Contacts of the helix formed by residues 396 - 401 (chain A) in PDB entry 2ZDZ
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 GLY 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ASP 3.3 11.2 - - - -
293A THR* 3.2 17.9 - - - -
295A ASN 3.3 13.8 + - - -
296A LEU* 4.5 1.0 - - - +
394A VAL 3.1 8.9 + - - -
395A MET* 1.3 75.8 - - - +
397A ALA* 1.3 65.8 + - - -
398A VAL 3.1 3.6 - - - -
399A ILE* 2.9 13.2 + - - +
400A MET* 3.0 13.5 + - - +
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Residues in contact with ALA 397 (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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1A 310 4.1 16.6 - - + +
76A TYR* 4.6 9.9 - - + -
216A LEU* 4.7 5.8 - - + -
290A ASP 4.1 1.2 + - - -
291A SER* 5.3 1.5 - - - +
293A THR 2.8 14.5 + - - +
294A THR* 3.3 13.4 + - + +
396A GLY* 1.3 70.5 - - - -
398A VAL* 1.3 56.8 + - - +
400A MET* 4.3 8.1 - - - +
401A GLU* 2.8 57.5 + - + +
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Residues in contact with VAL 398 (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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294A THR* 3.1 20.3 + - + +
296A LEU* 3.7 26.0 - - + +
362A ILE* 3.9 14.8 - - + +
366A GLN* 3.4 39.2 - - - +
367A TYR* 3.8 24.9 - - + -
369A ARG* 6.0 1.3 - - + -
385A ALA* 3.4 38.8 - - + +
397A ALA* 1.3 76.4 - - - +
399A ILE* 1.3 62.3 + - - +
401A GLU* 4.2 3.5 + - - -
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Residues in contact with ILE 399 (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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296A LEU* 3.8 31.0 - - + -
345A ILE* 6.0 0.4 - - + -
347A LEU* 3.8 21.5 - - + -
360A ILE* 3.8 15.5 - - + -
362A ILE* 3.9 33.5 - - + +
395A MET* 3.8 40.6 - - + -
396A GLY 2.9 8.4 + - - +
398A VAL* 1.3 76.1 - - - +
400A MET* 1.3 66.8 + - + +
401A GLU 3.2 1.0 + - - -
402A GLY* 3.3 4.5 + - - -
403A PHE* 3.0 28.9 - - + -
416A PHE* 4.6 4.9 - - + -
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Residues in contact with MET 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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214A LEU* 3.8 36.6 - - + +
216A LEU* 3.9 27.6 + - + +
289A VAL* 4.0 17.3 - - + -
290A ASP 4.0 6.5 - - - +
291A SER* 3.7 30.1 - - - -
395A MET 4.2 5.6 - - - +
396A GLY 3.0 14.8 + - - +
397A ALA* 4.0 1.6 - - - +
399A ILE* 1.3 79.7 - - + +
401A GLU* 1.3 57.1 + - - +
402A GLY 3.2 0.2 - - - -
403A PHE* 2.9 32.5 + - - +
405A VAL* 4.3 19.4 - - + +
407A PHE* 3.9 16.6 - - + -
416A PHE* 5.7 0.2 - - + -
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Residues in contact with GLU 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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76A TYR* 2.6 35.4 + - - +
216A LEU* 3.2 28.5 - - + +
217A CYS* 4.8 3.6 - - - +
218A GLY* 3.7 17.9 - - - +
232A VAL* 5.0 2.6 - - - +
365A GLN 5.7 0.2 - - - +
366A GLN* 4.5 18.8 + - + +
397A ALA* 2.8 34.1 + - + +
398A VAL* 4.5 4.6 - - - +
399A ILE 3.2 0.4 + - - -
400A MET* 1.3 71.1 - - - +
402A GLY* 1.3 58.7 + - - +
403A PHE 3.3 0.4 + - - -
419A SER* 4.7 1.6 - - - -
422A HIS* 3.6 17.7 + - - +
423A VAL 5.0 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