Contacts of the helix formed by residues 375 - 383 (chain K) in PDB entry 1HZH
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 SER 375 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370H TYR* 3.6 32.4 - - - +
371H THR* 3.2 16.3 + - - -
372H LEU* 3.6 26.7 - - - +
470H LYS* 5.4 0.2 + - - -
374K PRO* 1.3 74.6 - - - +
376K ARG* 1.3 67.6 + - - +
377K ASP* 3.9 10.4 + - - +
378K GLU* 2.9 18.7 + - - +
381K LEU* 3.4 9.1 + - - +
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Residues in contact with ARG 376 (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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373H PRO* 5.1 15.3 - - - +
473H SER 5.8 1.6 + - - -
475H SER* 4.2 17.8 + - - +
374K PRO 3.5 3.4 + - - +
375K SER* 1.3 72.9 + - - +
377K ASP* 1.3 67.4 + - - +
381K LEU* 3.2 34.8 + - + +
382K THR* 4.4 3.6 + - - +
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Residues in contact with ASP 377 (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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370H TYR* 3.9 12.6 + - + -
470H LYS* 2.5 39.4 + - - +
375K SER* 3.1 5.9 + - - +
376K ARG* 1.3 81.7 - - - +
378K GLU* 1.3 63.7 + - - +
381K LEU 3.3 0.7 + - - -
382K THR* 3.3 26.8 + - - +
383K LYS* 5.0 0.3 - - - +
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Residues in contact with GLU 378 (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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368H GLN* 5.2 0.8 + - - +
370H TYR* 3.5 46.7 - - + +
391H LEU* 5.2 0.9 - - - +
393H LYS* 4.1 9.7 + - - +
374K PRO* 3.8 14.5 - - + +
375K SER 2.9 12.9 + - - +
377K ASP* 1.3 75.1 - - - +
381K LEU* 1.3 56.6 + - - +
382K THR 2.8 12.8 + - - -
383K LYS* 2.9 21.9 + - + +
385K GLN 4.1 6.3 - - - +
386K VAL* 3.7 14.0 - - + +
387K SER* 2.5 53.9 + - - +
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Residues in contact with LEU 381 (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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374K PRO* 4.2 11.4 - - + +
375K SER 3.9 7.6 - - - +
376K ARG* 3.2 26.6 + - + +
377K ASP 3.1 0.8 - - - -
378K GLU* 1.3 77.8 - - - +
382K THR* 1.3 57.6 + - + +
383K LYS 3.3 0.4 - - - -
386K VAL* 3.9 20.6 - - + -
445K LYS* 3.0 27.6 + - + +
448K TRP* 4.0 25.1 - - + +
449K GLN* 4.1 18.8 + - - +
474K LEU* 6.1 3.4 - - + -
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Residues in contact with THR 382 (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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376K ARG 4.6 3.6 - - - +
377K ASP* 3.3 22.1 + - - +
378K GLU 2.8 1.0 + - - -
381K LEU* 1.3 79.3 - - - +
383K LYS* 1.3 75.0 + - - +
384K ASN* 5.4 0.9 - - - +
445K LYS* 3.7 8.7 + - - +
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Residues in contact with LYS 383 (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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368H GLN* 3.7 39.8 + - - +
370H TYR* 3.8 13.7 - - - +
378K GLU* 2.9 18.1 + - + +
381K LEU 3.9 0.2 - - - +
382K THR* 1.3 90.9 - - - +
384K ASN* 1.3 64.5 + - - +
385K GLN 3.4 14.7 - - - +
386K VAL* 4.6 0.7 - - - +
445K LYS* 3.2 27.9 - - - +
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Residues in contact with ASN 384 (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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382K THR 5.4 0.6 - - - +
383K LYS* 1.3 76.9 - - - +
385K GLN* 1.3 60.4 + - + +
444K ASP* 3.5 8.3 - - - +
445K LYS* 2.7 38.7 + - - +
446K SER* 5.5 0.2 + - - -
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Residues in contact with GLN 385 (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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393H LYS* 5.3 4.3 + - - -
378K GLU* 4.1 6.6 - - - +
383K LYS* 3.7 17.0 - - - +
384K ASN* 1.3 88.6 - - + +
386K VAL* 1.3 63.2 + - - +
418K ASN* 4.6 5.3 + - - -
442K THR* 3.9 26.9 + - + +
443K VAL* 3.3 11.2 - - - +
444K ASP* 3.9 20.5 + - - +
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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
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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