Contacts of the helix formed by residues 399 - 415 (chain B) in PDB entry 2H5G
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 GLN 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B LEU* 2.9 28.0 + - + +
398B ASP* 1.3 81.4 - - + +
400B ARG* 1.3 64.2 + - - +
401B ASP 3.2 3.7 + - - -
402B GLU* 3.2 37.6 + - + +
403B ILE* 3.0 24.1 + - + +
515B ILE* 5.3 2.8 - - + +
519B LEU* 3.9 32.6 - - + +
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Residues in contact with ARG 400 (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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396B LEU 3.5 11.5 + - - +
397B THR* 3.0 21.1 + - - +
398B ASP 3.3 2.0 - - - +
399B GLN* 1.3 75.6 - - - +
401B ASP* 1.3 64.9 + - - +
403B ILE* 3.2 6.3 + - - +
404B LEU* 2.9 49.0 + - + +
430B THR* 3.4 30.3 - - - +
433B LEU* 3.8 16.8 - - + -
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Residues in contact with ASP 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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398B ASP 4.9 1.5 + - - -
399B GLN 3.2 0.8 + - - -
400B ARG* 1.3 85.3 - - - +
402B GLU* 1.3 67.1 + - - +
404B LEU* 3.4 9.9 + - - +
405B LEU* 3.0 32.5 + - + +
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Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASP 3.9 4.5 - - - +
399B GLN* 3.2 64.0 + - + +
401B ASP* 1.3 82.1 + - - +
403B ILE* 1.3 63.1 + - - +
405B LEU* 3.4 11.9 + - + +
406B ALA* 3.0 25.5 + - - +
515B ILE* 3.8 17.0 - - + +
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Residues in contact with ILE 403 (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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396B LEU* 3.6 40.6 - - + +
399B GLN* 3.0 17.5 + - + +
400B ARG* 3.5 6.5 - - - +
402B GLU* 1.3 75.7 - - - +
404B LEU* 1.3 57.6 + - + +
406B ALA* 3.3 4.3 + - - +
407B ASN* 2.9 28.2 + - - +
428B LEU* 3.8 25.6 - - + -
433B LEU* 3.8 19.5 - - + -
512B SER* 5.5 0.6 - - - -
515B ILE* 4.0 16.9 - - + +
516B LEU* 4.1 12.8 - - + -
519B LEU* 3.7 30.5 - - + -
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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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400B ARG* 2.9 42.1 + - + +
401B ASP* 3.7 10.3 - - - +
403B ILE* 1.3 74.6 - - - +
405B LEU* 1.3 52.6 + - - +
407B ASN* 3.5 4.4 + - - +
408B LYS* 2.8 33.8 + - - +
428B LEU* 3.4 31.0 - - + +
429B SER* 4.3 6.1 - - - -
430B THR* 4.3 10.8 - - - +
433B LEU* 3.8 19.3 - - + -
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Residues in contact with LEU 405 (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 ASP* 3.0 18.9 + - + +
402B GLU* 3.5 11.4 - - + +
404B LEU* 1.3 75.6 - - - +
406B ALA* 1.3 64.0 + - - +
408B LYS* 3.3 9.5 + - + +
409B LYS* 3.1 48.6 + - + +
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Residues in contact with ALA 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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402B GLU 3.0 16.2 + - - +
403B ILE 3.5 4.5 - - - +
405B LEU* 1.3 77.1 - - - +
407B ASN* 1.3 61.7 + - - +
409B LYS* 3.4 8.5 + - - +
410B ASP* 3.3 10.6 + - - +
511B HIS* 3.2 48.3 - - + +
512B SER* 4.1 1.3 - - - +
515B ILE* 3.8 16.8 - - + -
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Residues in contact with ASN 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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403B ILE 2.9 16.2 + - - +
404B LEU* 3.7 7.4 - - - +
406B ALA* 1.3 74.5 - - - +
408B LYS* 1.3 58.2 + - - +
