Contacts of the helix formed by residues 406 - 420 (chain B) in PDB entry 1L0N
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 406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B VAL* 5.2 0.2 - - - -
361B LYS* 5.0 0.7 - - - -
404B ALA 3.1 4.4 + - - +
405B VAL* 1.3 81.4 - - - +
407B ASP* 1.3 66.9 + - - +
408B ALA* 3.2 9.6 - - + +
409B ASP* 2.7 31.4 + - - +
410B VAL* 3.3 10.4 + - - +
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Residues in contact with ASP 407 (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 LEU* 4.0 2.1 - - + +
353B SER 2.9 22.1 - - - +
354B ASN* 3.4 25.6 + - - +
357B VAL* 3.5 35.0 - - + +
358B GLN* 5.9 0.3 + - - -
361B LYS* 5.2 1.0 + - - -
406B ALA* 1.3 72.9 - - - +
408B ALA* 1.3 58.8 + - - +
410B VAL* 3.1 7.3 + - - +
411B ILE* 2.9 37.7 + - + +
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Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ALA* 3.2 6.9 - - + +
407B ASP* 1.3 76.7 - - - +
409B ASP* 1.3 61.8 + - - +
411B ILE* 3.8 13.2 - - + +
412B ASN* 2.8 45.4 + - - +
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Residues in contact with ASP 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ALA* 3.8 25.5 - - + +
404B ALA 3.8 3.8 - - - +
405B VAL* 3.6 8.6 - - + -
406B ALA* 2.7 37.5 + - - +
408B ALA* 1.3 79.2 - - - +
410B VAL* 1.3 58.1 + - - +
412B ASN* 3.2 9.9 + - - +
413B ALA 2.9 24.8 + - - -
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Residues in contact with VAL 410 (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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271B ALA* 4.5 8.1 - - - +
274B VAL* 3.7 29.4 - - + -
275B LEU* 4.0 30.7 - - + +
278B VAL* 4.4 8.3 - - + -
347B ILE* 4.9 0.9 - - + -
352B LEU* 3.7 20.0 - - + -
357B VAL* 4.2 9.9 - - + -
405B VAL* 3.8 9.4 - - + -
406B ALA 3.6 12.3 - - - +
407B ASP 3.1 7.1 + - - +
409B ASP* 1.3 76.7 - - - +
411B ILE* 1.3 65.8 + - - +
413B ALA* 3.1 12.0 + - - +
414B ALA* 3.1 11.3 + - - +
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Residues in contact with ILE 411 (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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347B ILE* 3.7 22.9 - - - +
348B ALA* 3.9 13.2 - - - +
350B GLY* 4.4 17.7 - - - +
352B LEU* 3.8 25.1 - - + +
407B ASP* 2.9 34.0 + - + +
408B ALA* 3.8 11.0 - - + +
410B VAL* 1.3 74.3 - - - +
412B ASN* 1.4 67.1 + - - +
414B ALA* 2.9 17.5 + - - +
415B LYS* 2.9 21.3 + - - +
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Residues in contact with ASN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ALA* 2.8 37.4 + - - +
409B ASP* 3.6 9.5 + - - +
411B ILE* 1.4 73.9 - - - +
413B ALA* 1.4 55.2 + - - +
415B LYS* 3.2 28.3 + - - +
416B LYS* 2.8 28.8 + - - +
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Residues in contact with ALA 413 (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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268B GLU* 5.7 2.9 - - + -
271B ALA* 4.5 4.0 - - + -
272B PHE* 3.6 56.2 - - + +
275B LEU* 3.8 8.5 - - + -
409B ASP 2.9 16.0 + - - +
410B VAL* 3.1 7.8 + - - +
412B ASN* 1.4 69.8 - - - +
414B ALA* 1.3 66.5 + - - +
416B LYS* 3.0 6.7 + - - +
417B PHE* 2.9 19.1 + - - +
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Residues in contact with ALA 414 (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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275B LEU* 3.5 15.6 - - + +
344B VAL* 4.3 9.4 - - + +
347B ILE* 3.9 22.4 - - + -
348B ALA* 3.7 20.6 - - + +
410B VAL 3.1 6.4 + - - +
411B ILE 2.9 9.9 + - - +
413B ALA* 1.3 75.8 - - - +
415B LYS* 1.3 58.4 + - - +
417B PHE* 2.9 8.6 + - - +
418B VAL* 2.9 30.8 + - - +
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Residues in contact with LYS 415 (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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348B ALA* 3.6 31.3 - - + +
411B ILE* 2.9 17.8 + - - +
412B ASN* 3.4 29.1 + - - +
413B ALA 3.1 0.2 - - - -
414B ALA* 1.3 78.3 - - - +
416B LYS* 1.3 61.6 + - - +
418B VAL* 3.6 3.7 + - + +
419B SER* 3.1 26.7 + - - +
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Residues in contact with LYS 416 (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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259B ALA* 4.7 1.9 - - - +
260B GLU* 4.2 16.2 - - - +
261B SER 4.1 15.7 + - - -
268B GLU* 2.7 36.8 + - - +
272B PHE* 4.2 10.5 - - + -
412B ASN 2.8 13.5 + - - +
413B ALA* 3.0 10.7 + - - +
415B LYS* 1.3 76.5 - - - +
417B PHE* 1.3 65.4 + - - +
419B SER* 4.0 3.4 + - - -
420B GLY* 3.3 19.2 + - - -
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Residues in contact with PHE 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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257B LEU* 4.3 10.8 - - + -
258B VAL* 3.9 7.0 - - - -
259B ALA* 3.7 23.6 - - + +
260B GLU 5.6 0.7 - - - -
272B PHE* 5.0 2.0 - - + -
322B PHE* 3.5 37.0 - + + -
323B GLY* 3.7 18.8 - - - -
324B PHE* 4.2 15.5 - + - -
341B TYR* 3.5 32.1 - + - -
344B VAL* 3.5 31.0 - - + -
413B ALA 2.9 12.0 + - - +
414B ALA* 2.9 7.4 + - - +
416B LYS* 1.3 80.5 - - - +
418B VAL* 1.3 60.9 + - - +
419B SER 3.1 0.9 + - - -
420B GLY 3.4 2.6 + - - -
422B LYS* 2.9 32.1 + - - -
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B TYR* 3.3 12.8 + - + +
344B VAL* 3.9 18.4 - - + -
345B LYS* 3.9 33.7 - - + +
348B ALA* 3.8 21.3 - - + -
414B ALA 2.9 18.6 + - - +
415B LYS* 4.1 5.8 - - + +
416B LYS 3.4 0.2 - - - -
417B PHE* 1.3 81.8 - - + +
419B SER* 1.3 56.0 + - - +
422B LYS* 2.5 19.0 + - - +
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Residues in contact with SER 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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415B LYS* 3.1 18.0 + - - +
416B LYS* 4.0 4.0 + - - -
417B PHE 3.2 0.6 - - - -
418B VAL* 1.3 80.2 - - - +
420B GLY* 1.3 63.7 + - - +
421B ARG 3.9 0.7 + - - -
422B LYS* 4.0 0.7 - - - -
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Residues in contact with GLY 420 (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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259B ALA* 4.7 6.7 - - - -
260B GLU 5.7 1.6 - - - -
416B LYS 3.3 16.7 + - - -
417B PHE 3.4 3.7 + - - -
419B SER* 1.3 78.7 - - - +
421B ARG* 1.3 68.5 + - - -
422B LYS* 3.1 23.7 + - - +
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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