Contacts of the helix formed by residues 401 - 411 (chain B) in PDB entry 2JI8
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 401 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400B GLY* 1.3 72.1 - - - -
402B ASN* 1.3 67.6 + - - +
403B ALA 3.2 0.4 - - - +
404B LEU* 3.2 2.8 + - - +
405B ASP* 3.0 32.8 + - - -
483B TYR* 3.6 31.0 - - + -
553B SER 4.1 7.2 - - - -
554B GLY* 4.3 1.6 - - - +
1563B TPP 3.1 25.7 + - - +
1566B FYN 4.0 17.3 - - - -
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Residues in contact with ASN 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 3.4 21.9 - - + -
401B ALA* 1.3 80.2 - - - +
403B ALA* 1.3 56.8 + - - +
405B ASP* 4.7 1.6 - - - +
406B ASN* 2.9 47.4 + - - +
483B TYR* 3.2 17.8 + - - +
549B ALA 4.7 0.7 - - - +
550B GLY* 3.4 9.9 - - - -
551B VAL* 3.0 48.3 + - - +
554B GLY* 4.2 7.4 - - - -
1563B TPP 2.7 24.5 + - - +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 3.8 8.5 - - + -
381B LEU* 5.2 0.4 - - - -
398B ASN* 3.0 9.1 + - - -
399B GLU 4.1 3.6 - - - +
400B GLY* 4.6 0.2 - - - -
401B ALA 3.2 0.6 - - - -
402B ASN* 1.3 76.4 - - - +
404B LEU* 1.3 60.6 + - - +
406B ASN* 5.2 0.2 - - - -
407B THR* 2.6 30.6 + - - -
449B VAL* 4.1 1.9 - - + +
450B GLU 4.4 0.9 - - - -
451B GLY* 3.7 29.4 - - - +
477B MET* 3.9 21.1 - - + -
1563B TPP 3.2 14.6 + - - +
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Residues in contact with LEU 404 (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 ASN* 3.2 44.7 - - - +
399B GLU* 4.0 3.4 - - - -
400B GLY* 3.3 20.9 - - - +
401B ALA 3.2 3.2 + - - +
403B ALA* 1.3 77.5 - - - +
405B ASP* 1.3 74.3 + - - +
406B ASN 3.3 0.2 - - - -
407B THR 3.3 1.0 + - - -
408B ARG* 3.0 32.0 + - - +
419B ARG* 3.7 11.7 - - - +
421B ASP* 3.9 11.4 - - + +
422B SER* 4.3 9.4 - - - +
1566B FYN 3.2 47.1 - - + +
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Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ALA 3.0 14.0 + - - +
402B ASN* 4.4 2.9 - - - +
404B LEU* 1.3 91.3 - - - +
406B ASN* 1.3 64.3 + - - +
408B ARG* 3.0 30.0 + - - +
409B MET* 3.3 22.5 + - - +
553B SER 4.1 3.5 - - - +
554B GLY* 3.6 5.7 - - - -
555B ARG* 2.6 56.3 + - + +
556B ILE 4.2 1.2 + - - -
1566B FYN 3.6 12.1 + - - +
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Residues in contact with ASN 406 (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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377B TYR* 3.6 27.8 - - + +
378B SER* 5.6 1.6 + - - -
381B LEU* 3.7 18.4 - - + -
402B ASN* 2.9 38.9 + - - +
405B ASP* 1.3 76.3 - - - +
407B THR* 1.3 58.6 + - - +
409B MET* 3.5 21.8 + - - +
410B ILE* 2.9 39.6 + - + +
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Residues in contact with THR 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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381B LEU* 3.4 17.0 - - - +
396B LEU* 3.8 19.1 - - + -
398B ASN* 3.2 28.3 - - - +
403B ALA 2.6 19.1 + - - -
404B LEU 3.3 1.2 + - - -
406B ASN* 1.3 74.8 - - - +
408B ARG* 1.3 60.7 + - - +
410B ILE* 4.7 0.2 - - - -
411B VAL* 3.0 50.3 + - + +
419B ARG* 3.8 2.1 + - - +
449B VAL* 3.4 18.9 - - + +
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Residues in contact with ARG 408 (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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248B GLY* 3.9 22.4 - - - +
251B LYS* 2.8 47.9 + - + +
404B LEU* 3.0 25.9 + - - +
405B ASP* 3.0 39.7 + - - +
406B ASN 3.3 0.2 - - - -
407B THR* 1.3 76.4 - - - +
409B MET* 1.3 59.7 + - - +
411B VAL 4.3 0.2 - - - +
419B ARG* 3.4 25.6 - - - +
421B ASP* 5.2 2.0 + - - -
555B ARG* 4.0 0.4 - - - +
1566B FYN 3.0 79.1 + - - +
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Residues in contact with MET 409 (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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251B LYS* 5.0 1.6 + - - -
362B LEU* 3.5 30.5 - - + -
365B LYS* 6.2 1.3 - - + -
378B SER* 5.6 2.0 - - - +
405B ASP 3.3 13.3 + - - +
406B ASN* 3.6 21.5 - - - +
408B ARG* 1.3 82.6 - - - +
410B ILE* 1.3 73.4 + - + +
412B ASP* 4.7 2.4 - - - +
555B ARG* 5.9 4.3 - - - -
1566B FYN 3.1 91.0 + - + +
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Residues in contact with ILE 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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362B LEU* 4.1 17.3 - - + +
366B MET* 3.8 18.6 - - + -
377B TYR 3.8 22.9 - - - +
378B SER* 3.9 18.6 - - - +
381B LEU* 3.4 35.4 - - + +
385B ARG* 3.4 21.8 + - + +
406B ASN* 2.9 30.7 + - + +
407B THR 4.6 0.2 - - - +
409B MET* 1.3 96.4 - - + +
411B VAL* 1.3 58.6 + - - +
412B ASP* 3.2 10.8 + - - +
1566B FYN 5.3 0.9 + - - -
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LYS* 3.6 21.2 - - - -
381B LEU* 4.2 10.3 - - + +
384B VAL* 4.0 22.9 - - + +
385B ARG* 4.1 12.3 - - - +
388B MET* 3.9 32.5 - - + -
396B LEU* 4.2 16.3 - - + +
407B THR* 3.0 42.3 + - + +
409B MET 3.8 0.2 - - - -
410B ILE* 1.3 70.2 - - + +
412B ASP* 1.3 65.1 + - - +
413B MET* 3.5 8.3 + - - +
419B ARG* 5.8 0.3 + - - -
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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