410B ASP* 3.1 4.2 + - - +
411B LEU* 2.9 50.1 + - - +
426B LEU* 2.8 29.2 + - - +
427B SER* 4.2 0.2 - - - -
428B LEU* 2.8 48.5 + - + +
484B PRO* 3.9 1.0 - - - +
512B SER* 2.9 27.1 + - - +
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Residues in contact with LYS 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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404B LEU 2.8 21.8 + - - +
405B LEU* 3.4 10.8 - - + +
407B ASN* 1.3 74.5 + - - +
409B LYS* 1.3 57.5 + - + +
411B LEU* 3.4 11.8 + - - +
412B GLU* 2.9 55.5 + - + +
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Residues in contact with LYS 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 LEU* 3.1 32.7 + - + +
406B ALA* 3.5 12.1 - - - +
407B ASN 3.2 0.4 - - - -
408B LYS* 1.3 73.5 - - + +
410B ASP* 1.3 59.6 + - - +
412B GLU* 3.4 12.6 + - - +
413B GLU* 3.0 38.4 + - - +
511B HIS* 3.8 33.8 + - + +
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Residues in contact with ASP 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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406B ALA 3.3 0.8 + - - -
407B ASN 3.1 7.7 + - - +
409B LYS* 1.3 78.4 - - - +
411B LEU* 1.3 57.9 + - - +
413B GLU* 3.3 6.8 + - - +
414B ALA* 2.9 30.3 + - - +
426B LEU* 3.8 13.7 - - + +
507B LYS 4.8 0.7 - - - +
508B GLU 3.4 23.5 - - - +
509B ALA* 3.4 5.2 - - - +
510B ALA* 3.7 2.4 + - - +
511B HIS* 3.0 35.9 + - - -
512B SER* 2.6 39.9 + - - +
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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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407B ASN* 2.9 40.1 + - - +
408B LYS* 3.7 9.2 - - + +
410B ASP* 1.3 73.1 - - - +
412B GLU* 1.3 60.4 + - + +
414B ALA* 3.3 3.9 + - - +
415B GLU* 2.9 31.4 + - - +
423B LEU* 4.0 21.0 - - + +
426B LEU* 3.9 20.2 - - + -
427B SER* 3.8 28.7 - - - +
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Residues in contact with GLU 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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408B LYS* 2.9 44.1 + - + +
409B LYS* 3.6 10.8 - - - +
410B ASP 3.3 0.2 - - - -
411B LEU* 1.3 78.1 - - + +
413B GLU* 1.3 63.7 + - + +
415B GLU* 3.4 20.9 - - - +
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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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409B LYS* 3.0 24.4 + - - +
410B ASP* 3.3 5.9 + - - +
412B GLU* 1.3 78.4 - - + +
414B ALA* 1.3 57.8 + - - +
415B GLU 3.5 0.2 - - - -
417B ARG* 2.9 36.1 + - - +
511B HIS* 3.5 29.6 + - - -
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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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410B ASP 2.9 17.4 + - - +
411B LEU 3.7 4.3 - - - +
412B GLU 3.2 0.2 - - - -
413B GLU* 1.3 78.8 - - - +
415B GLU* 1.3 65.3 + - - +
416B GLY 3.2 0.7 + - - -
417B ARG* 2.9 3.9 + - - +
418B LEU* 2.9 48.3 + - + +
423B LEU* 4.3 10.0 - - + +
426B LEU* 3.7 20.4 - - + -
508B GLU* 5.4 3.4 - - + +
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Residues in contact with GLU 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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411B LEU 2.9 13.5 + - - +
412B GLU* 3.4 19.8 - - - +
413B GLU 3.5 0.2 - - - -
414B ALA* 1.3 74.0 - - - +
416B GLY* 1.3 63.7 + - - +
417B ARG* 3.3 15.4 + - - +
423B LEU* 4.8 10.9 - - - +
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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