Contacts of the helix formed by residues 377 - 386 (chain X) in PDB entry 4HSC
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 ASN 377 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373X ASP 5.1 0.2 - - - +
374X VAL* 3.2 6.9 + - - +
375X LYS 3.2 3.5 + - - +
376X THR* 1.3 81.0 + - - +
378X GLY* 1.3 84.0 + - - +
379X LYS 3.2 4.2 + - - -
380X TYR* 3.1 63.7 + - + -
381X SER* 3.2 21.3 + - - -
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Residues in contact with GLY 378 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377X ASN* 1.3 83.1 + - - +
379X LYS* 1.3 60.0 + - - -
381X SER* 4.0 1.2 - - - -
382X ASP* 3.4 24.1 + - - +
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Residues in contact with LYS 379 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358X SER* 4.7 10.1 - - - +
360X ASP* 4.4 15.9 - - - +
377X ASN* 3.2 4.0 + - - -
378X GLY* 1.3 70.7 - - - -
380X TYR* 1.3 67.6 + - + +
381X SER 3.2 0.2 - - - -
382X ASP* 3.5 26.5 + - + +
383X ILE* 2.9 44.4 + - + +
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Residues in contact with TYR 380 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360X ASP* 4.1 25.6 - - + -
363X ALA* 3.5 21.3 - - + +
364X ALA* 3.9 25.7 - - + +
367X ALA* 4.0 28.5 - - + -
374X VAL* 4.4 9.4 - - + +
377X ASN* 3.1 42.9 + - + +
379X LYS* 1.3 78.8 - - + +
381X SER* 1.3 58.6 + - - +
383X ILE* 3.3 2.4 + - - +
384X LEU* 3.0 39.4 + - + +
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Residues in contact with SER 381 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374X VAL 4.1 10.7 + - - -
375X LYS* 4.5 11.2 + - - -
377X ASN 3.2 18.0 + - - -
378X GLY 4.0 2.2 - - - -
380X TYR* 1.3 78.8 - - - +
382X ASP* 1.3 61.9 + - - +
384X LEU* 3.9 9.6 - - - +
385X GLU* 2.9 35.0 + - - +
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Residues in contact with ASP 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378X GLY 3.4 15.3 + - - +
379X LYS* 3.5 32.3 + - + +
380X TYR 3.3 0.4 - - - -
381X SER* 1.3 79.0 + - - +
383X ILE* 1.3 58.9 + - - +
385X GLU* 3.3 8.3 + - - +
386X ASN* 2.6 36.2 + - - +
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Residues in contact with ILE 383 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354X THR* 4.2 1.0 + - + -
356X SER* 4.0 18.8 - - - +
358X SER* 3.4 31.0 - - - +
360X ASP* 3.8 11.4 - - + -
361X VAL* 3.6 39.5 - - + +
364X ALA* 4.0 14.8 - - + -
365X PHE* 4.4 3.1 - - + -
379X LYS* 2.9 32.2 + - + +
380X TYR 3.5 4.0 - - - +
382X ASP* 1.3 76.4 - - - +
384X LEU* 1.3 55.7 + - - +
386X ASN* 2.8 24.9 + - - +
387X SER* 2.8 22.3 + - - +
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Residues in contact with LEU 384 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364X ALA* 4.1 11.4 - - + +
365X PHE* 4.0 20.9 - - + -
368X ALA* 3.9 31.0 - - + -
374X VAL* 4.2 21.1 - - + -
380X TYR* 3.0 27.3 + - + +
381X SER* 3.9 7.9 - - - +
383X ILE* 1.3 75.0 - - - +
385X GLU* 1.3 58.4 + - - +
387X SER* 2.8 29.2 + - - +
389X PHE* 3.8 34.9 - - + -
407X LYS* 5.0 2.3 - - - +
409X PHE* 6.0 1.3 - - + -
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Residues in contact with GLU 385 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381X SER* 2.9 19.0 + - - +
382X ASP* 3.3 14.7 - - - +
383X ILE 3.2 0.2 - - - -
384X LEU* 1.3 76.2 - - - +
386X ASN* 1.3 63.8 + - - +
387X SER 3.2 0.2 - - - -
407X LYS* 3.2 21.7 + - - +
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Residues in contact with ASN 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354X THR* 2.8 26.8 + - - +
355X SER* 4.5 2.4 + - - -
356X SER* 4.8 9.4 + - - +
382X ASP* 2.6 27.7 + - - +
383X ILE* 2.8 15.1 + - - +
385X GLU* 1.3 84.9 + - - +
387X SER* 1.3 51.7 + - - -
407X LYS* 4.1 5.4 - - - +
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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
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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