Contacts of the helix formed by residues 393 - 397 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363G GLU* 3.3 36.8 - - + +
364G GLY 4.0 15.7 - - - +
365G ALA* 4.0 15.0 - - - +
388G ASP 3.9 9.4 - - - +
389G VAL* 3.9 11.9 - - - -
390G GLN* 3.1 51.6 + - + +
392G GLY* 1.3 81.0 - - - +
394G THR* 1.3 65.2 + - - +
395G ILE* 4.2 13.2 - - + -
396G ALA* 3.0 13.8 + - + +
397G LYS* 3.4 12.7 + - - +
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Residues in contact with THR 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356G TYR* 4.1 12.8 - - + -
359G THR* 3.8 18.3 - - + +
363G GLU* 2.7 34.3 + - - -
392G GLY 3.7 1.4 + - - -
393G MET* 1.3 72.2 - - - +
395G ILE* 1.3 58.0 + - + +
397G LYS* 3.1 10.8 + - - +
398G GLU* 2.9 59.9 + - - +
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Residues in contact with ILE 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272G LYS* 2.9 25.3 + - - +
356G TYR* 3.7 34.3 - - + +
359G THR* 4.9 1.1 - - - -
360G GLY* 3.8 16.8 - - - +
363G GLU* 4.5 1.1 + - - +
365G ALA* 3.7 30.1 - - + -
386G PHE* 3.8 26.7 - - + -
389G VAL* 4.0 11.9 - - + -
393G MET* 4.2 9.0 - - + -
394G THR* 1.3 77.1 - - - +
396G ALA* 1.3 57.2 + - - +
397G LYS 3.4 0.4 - - - -
398G GLU 4.6 4.0 - - - -
400G ILE* 5.8 4.5 - - + -
404G VAL* 5.8 1.1 - - + -
406G GLN* 3.5 30.9 - - + +
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Residues in contact with ALA 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272G LYS* 3.5 9.7 - - - +
307G ARG* 3.4 27.9 - - + +
389G VAL* 3.8 15.0 - - + -
390G GLN 3.2 28.9 - - - +
391G ASP* 3.9 10.4 - - - +
393G MET 3.0 8.4 + - - +
395G ILE* 1.3 79.1 - - - +
397G LYS* 1.3 60.6 + - - +
406G GLN* 5.0 0.7 - - - -
408G LEU* 4.8 6.5 - - + -
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Residues in contact with LYS 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272G LYS* 4.1 12.2 - - - +
391G ASP 3.5 19.1 - - - +
392G GLY* 3.5 25.6 + - - -
393G MET 3.4 12.1 - - - +
394G THR* 3.1 7.0 + - - +
396G ALA* 1.3 82.1 - - - +
398G GLU* 1.3 67.4 + - + +
399G GLU 4.0 1.2 + - - -
423G SER* 5.8 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