Contacts of the helix formed by residues 399 - 411 (chain B) in PDB entry 4Z2C
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 THR 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A THR* 5.0 1.1 - - - -
432A LEU* 5.8 2.0 - - + -
397B SER* 4.1 1.2 - - - -
398B GLU* 1.3 87.5 - - + +
400B ASP* 1.3 66.1 + - - +
401B ALA* 3.0 14.3 + - - +
402B GLU* 3.1 31.8 + - - +
403B ALA* 3.3 5.4 + - - +
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Residues in contact with ASP 400 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A ARG* 3.4 48.3 + - - +
430A THR* 3.4 24.7 + - - +
399B THR* 1.3 73.8 - - - +
401B ALA* 1.3 56.2 + - - +
403B ALA* 3.4 10.0 - - - +
404B GLN* 2.9 30.8 + - - +
422B LEU* 3.8 8.1 - - + +
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Residues in contact with ALA 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 THR* 3.0 9.5 + - - +
400B ASP* 1.3 78.3 - - - +
402B GLU* 1.3 58.2 + - - +
404B GLN* 3.2 11.8 + - - +
405B ALA* 2.9 28.0 + - - +
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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
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396B ALA 4.6 1.2 - - - +
397B SER* 3.4 11.6 - - - -
398B GLU* 2.5 36.0 + - - +
399B THR* 3.1 26.0 + - - +
401B ALA* 1.3 76.4 - - - +
403B ALA* 1.3 60.1 + - - +
405B ALA* 3.8 7.6 - - - +
406B GLU* 2.9 30.5 + - - +
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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
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430A THR* 5.3 4.0 - - + -
393B ILE* 4.2 3.2 - - + +
394B ILE* 4.7 10.3 - - + +
397B SER* 3.6 24.5 - - - -
399B THR 3.3 0.9 + - - +
400B ASP* 3.4 17.3 - - - +
401B ALA 3.1 0.4 - - - -
402B GLU* 1.3 80.2 - - - +
404B GLN* 1.3 59.6 + - - +
406B GLU* 3.2 5.6 + - - +
407B LEU* 2.9 37.3 + - + +
422B LEU* 4.3 16.4 - - + -
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Residues in contact with GLN 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 ASP 2.9 14.1 + - - +
401B ALA* 3.2 12.1 + - - +
403B ALA* 1.3 76.1 - - - +
405B ALA* 1.3 57.3 + - - +
407B LEU* 3.3 3.6 + - - +
408B MET* 2.9 42.2 + - - +
415B GLU* 3.5 29.3 + - - +
418B SER* 3.2 30.4 + - - +
419B GLN* 3.3 24.2 + - - +
422B LEU* 3.9 14.5 - - + +
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Residues in contact with ALA 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 ALA 2.9 15.3 + - - +
402B GLU* 3.9 8.1 - - - +
404B GLN* 1.3 77.2 - - - +
406B GLU* 1.3 57.8 + - - +
408B MET* 3.3 10.5 + - - +
409B SER* 2.9 29.6 + - - -
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Residues in contact with GLU 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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393B ILE* 3.6 29.9 - - + +
402B GLU 2.9 19.7 + - - +
403B ALA* 3.2 0.6 + - - +
405B ALA* 1.3 74.5 - - - +
407B LEU* 1.3 59.7 + - - +
409B SER* 3.8 4.9 - - - -
410B LYS* 2.9 32.2 + - - +
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390B VAL* 4.3 16.8 - - + +
393B ILE* 4.0 20.9 - - + -
394B ILE* 5.9 2.7 - - + -
403B ALA* 2.9 19.4 + - + +
404B GLN* 3.7 4.7 - - - +
406B GLU* 1.3 75.2 - - - +
408B MET* 1.3 58.3 + - - +
410B LYS* 4.7 0.4 - - - -
411B PHE* 2.9 65.3 + - + +
412B LYS 4.0 0.3 + - - -
413B LEU* 4.2 8.8 - - + +
418B SER* 4.5 15.0 - - - +
421B ILE* 4.6 12.8 - - + -
422B LEU* 3.9 32.5 - - + -
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Residues in contact with MET 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 GLN* 2.9 35.0 + - - +
405B ALA* 3.6 8.5 - - - +
407B LEU* 1.3 76.3 - - - +
409B SER* 1.3 60.3 + - - +
412B LYS* 3.4 6.9 - - - -
413B LEU* 3.3 43.8 + - - +
414B SER* 3.6 4.0 - - - +
415B GLU* 3.8 22.2 - - + +
418B SER* 3.4 25.6 - - - +
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Residues in contact with SER 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 ALA 2.9 18.5 + - - -
406B GLU* 3.8 6.3 - - - -
407B LEU 3.2 0.2 - - - -
408B MET* 1.3 78.1 - - - +
410B LYS* 1.3 63.9 + - - +
412B LYS* 4.1 4.0 + - - +
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Residues in contact with LYS 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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389B GLU* 4.9 8.1 - - - +
393B ILE* 5.3 10.5 - - + -
406B GLU 2.9 17.6 + - - +
407B LEU* 4.7 0.2 - - - -
409B SER* 1.3 79.5 - - - +
411B PHE* 1.3 81.8 + - + +
412B LYS* 3.4 1.4 + - - +
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Residues in contact with PHE 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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382B ILE* 4.1 30.9 - - + +
383B ALA* 6.2 3.6 - - - -
386B HIS* 3.5 39.0 - + + -
389B GLU* 3.7 37.7 - - + -
390B VAL* 4.2 12.3 - - + -
393B ILE* 5.0 2.5 - - + -
407B LEU* 2.9 44.4 + - + +
410B LYS* 1.3 86.6 - - + +
412B LYS* 1.3 71.5 + - - +
413B LEU* 3.5 22.4 - - + +
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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