Contacts of the helix formed by residues 400 - 413 (chain B) in PDB entry 2A72
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 ASP 400 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A HIS* 3.1 36.9 + - + +
399B LEU* 1.3 75.5 - - - +
401B SER* 1.3 58.9 + - - +
402B LYS* 3.6 12.4 - - - +
403B SER* 2.7 42.7 + - - -
404B TYR* 2.9 27.2 + - - +
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Residues in contact with SER 401 (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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399B LEU 3.8 1.2 + - - -
400B ASP* 1.3 74.1 - - - +
402B LYS* 1.3 58.5 + - - +
404B TYR* 3.3 6.0 + - - +
405B ASP* 2.8 45.0 + - - +
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Residues in contact with LYS 402 (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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400B ASP* 3.3 11.1 + - - +
401B SER* 1.3 81.2 + - - +
403B SER* 1.3 61.3 + - - +
405B ASP* 3.3 7.5 + - - +
406B LYS* 3.1 53.1 + - - +
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Residues in contact with SER 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASP* 4.0 33.8 - - - +
422A ALA* 3.9 5.2 + - - -
425A HIS* 4.4 0.4 - - - +
399B LEU* 3.4 17.9 - - - +
400B ASP* 2.7 29.5 + - - -
402B LYS* 1.3 76.3 - - - +
404B TYR* 1.3 62.5 + - - +
406B LYS* 3.5 7.1 + - - +
407B THR* 2.5 34.9 + - - -
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Residues in contact with TYR 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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385B TRP* 4.3 6.7 - + - -
389B LEU* 2.7 55.9 + - + +
397B ILE 4.2 9.2 + - - -
398B ASN* 5.1 0.7 - - - -
399B LEU* 3.6 40.1 - - + +
400B ASP 2.9 15.3 + - - +
401B SER* 3.7 7.2 - - - +
403B SER* 1.3 76.5 + - - +
405B ASP* 1.3 65.6 + - - +
407B THR* 3.1 4.2 + - - -
408B THR* 2.9 45.8 + - + +
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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 SER* 2.8 33.9 + - - +
402B LYS* 3.6 7.5 + - - +
404B TYR* 1.3 75.4 - - - +
406B LYS* 1.3 63.5 + - + +
408B THR* 2.9 24.2 + - - +
409B HIS* 3.0 22.8 - - + +
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Residues in contact with LYS 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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421A ASP* 3.3 34.2 + - + +
402B LYS* 3.1 40.6 + - - +
403B SER* 3.9 5.1 - - - +
405B ASP* 1.3 77.5 - - + +
407B THR* 1.3 58.9 + - - +
409B HIS* 3.3 5.6 + - - +
410B ASN* 2.9 41.0 + - - +
420B GLU* 3.6 34.5 + - - +
421B ASP* 4.2 16.8 - - - +
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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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418A THR 4.2 14.4 + - - +
419A PHE* 3.6 38.0 - - + -
421A ASP* 5.8 0.5 - - - +
422A ALA* 3.7 17.7 + - + +
385B TRP* 4.5 5.4 - - + -
389B LEU* 4.1 13.5 - - + -
399B LEU* 4.2 2.3 - - - +
403B SER 2.5 23.3 + - - -
404B TYR* 3.5 6.7 - - - -
406B LYS* 1.3 77.8 - - - +
408B THR* 1.3 64.1 + - - +
410B ASN* 3.1 3.6 + - - +
411B VAL* 2.9 30.9 + - + +
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Residues in contact with THR 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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385B TRP* 3.7 32.5 - - + -
404B TYR* 2.9 31.7 + - + +
405B ASP* 2.9 15.3 + - - +
407B THR* 1.3 74.3 - - - +
409B HIS* 1.3 68.9 + - - +
411B VAL* 3.2 1.8 + - - +
412B LYS* 2.9 41.6 + - - +
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Residues in contact with HIS 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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405B ASP* 3.0 28.4 + - + +
406B LYS* 3.6 9.9 - - - +
408B THR* 1.3 86.8 + - - +
410B ASN* 1.3 59.1 + - - +
412B LYS* 4.9 1.1 - - - -
413B GLU* 2.8 40.6 + - + +
417B TYR* 3.2 51.3 + + + -
420B GLU* 5.5 2.0 - - - +
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Residues in contact with ASN 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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417A TYR 4.5 3.0 + - - -
418A THR* 3.1 47.5 + - + +
381B VAL* 5.6 0.7 - - - +
406B LYS* 2.9 25.9 + - - +
407B THR 3.1 7.2 + - - +
409B HIS* 1.3 77.0 - - - +
411B VAL* 1.3 60.5 + - - +
413B GLU 4.5 3.3 - - - +
414B PRO* 3.3 26.1 - - - +
415B GLY 5.8 1.2 + - - +
417B TYR* 3.9 24.3 + - - +
420B GLU* 5.2 1.7 - - - +
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Residues in contact with VAL 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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418A THR* 3.8 19.1 - - + -
419A PHE* 4.3 6.7 - - + -
381B VAL* 4.2 8.7 - - + -
382B GLN* 3.1 42.8 + - - +
385B TRP* 3.6 53.4 - - + -
407B THR 2.9 18.4 + - - +
408B THR* 3.8 4.0 - - - +
410B ASN* 1.3 74.8 - - - +
412B LYS* 1.3 70.5 + - + +
414B PRO* 3.6 11.4 - - - +
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Residues in contact with LYS 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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374A ILE* 5.3 1.2 - - - +
382B GLN* 4.4 6.7 + - - -
385B TRP* 3.7 35.8 - - + +
386B GLN* 5.7 1.0 - - - +
408B THR* 2.9 26.2 + - - +
409B HIS* 4.9 0.7 - - - -
411B VAL* 1.3 87.0 - - + +
413B GLU* 1.3 77.5 + - + +
414B PRO* 3.4 5.8 - - - +
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Residues in contact with GLU 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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374A ILE* 4.0 8.1 - - - +
409B HIS* 2.8 24.3 + - - +
410B ASN* 4.0 2.1 - - - +
412B LYS* 1.3 94.7 - - + +
414B PRO* 1.3 68.0 - - - +
415B GLY 3.2 0.7 + - - -
416B ARG* 2.8 62.0 + - + +
417B TYR* 4.0 16.2 + - + +
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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