Contacts of the helix formed by residues 416 - 431 (chain B) in PDB entry 1JS6
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 SER 416 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B ARG* 3.4 7.6 - - - +
415B GLY* 1.3 71.3 - - - -
417B ASP* 1.3 64.6 + - - +
418B GLY* 3.4 5.2 + - - -
419B LEU* 3.1 33.5 + - - +
420B ASN* 3.0 17.7 + - - -
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Residues in contact with ASP 417 (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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412B ARG* 3.0 18.6 + - - +
416B SER* 1.3 74.9 - - - +
418B GLY* 1.3 57.5 + - - +
420B ASN* 3.3 2.7 + - - +
421B GLU* 2.8 39.7 + - - +
442B GLY 3.8 12.0 - - - +
443B GLN* 3.5 7.8 - - - +
444B PHE* 2.8 41.0 + - + +
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Residues in contact with GLY 418 (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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416B SER* 3.1 7.5 + - - -
417B ASP* 1.3 80.4 - - - +
419B LEU* 1.3 61.4 + - - +
421B GLU* 3.4 12.5 + - - +
422B ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 419 (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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413B LEU* 3.3 42.0 - - + +
414B LYS 4.1 13.5 - - - +
415B GLY* 4.7 2.2 - - - -
416B SER* 3.1 25.5 + - - +
418B GLY* 1.3 77.2 - - - +
420B ASN* 1.3 57.4 + - - +
422B ALA* 3.2 8.3 - - + +
423B LEU* 3.1 20.6 + - - +
474B LEU* 3.4 32.6 - - + +
475B LEU* 4.3 16.6 - - + -
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Residues in contact with ASN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 3.3 31.4 - - - +
413B LEU* 2.6 51.1 + - - +
416B SER 3.0 22.6 + - - +
417B ASP 3.8 4.0 - - - +
419B LEU* 1.3 74.0 - - - +
421B GLU* 1.3 65.1 + - - +
422B ALA 2.9 2.0 - - - -
423B LEU* 3.1 8.8 + - - +
424B LEU* 3.0 19.6 + - - +
444B PHE* 3.6 27.4 - - + +
446B LEU* 4.0 11.6 - - + +
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Residues in contact with GLU 421 (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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417B ASP* 2.8 29.1 + - - +
418B GLY* 3.7 12.1 + - - +
420B ASN* 1.3 71.6 - - - +
422B ALA* 1.3 57.2 + - - +
424B LEU* 3.5 3.3 + - - +
425B GLU* 3.0 42.2 + - + +
444B PHE* 3.5 38.1 - - + -
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLY 3.1 12.8 + - - +
419B LEU* 3.2 13.7 - - + +
420B ASN 2.9 0.2 - - - -
421B GLU* 1.3 76.5 - - - +
423B LEU* 1.3 66.7 + - - +
425B GLU* 3.1 13.3 + - - +
426B ARG* 3.0 27.5 + - + +
474B LEU* 3.9 22.2 - - + -
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Residues in contact with LEU 423 (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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398B PHE* 4.2 13.5 - - + -
411B PHE* 4.8 2.5 - - + -
413B LEU* 4.1 24.2 - - + +
419B LEU 3.1 8.6 + - - +
420B ASN* 3.1 12.8 + - - +
422B ALA* 1.3 74.1 - - - +
424B LEU* 1.3 59.2 + - - +
426B ARG* 3.1 5.8 + - + -
427B ILE* 2.9 45.7 + - + +
446B LEU* 4.3 14.8 - - + -
467B ILE* 4.0 10.1 - - + +
470B LEU* 4.0 15.5 - - + +
471B ALA* 3.6 36.3 - - + +
474B LEU* 3.7 14.5 - - + +
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Residues in contact with LEU 424 (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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420B ASN 3.0 11.3 + - - +
421B GLU 3.6 9.0 - - - +
423B LEU* 1.3 78.3 - - - +
425B GLU* 1.3 63.6 + - + +
427B ILE* 3.2 10.0 + - + +
428B ASN* 3.1 41.2 + - - +
435B LEU* 4.0 28.7 - - + +
436B VAL 4.8 0.7 - - - +
437B PRO* 3.3 43.7 - - + -
444B PHE* 3.5 12.6 - - + -
446B LEU* 4.4 15.9 - - + +
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Residues in contact with GLU 425 (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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421B GLU* 3.0 29.9 + - + +
422B ALA* 3.1 11.5 + - - +
424B LEU* 1.3 76.0 - - + +
426B ARG* 1.3 64.2 + - + +
428B ASN* 3.6 5.0 + - - +
429B SER* 2.8 31.9 + - - +
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Residues in contact with ARG 426 (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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422B ALA* 3.0 16.4 + - + +
423B LEU* 3.6 8.7 - - - +
425B GLU* 1.3 80.2 - - + +
427B ILE* 1.3 60.5 + - - +
429B SER* 4.1 4.9 - - - -
430B ALA* 3.3 22.3 + - - +
470B LEU* 3.7 26.3 - - + +
473B GLU* 4.1 18.5 + - - +
474B LEU* 3.6 55.3 + - - +
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Residues in contact with ILE 427 (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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423B LEU* 2.9 41.2 + - + +
424B LEU* 3.2 8.0 + - + +
426B ARG* 1.3 77.3 - - - +
428B ASN* 1.3 65.0 + - - +
430B ALA* 3.3 16.3 + - - +
431B ARG 3.6 4.5 + - - -
432B LYS 4.5 0.2 + - - -
433B ILE* 3.7 39.4 - - + +
435B LEU* 4.1 17.0 - - + -
446B LEU* 4.0 19.1 - - + -
466B HIS* 4.4 7.2 - - + +
467B ILE* 4.0 20.0 - - + -
470B LEU* 3.6 18.8 - - + -
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Residues in contact with ASN 428 (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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30B TYR* 6.2 1.1 - - + -
424B LEU* 3.1 38.7 + - - +
425B GLU* 4.1 4.6 - - - +
427B ILE* 1.3 77.8 - - - +
429B SER* 1.3 64.9 + - - +
431B ARG* 2.8 42.9 + - - +
433B ILE 4.5 3.9 - - - +
434B HIS* 3.5 28.1 + - - -
435B LEU 3.6 17.8 + - - +
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Residues in contact with SER 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLU* 2.8 24.9 + - - +
426B ARG* 4.1 6.1 - - - -
428B ASN* 1.3 77.5 - - - +
430B ALA* 1.3 61.9 + - - +
431B ARG* 3.3 16.0 + - - +
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Residues in contact with ALA 430 (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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426B ARG 3.3 12.5 + - - +
427B ILE 3.3 12.0 + - - +
428B ASN 3.1 1.0 - - - -
429B SER* 1.3 77.2 - - - +
431B ARG* 1.3 68.4 + - - +
432B LYS* 3.3 8.2 + - + +
466B HIS* 3.7 26.7 - - + +
470B LEU* 4.4 7.0 - - + -
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Residues in contact with ARG 431 (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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28B GLN* 3.0 54.1 - - - +
29B VAL* 5.1 2.8 + - - -
30B TYR* 3.6 35.8 + - - +
31B PRO 3.3 17.2 + - - -
32B ASP* 2.4 33.1 + - - +
427B ILE 3.6 2.8 + - - -
428B ASN* 2.8 37.4 + - - +
429B SER* 3.1 16.9 - - - +
430B ALA* 1.3 78.8 - - - +
432B LYS* 1.3 62.5 + - - +
433B ILE 3.8 3.4 - - - -
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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