Contacts of the helix formed by residues 393 - 398 (chain C) in PDB entry 3SZ9
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C GLU* 3.1 36.1 - - + +
364C GLY 4.0 4.7 - - - +
365C ALA* 3.8 42.0 - - - +
388C ASP 4.1 5.2 - - - +
389C VAL* 4.0 6.5 - - - -
390C GLN* 3.1 49.6 + - + +
392C GLY* 1.3 80.2 - - - +
394C THR* 1.3 65.8 + - - +
395C ILE* 3.3 8.1 - - + +
396C ALA* 3.0 13.2 + - + +
397C LYS* 3.3 16.3 + - - +
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Residues in contact with THR 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C TYR* 4.2 11.0 - - + -
359C THR* 4.0 17.5 - - + +
363C GLU* 2.4 28.3 + - - -
392C GLY 3.7 1.2 + - - -
393C MET* 1.3 71.8 - - - +
395C ILE* 1.3 56.8 + - - +
397C LYS* 3.1 15.1 + - - +
398C GLU* 2.9 59.1 + - - +
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Residues in contact with ILE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LYS* 2.8 29.5 + - - -
356C TYR* 3.6 28.7 - - + +
359C THR* 4.5 4.5 - - + -
360C GLY* 3.7 9.9 - - - +
363C GLU* 3.0 21.4 + - - +
365C ALA* 3.8 23.6 - - + -
386C PHE* 3.8 30.5 - - + -
389C VAL* 4.0 7.2 - - + -
393C MET* 4.3 8.3 - - + -
394C THR* 1.3 75.9 - - - +
396C ALA* 1.3 56.7 + - - +
397C LYS 3.4 0.2 - - - -
398C GLU 4.8 0.4 - - - -
400C ILE* 4.1 21.3 - - + -
406C GLN* 3.4 21.9 - - + +
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Residues in contact with ALA 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LYS* 3.6 9.9 - - - +
307C ARG* 3.3 27.9 + - + -
389C VAL* 3.6 17.3 - - + -
390C GLN 3.2 28.3 - - - +
391C ASP* 3.9 10.4 - - - +
393C MET 3.0 7.6 + - - +
395C ILE* 1.3 79.9 - - - +
397C LYS* 1.3 59.7 + - - +
406C GLN* 4.8 0.7 - - - -
408C LEU* 4.5 6.7 - - + -
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Residues in contact with LYS 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LYS* 3.9 14.5 - - - +
391C ASP 3.5 15.0 - - - +
392C GLY* 3.5 27.6 + - - -
393C MET 3.3 12.4 + - - +
394C THR* 3.1 14.2 + - - +
396C ALA* 1.3 81.0 - - - +
398C GLU* 1.3 70.1 + - + +
399C GLU 4.1 0.7 + - - -
423C SER* 5.3 1.7 + - - -
425C TYR* 4.2 10.6 - - - -
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Residues in contact with GLU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LYS* 2.9 21.4 + - - -
356C TYR* 2.6 42.5 + - + +
394C THR* 2.9 30.9 + - + +
395C ILE 4.1 1.0 - - - +
397C LYS* 1.3 88.1 + - + +
399C GLU* 1.3 64.1 + - - +
400C ILE* 3.4 7.6 + - - +
425C TYR* 5.1 2.0 - - - -
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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