Contacts of the helix formed by residues 376 - 381 (chain K) in PDB entry 4ZZ7
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 376 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339K ALA* 4.5 6.3 - - - +
342K GLN* 3.5 43.3 - - + +
343K GLY 4.4 1.8 - - - -
344K ALA* 4.0 21.1 - - - +
371K HIS 3.7 16.2 - - - +
372K VAL* 3.8 12.3 - - - -
373K THR* 3.1 48.7 + - + +
375K GLU* 1.3 80.2 - - + +
377K THR* 1.3 65.5 + - - +
378K SER* 4.1 13.2 - - - +
379K TYR* 3.4 5.9 + - + +
380K GLN* 3.1 26.4 + - - +
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Residues in contact with THR 377 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335K TYR* 4.9 4.7 - - + -
338K SER* 4.1 10.9 + - - -
342K GLN* 3.1 20.7 + - - +
375K GLU 3.9 0.9 + - - -
376K MET* 1.3 69.2 - - - +
378K SER* 1.3 67.0 + - - +
380K GLN* 3.2 11.9 + - - +
381K GLU* 3.0 56.2 + - + +
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Residues in contact with SER 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K LYS* 3.5 9.0 + - - -
335K TYR* 3.8 43.7 - - - -
338K SER* 4.1 6.5 + - - -
339K ALA* 3.6 18.3 - - - +
369K ILE* 5.9 0.2 - - - -
372K VAL* 5.8 0.2 - - - +
376K MET* 4.1 10.4 - - - +
377K THR* 1.3 80.6 - - - +
379K TYR* 1.3 57.7 + - - +
381K GLU 3.0 19.4 - - - +
383K ILE* 4.0 8.1 - - - +
389K GLN* 3.3 18.6 + - - +
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Residues in contact with TYR 379 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K LYS* 3.2 13.7 - - - +
252K HIS* 3.0 32.7 + + - -
285K VAL* 4.1 11.0 - - + -
372K VAL* 4.3 8.5 - - + -
373K THR 3.5 19.3 - - - +
374K PRO* 3.7 30.5 - - + -
376K MET* 3.4 7.5 + - + +
377K THR 3.2 0.8 - - - -
378K SER* 1.3 82.6 + - - +
380K GLN* 1.3 66.0 + - + +
389K GLN* 3.8 11.2 - - - +
391K VAL* 4.0 28.5 - - + -
402K LEU* 3.1 34.7 + - + +
406K HIS* 3.2 31.3 + + - -
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Residues in contact with GLN 380 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374K PRO 2.8 27.3 + - - +
375K GLU* 3.6 15.2 + - - +
376K MET 3.1 17.4 + - - +
377K THR* 3.2 10.4 + - - +
379K TYR* 1.3 80.6 - - + +
381K GLU* 1.3 63.6 + - + +
406K HIS* 3.0 29.9 - - + +
407K GLU* 4.3 10.2 - - - +
408K TYR* 4.8 1.6 - - - -
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Residues in contact with GLU 381 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K LYS* 3.1 14.9 + - - -
335K TYR* 2.6 43.2 + - + +
377K THR* 3.0 37.1 + - + +
378K SER 3.0 18.4 - - - +
380K GLN* 1.3 83.3 - - + +
382K GLU* 1.3 60.9 + - - +
383K ILE* 3.5 0.8 + - - -
407K GLU* 5.8 0.7 - - - -
408K TYR* 5.2 2.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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