Contacts of the helix formed by residues 409 - 417 (chain B) in PDB entry 1JB0
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 ASN 409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B PRO* 3.3 19.1 - - - +
323B GLN* 3.2 27.9 + - - +
325B ILE* 2.8 22.5 - - + +
406B ASN* 2.6 46.9 + - - +
407B LYS 3.4 2.0 + - - -
408B GLY* 1.3 79.3 - - - +
410B VAL* 1.3 53.1 + - - +
411B LEU* 2.9 17.0 + - - +
412B ASP 3.0 8.7 + - - -
413B ARG* 2.8 33.3 + - - +
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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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320B MET* 4.0 14.4 - - + -
321B PRO* 2.9 23.3 + - + +
322B HIS* 3.9 15.9 - - + +
325B ILE* 3.9 16.8 - - + -
409B ASN* 1.3 71.4 - - - +
411B LEU* 1.3 57.7 + - - +
413B ARG* 3.3 8.1 + - - +
414B VAL* 2.9 35.0 + - - +
1220B CLA 3.6 55.4 - - + +
1227B CLA 3.9 11.8 - - + +
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Residues in contact with LEU 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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325B ILE* 4.7 6.3 - - + -
328B THR* 3.9 13.9 - - + -
335B PHE* 4.5 7.4 - - + -
396B PHE* 3.8 17.7 - - + -
397B LEU* 4.2 21.3 - - + -
401B TYR* 3.6 27.6 - - + -
406B ASN* 4.0 4.5 - - - +
409B ASN* 2.9 11.9 + - - +
410B VAL* 1.3 80.9 - - - +
412B ASP* 1.3 63.7 + - - +
414B VAL* 3.3 8.8 + - + +
415B LEU* 3.1 37.6 + - + +
1220B CLA 4.7 16.4 - - + -
4009B BCR 5.9 3.8 - - + -
4010B BCR 4.5 11.7 - - + -
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Residues in contact with ASP 412 (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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401B TYR* 3.8 18.0 + - - +
406B ASN 3.2 22.0 - - - +
407B LYS* 3.6 11.4 - - - +
408B GLY* 2.8 23.8 + - - +
409B ASN* 3.0 7.7 + - - +
411B LEU* 1.3 76.5 - - - +
413B ARG* 1.3 67.2 + - - +
415B LEU* 3.2 6.1 + - - +
416B GLN* 2.6 56.0 + - - +
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Residues in contact with ARG 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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315B GLU* 2.8 29.5 + - - -
320B MET* 3.7 4.4 - - - +
321B PRO* 3.2 33.9 - - - +
408B GLY* 3.9 11.3 + - - +
409B ASN 2.8 16.3 + - - +
410B VAL* 3.5 12.3 - - - +
412B ASP* 1.3 78.6 - - - +
414B VAL* 1.3 55.1 + - - +
416B GLN* 3.1 19.3 + - + +
417B HIS* 2.8 26.5 + - - -
1227B CLA 3.0 49.7 + - + +
5004B LHG 3.4 17.6 + - - -
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Residues in contact with VAL 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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410B VAL 2.9 18.5 + - - +
411B LEU* 3.6 10.3 - - + +
412B ASP 3.3 0.2 - - - -
413B ARG* 1.3 74.7 - - - +
415B LEU* 1.3 66.4 + - + +
417B HIS* 3.1 21.1 + - - -
418B LYS* 3.2 10.7 + - - -
421B ILE* 3.7 17.7 - - + +
545B LEU* 4.5 11.7 - - + -
1220B CLA 3.6 23.3 - - + -
1227B CLA 3.8 22.2 - - + -
4009B BCR 3.4 33.0 - - + -
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Residues in contact with LEU 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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397B LEU* 4.4 16.8 - - + -
401B TYR* 3.4 45.8 - - + +
411B LEU* 3.1 23.3 + - + +
412B ASP* 3.5 6.7 - - - +
414B VAL* 1.3 77.0 - - + +
416B GLN* 1.3 63.7 + - - +
417B HIS 3.2 0.9 + - - -
418B LYS* 3.2 21.2 + - + +
545B LEU* 3.9 32.3 - - + +
548B ARG* 5.2 2.0 - - - -
141F ARG* 3.4 44.0 - - + +
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Residues in contact with GLN 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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412B ASP* 2.6 46.7 + - - +
413B ARG* 3.1 12.7 + - + +
415B LEU* 1.3 78.3 - - - +
417B HIS* 1.3 57.7 + - - +
418B LYS 3.6 0.4 - - - -
1227B CLA 4.8 7.6 - - - -
141F ARG* 3.0 54.9 + - - +
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Residues in contact with HIS 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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706A TRP* 6.2 2.2 - - + -
413B ARG 2.8 28.6 + - - -
414B VAL* 3.1 21.2 + - - -
416B GLN* 1.3 77.7 - - - +
418B LYS* 1.3 64.8 + - - +
419B GLU* 3.3 4.7 - - - -
420B ALA* 3.0 23.2 + - + -
421B ILE* 3.2 26.9 + - + +
1227B CLA 2.4 91.4 + + + -
1228B CLA 5.9 1.6 - - - -
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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