Contacts of the helix formed by residues 384 - 392 (chain H) in PDB entry 6MZL
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 384 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380H LEU 3.3 1.6 + - - -
381H ALA 3.2 13.3 + - - -
382H GLU 3.2 4.6 - - - -
383H LEU* 1.3 80.8 - - - +
385H HIS* 1.3 65.2 + - - +
386H ASP 3.7 0.4 - - - -
387H VAL* 3.3 6.2 - - - +
388H ILE* 3.2 27.2 + - - +
430H HIS* 5.2 1.8 - - - -
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Residues in contact with HIS 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383H LEU 4.0 1.2 + - - -
384H GLY* 1.3 70.0 - - - +
386H ASP* 1.3 86.5 + - - +
388H ILE* 3.1 8.0 + - - +
389H LYS* 3.0 43.3 + - - +
433H PRO 5.6 0.2 - - - -
434H VAL* 3.4 32.0 - - + +
437H LYS* 3.4 44.8 + - + +
354I ARG* 4.5 15.8 + - - -
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Residues in contact with ASP 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385H HIS* 1.3 100.6 - - - +
387H VAL* 1.3 54.7 + - - +
388H ILE 3.2 0.2 - - - -
389H LYS* 3.3 27.9 + - + +
390H THR* 2.4 47.0 + - + -
350I ASN* 5.9 2.3 - - - -
354I ARG* 4.2 20.8 + - - +
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Residues in contact with VAL 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H THR* 5.3 4.9 - - + -
380H LEU* 3.4 50.5 - - + +
383H LEU* 3.7 27.1 - - + +
384H GLY 3.3 10.3 - - - +
386H ASP* 1.3 76.2 - - - +
388H ILE* 1.3 57.6 + - + +
390H THR* 3.9 0.2 - - - -
391H LEU* 2.8 53.9 + - + +
392H ILE* 3.6 0.3 + - - +
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Residues in contact with ILE 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377H ILE 5.3 0.9 - - - +
380H LEU* 3.6 22.7 - - + +
381H ALA* 3.8 14.4 - - + +
384H GLY 3.2 16.4 - - - +
385H HIS* 3.1 6.6 + - - +
387H VAL* 1.3 76.9 - - + +
389H LYS* 1.3 63.7 + - - +
392H ILE* 3.2 40.6 + - + -
393H LEU* 3.3 9.5 + - - +
430H HIS* 4.3 15.9 - - + +
431H CYS* 3.7 36.0 - - + -
434H VAL* 3.9 17.2 - - + +
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Residues in contact with LYS 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385H HIS* 3.0 39.3 + - - +
386H ASP* 3.3 25.8 + - + +
388H ILE* 1.3 77.6 - - - +
390H THR* 1.3 62.6 + - + +
393H LEU* 3.4 28.7 - - + +
434H VAL* 4.8 12.3 - - + +
437H LYS* 5.7 2.8 - - - +
438H LEU* 3.6 49.2 - - + +
354I ARG* 4.7 15.8 - - - +
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Residues in contact with THR 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386H ASP* 2.4 37.2 + - + +
387H VAL* 3.9 0.2 - - - -
389H LYS* 1.3 89.4 - - + +
391H LEU* 1.3 78.5 + - - +
392H ILE 3.7 0.2 - - - -
393H LEU* 5.7 0.3 - - - +
394H PRO* 3.2 19.8 - - - +
348I THR* 4.2 28.3 - - + -
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Residues in contact with LEU 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356H THR* 5.5 9.4 - - + -
360H THR* 5.6 8.5 - - + +
363H TRP* 3.2 24.5 - - + -
380H LEU* 4.9 9.4 - - + -
387H VAL* 2.8 44.1 + - + +
390H THR* 1.3 92.4 - - - +
392H ILE* 1.3 68.4 + - + +
394H PRO* 3.4 11.1 - - - +
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Residues in contact with ILE 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363H TRP* 3.5 27.9 - - + +
377H ILE* 5.4 7.0 - - + -
380H LEU* 3.8 32.5 - - + -
387H VAL 4.0 2.2 - - - +
388H ILE* 3.2 46.9 + - + +
391H LEU* 1.3 84.5 - - + +
393H LEU* 1.3 67.3 + - - +
394H PRO 3.3 0.6 - - - -
396H LEU* 3.1 26.2 + - + +
427H LEU* 4.4 22.0 - - + -
431H CYS* 4.7 9.4 - - + -
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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
------------------------------------------------------------
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