Contacts of the helix formed by residues 399 - 412 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A SER* 3.8 2.8 - - - +
398A GLU* 1.3 81.3 - - - +
400A ASP* 1.3 65.3 + - + +
401A ALA* 3.7 20.9 - - + +
402A GLU* 3.2 33.3 + - - +
403A ALA* 3.5 8.5 + - - +
430B THR* 5.1 0.9 - - - +
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Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A GLU 4.0 0.9 + - - -
399A THR* 1.3 76.5 - - - +
401A ALA* 1.3 60.9 + - - +
403A ALA* 3.3 4.6 + - - +
404A GLN* 2.9 30.1 + - - +
422A LEU* 4.1 6.8 - - + +
427B ARG* 3.0 65.0 + - - +
430B THR* 4.0 11.6 - - - +
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A THR* 3.3 14.8 - - + +
400A ASP* 1.3 79.8 - - - +
402A GLU* 1.3 58.2 + - - +
404A GLN* 3.5 7.5 + - - +
405A ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ALA 4.5 2.2 - - - +
397A SER* 3.2 10.3 - - - -
398A GLU* 2.4 36.4 + - - +
399A THR* 3.2 30.5 + - - +
401A ALA* 1.3 76.3 - - - +
403A ALA* 1.3 60.1 + - - +
405A ALA* 3.8 6.9 - - - +
406A GLU* 2.9 37.3 + - + +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ILE* 4.3 3.6 - - - +
394A ILE* 4.6 10.8 - - + +
397A SER* 3.6 24.0 - - - -
399A THR 3.5 5.8 + - - +
400A ASP* 3.3 13.7 + - - +
401A ALA 3.3 0.2 - - - -
402A GLU* 1.3 79.0 - - - +
404A GLN* 1.3 59.8 + - - +
406A GLU* 3.4 4.0 + - - +
407A LEU* 2.9 37.9 + - + +
422A LEU* 4.2 16.8 - - + -
430B THR* 5.3 2.2 - - + -
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Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ASP 2.9 17.6 + - - +
401A ALA* 3.7 7.4 - - - +
403A ALA* 1.3 77.4 - - - +
405A ALA* 1.3 55.8 + - - +
407A LEU* 3.3 6.3 + - - +
408A MET* 2.9 42.3 + - - +
415A GLU* 4.0 23.2 - - - +
418A SER* 3.2 23.6 - - - +
419A GLN* 3.8 21.7 - - - +
422A LEU* 3.7 17.6 - - + +
427B ARG* 4.6 3.1 + - - -
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ALA 2.9 19.0 + - - +
402A GLU* 3.8 9.0 - - - +
404A GLN* 1.3 78.6 - - - +
406A GLU* 1.3 58.8 + - + +
408A MET* 3.5 9.4 + - - +
409A SER* 2.9 29.5 + - - -
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Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ILE* 3.6 24.8 - - + +
402A GLU* 2.9 21.7 + - + +
403A ALA* 3.9 0.4 - - - +
405A ALA* 1.3 75.9 - - + +
407A LEU* 1.3 59.9 + - - +
409A SER* 4.2 12.0 - - - -
410A LYS* 2.9 35.2 + - - +
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Residues in contact with LEU 407 (chain A).
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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390A VAL* 4.2 18.8 - - + +
393A ILE* 4.2 16.6 - - + -
394A ILE* 5.8 4.5 - - + +
403A ALA* 2.9 23.2 + - + +
404A GLN* 3.6 4.7 - - - +
406A GLU* 1.3 76.9 - - - +
408A MET* 1.3 56.9 + - - +
410A LYS* 4.7 0.2 - - - -
411A PHE* 2.9 64.9 + - + +
413A LEU* 4.4 6.3 - - + +
418A SER* 4.4 13.2 - - - +
421A ILE* 4.3 22.0 - - + -
422A LEU* 4.0 31.4 - - + -
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Residues in contact with MET 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A GLN* 2.9 31.2 + - - +
405A ALA* 3.7 7.4 - - - +
407A LEU* 1.3 77.2 - - - +
409A SER* 1.3 61.1 + - - +
412A LYS* 3.0 20.8 + - - -
413A LEU* 3.2 30.0 + - - +
414A SER* 3.4 16.6 - - - +
415A GLU* 3.7 32.3 - - + +
418A SER* 3.4 10.5 - - - +
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ALA 2.9 19.0 + - - -
406A GLU* 3.9 17.7 - - - -
407A LEU 3.3 0.2 - - - -
408A MET* 1.3 77.1 - - - +
410A LYS* 1.3 62.9 + - - +
412A LYS* 4.0 3.8 + - - +
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Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ILE* 4.0 21.1 - - + -
406A GLU* 2.9 21.5 + - - +
407A LEU 4.0 1.1 - - - +
409A SER* 1.3 80.2 - - - +
411A PHE* 1.3 68.9 + - + +
412A LYS* 3.1 6.3 + - - +
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Residues in contact with PHE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ILE* 4.1 21.5 - - + +
383A ALA* 5.8 3.8 - - + -
386A HIS* 3.2 50.7 - + + -
389A GLU* 3.9 21.3 - - + -
390A VAL* 4.1 8.5 - - + -
393A ILE* 4.1 12.3 - - + -
407A LEU* 2.9 45.3 + - + +
410A LYS* 1.3 78.4 - - + +
412A LYS* 1.3 71.6 + - - +
413A LEU* 3.3 32.9 - - + +
421A ILE* 5.5 2.9 - - + -
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Residues in contact with LYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A MET 3.0 12.0 + - - -
409A SER 4.0 3.3 + - - +
410A LYS 3.1 6.2 - - - +
411A PHE* 1.3 80.9 - - - +
413A LEU* 1.3 62.8 + - - +
417A GLN* 5.1 0.2 - - - +
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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