* 3.7 26.5 - - + -
314B PRO* 4.2 21.7 - - + +
317B LYS* 2.7 35.7 + - + +
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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