Contacts of the helix formed by residues 360 - 371 (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 ASP 360 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358X SER* 2.7 12.4 + - - +
359X ASN* 1.3 85.5 - - - +
361X VAL* 1.3 58.9 + - - +
362X GLU 3.4 2.0 - - - -
363X ALA* 3.0 11.7 + - + +
364X ALA* 2.8 25.8 + - - +
379X LYS* 4.4 14.4 - - + +
380X TYR* 4.1 19.4 - - + -
383X ILE* 3.8 11.0 - - + -
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Residues in contact with VAL 361 (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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256X MET* 5.1 1.6 - - + -
291X LYS* 3.8 26.2 - - + -
354X THR* 3.6 15.3 - - + -
356X SER* 3.8 20.2 - - - +
358X SER 3.4 18.6 - - - +
359X ASN 3.4 1.8 - - - -
360X ASP* 1.3 76.0 - - - +
362X GLU* 1.3 55.3 + - - +
364X ALA* 2.9 3.8 + - - +
365X PHE* 2.8 65.1 + - + -
383X ILE* 3.6 19.4 - - + +
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Residues in contact with GLU 362 (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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256X MET* 3.4 47.9 + - + +
258X TYR* 4.3 5.9 + - - -
293X MET* 3.8 7.4 - - + +
359X ASN 4.9 3.0 + - - +
360X ASP 3.4 0.8 - - - -
361X VAL* 1.3 77.8 - - - +
363X ALA* 1.3 59.3 + - - +
365X PHE* 3.4 2.8 + - - +
366X SER* 3.0 32.0 + - - +
454X GLU* 5.7 1.0 - - - +
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Residues in contact with ALA 363 (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* 3.0 14.5 + - + +
362X GLU* 1.3 81.0 - - - +
364X ALA* 1.3 58.2 + - - +
366X SER* 3.5 5.4 + - - -
367X ALA* 3.0 31.0 + - - +
380X TYR* 3.5 25.0 - - + +
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Residues in contact with ALA 364 (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 2.8 12.4 + - - +
361X VAL* 3.3 9.0 - - - +
363X ALA* 1.3 78.4 - - - +
365X PHE* 1.3 59.1 + - + +
367X ALA* 3.6 2.1 + - - +
368X ALA* 3.0 28.1 + - - +
374X VAL* 4.6 0.2 - - - +
380X TYR* 3.9 43.0 - - + +
383X ILE* 4.0 17.9 - - + -
384X LEU* 4.1 8.6 - - + +
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Residues in contact with PHE 365 (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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256X MET* 4.5 5.2 - - - -
291X LYS 3.8 12.1 - - - -
293X MET* 3.7 36.1 - - + -
352X LEU* 3.3 52.6 - - + +
353X GLU 3.9 0.7 - - - -
354X THR* 3.5 24.9 - - + -
361X VAL* 2.8 36.1 + - + +
362X GLU 3.7 4.5 - - - +
364X ALA* 1.3 71.6 - - + +
366X SER* 1.3 63.5 + - - +
368X ALA* 3.4 3.8 + - - +
369X LEU* 3.2 26.5 + - - +
383X ILE* 4.4 4.0 - - + -
384X LEU* 4.0 11.9 - - + -
387X SER* 3.3 23.1 - - - -
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Residues in contact with SER 366 (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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254X GLU* 2.7 33.4 + - - +
293X MET* 3.5 10.1 - - - +
362X GLU* 3.0 21.3 + - - +
363X ALA* 3.9 5.8 - - - -
365X PHE* 1.3 76.5 - - - +
367X ALA* 1.3 58.0 + - - +
369X LEU* 3.4 4.4 + - - +
370X LYS* 3.0 27.1 + - - +
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Residues in contact with ALA 367 (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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363X ALA 3.0 19.4 + - - +
364X ALA 3.8 2.7 - - - +
366X SER* 1.3 75.8 - - - +
368X ALA* 1.3 65.7 + - - +
370X LYS* 3.0 19.3 + - + +
371X GLY 3.1 10.2 + - - +
374X VAL* 3.0 25.8 - - + +
380X TYR* 4.0 19.1 - - + -
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Residues in contact with ALA 368 (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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352X LEU* 4.1 9.9 - - + -
364X ALA 3.0 18.6 + - - +
365X PHE 3.5 6.3 - - - +
367X ALA* 1.3 75.8 - - - +
369X LEU* 1.3 58.2 + - - +
370X LYS 3.3 0.2 + - - -
374X VAL* 3.1 15.3 - - + +
384X LEU* 3.9 25.8 - - + -
409X PHE* 3.1 16.8 - - + -
413X ARG* 2.8 32.1 + - - -
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Residues in contact with LEU 369 (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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252X TYR* 3.4 22.7 - - - +
254X GLU* 3.6 10.5 - - - +
293X MET* 3.8 18.4 - - - -
295X ALA* 3.9 24.0 - - + -
297X TYR* 3.7 28.1 + - + +
350X VAL* 4.3 16.4 - - + -
352X LEU* 3.9 8.3 - - + -
365X PHE 3.2 16.1 + - - +
366X SER 3.7 5.4 - - - +
367X ALA 3.3 0.2 - - - -
368X ALA* 1.3 80.2 - - - +
370X LYS* 1.3 62.4 + - - +
409X PHE* 3.8 22.4 - - + -
413X ARG* 4.0 5.2 + - - -
416X ILE* 5.1 1.3 - - + -
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Residues in contact with LYS 370 (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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366X SER 3.0 14.7 + - - +
367X ALA* 3.0 15.5 + - + +
369X LEU* 1.3 80.9 - - - +
371X GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 371 (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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367X ALA 3.1 13.3 + - - +
368X ALA 3.6 0.4 + - - -
369X LEU 3.4 2.6 - - - -
370X LYS* 1.3 80.0 - - - +
372X THR* 1.3 58.8 + - - -
373X ASP* 3.1 12.4 + - - -
374X VAL* 3.4 8.1 + - - +
413X ARG* 3.1 21.5 + - - -
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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