Contacts of the helix formed by residues 393 - 397 (chain L) in PDB entry 1ZUM
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 MET 393 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363L GLU* 3.4 39.5 - - + +
364L GLY 4.7 1.3 - - - -
365L ALA* 4.2 21.5 - - + -
388L ASP 4.9 1.3 - - - +
389L VAL* 3.2 26.2 - - + -
390L GLN* 2.9 46.0 + - + +
392L GLY* 1.3 81.0 - - - +
394L THR* 1.3 65.9 + - - +
395L ILE* 3.3 14.4 - - + +
396L ALA* 3.1 12.7 + - - +
397L LYS* 3.4 12.3 - - - +
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Residues in contact with THR 394 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356L TYR* 5.4 5.2 - - + -
359L THR* 3.9 14.6 - - + +
363L GLU* 2.9 30.1 + - - -
392L GLY 3.8 1.4 + - - -
393L MET* 1.3 66.5 - - - +
395L ILE* 1.3 58.0 - - - +
396L ALA 3.0 4.9 - - - -
397L LYS* 3.0 13.2 + - + +
398L GLU* 2.8 59.3 + - + +
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Residues in contact with ILE 395 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L LYS* 3.0 12.1 + - - -
356L TYR* 2.7 60.2 + - + +
359L THR* 4.6 4.5 - - + -
360L GLY* 3.6 25.8 - - - +
363L GLU* 4.8 1.3 - - - +
365L ALA* 3.6 29.8 - - + -
386L PHE* 3.9 22.0 - - + -
389L VAL* 4.2 4.9 - - + -
393L MET* 4.1 16.2 - - + -
394L THR* 1.3 74.3 - - - +
396L ALA* 1.3 58.0 + - - +
397L LYS 3.5 0.2 - - - -
406L GLN* 3.3 25.0 - - + +
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Residues in contact with ALA 396 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L LYS* 3.4 10.6 - - - +
307L ARG* 3.4 28.4 + - + +
389L VAL* 3.7 17.9 - - + -
390L GLN 3.4 27.6 - - - +
391L ASP* 4.1 9.3 - - - +
393L MET* 3.1 7.1 + - + +
394L THR 3.0 1.0 - - - -
395L ILE* 1.3 77.9 - - - +
397L LYS* 1.3 62.4 + - - +
406L GLN* 4.9 0.7 - - - -
408L LEU* 4.8 6.5 - - + -
423L SER* 5.3 0.5 + - - -
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Residues in contact with LYS 397 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272L LYS* 4.0 12.2 - - - +
391L ASP 3.5 20.0 - - - +
392L GLY* 3.6 19.7 + - - +
393L MET 3.4 13.5 - - - +
394L THR* 3.0 11.9 + - - +
396L ALA* 1.3 82.1 - - - +
398L GLU* 1.3 61.1 + - + +
399L GLU 4.0 1.0 + - - -
423L SER* 6.0 0.9 - - - -
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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