Contacts of the helix formed by residues 365 - 376 (chain A) in PDB entry 5HVO
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 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A LYS* 5.0 5.7 + - - -
364A VAL* 1.3 80.9 - - - +
366A PHE* 1.3 54.4 + - - +
367A ASP* 3.6 8.2 + - - +
368A GLU* 3.1 22.4 + - - +
369A LEU* 2.8 33.3 + - - +
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Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LYS* 3.7 55.6 - - + -
256A PHE* 3.8 25.6 - + - -
259A GLY* 4.5 8.5 - - - -
364A VAL 3.8 0.8 + - - -
365A SER* 1.3 73.6 - - - +
367A ASP* 1.3 68.7 + - - +
369A LEU* 3.7 16.2 - - + +
370A ILE* 3.0 59.6 + - + +
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLY* 4.9 3.6 - - - +
262A SER* 5.0 5.6 + - - -
264A LYS* 3.8 32.4 + - - +
265A VAL* 3.5 26.4 - - + +
268A ARG* 5.2 1.1 - - - +
365A SER* 3.2 8.3 + - - +
366A PHE* 1.3 87.4 - - - +
368A GLU* 1.3 59.0 + - - +
370A ILE* 3.1 9.0 - - - +
371A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ARG* 2.8 50.2 + - - +
272A LEU* 5.6 2.1 - - - +
360A MET* 6.0 2.4 - - - +
364A VAL* 3.1 27.6 - - + -
365A SER* 3.1 19.3 + - - +
367A ASP* 1.3 78.3 - - - +
369A LEU* 1.3 64.0 + - - +
371A ALA* 3.4 2.6 + - - +
372A LEU* 2.9 32.7 + - + +
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PHE* 5.0 3.8 - - + -
285A VAL* 3.8 26.7 - - + -
320A VAL* 6.0 0.2 - - + -
364A VAL* 3.7 14.1 - - + +
365A SER 2.8 20.2 + - - +
366A PHE* 3.7 21.1 - - + +
368A GLU* 1.3 74.0 - - - +
370A ILE* 1.3 52.1 + - - +
372A LEU* 3.1 9.8 + - + +
373A TYR* 2.8 74.4 + - + +
394A GLU* 3.9 3.1 - - - +
501A UDP 3.3 32.8 - - + +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PHE* 3.3 38.4 - - + +
259A GLY* 4.0 10.3 - - - -
260A LEU* 4.0 6.4 - - + +
265A VAL* 3.5 23.6 - - + -
366A PHE* 3.0 43.0 + - + +
367A ASP* 3.1 18.6 - - - +
369A LEU* 1.3 76.9 - - - +
371A ALA* 1.3 61.6 + - - +
373A TYR* 3.5 9.0 + - - +
374A ALA* 3.0 30.0 + - - +
398A THR* 3.8 19.6 - - + +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 4.2 4.0 - - + +
268A ARG* 3.5 36.1 - - + -
269A ILE* 3.8 21.9 - - + +
272A LEU* 3.7 4.5 - - + +
367A ASP 3.0 20.0 + - - +
368A GLU 3.7 3.4 - - - +
370A ILE* 1.3 79.7 - - - +
372A LEU* 1.3 56.2 + - - +
374A ALA* 3.2 2.6 + - - +
375A ALA* 2.9 30.8 + - - +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 4.0 17.4 - - + +
276A PHE* 6.6 0.2 - - + -
281A LEU* 4.8 9.6 - - + -
283A VAL* 3.7 20.4 - - + -
285A VAL* 5.0 3.4 - - + -
318A VAL* 4.1 26.7 - - + -
320A VAL* 3.6 31.2 - - + -
360A MET* 4.3 4.9 - - + -
364A VAL* 6.1 2.2 - - + -
368A GLU* 2.9 26.9 + - + +
369A LEU* 3.5 8.1 - - + +
371A ALA* 1.3 74.2 - - - +
373A TYR* 1.3 63.3 + - - +
375A ALA 3.5 1.4 + - - -
376A SER* 2.7 36.7 + - - +
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Residues in contact with TYR 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PHE* 4.6 3.4 - + - -
283A VAL* 4.3 11.9 - - + -
285A VAL* 3.7 23.1 - - + +
369A LEU* 2.8 51.0 + - + +
370A ILE* 3.6 8.1 - - - +
372A LEU* 1.3 72.5 - - + +
374A ALA* 1.3 61.8 + - - +
376A SER* 3.1 15.4 + - - -
379A CYS* 5.3 0.7 - - - -
391A VAL* 3.5 28.9 + - + +
394A GLU* 3.1 39.7 + - + -
395A TYR* 3.6 26.6 - + + -
398A THR* 3.2 30.1 - - + +
399A GLN* 2.9 16.8 + - - -
501A UDP 4.3 0.3 + - - -
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 4.3 8.7 - - + -
269A ILE* 3.4 33.2 - - + +
273A GLU* 5.1 0.3 - - - +
370A ILE 3.0 15.3 + - - +
371A ALA 3.2 1.3 + - - +
373A TYR* 1.3 79.8 - - - +
375A ALA* 1.3 57.2 + - - +
376A SER 3.5 0.3 + - - -
398A THR* 3.8 15.6 - - - +
399A GLN* 3.5 13.3 + - - +
402A ARG* 3.0 23.2 + - - +
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ILE* 4.5 13.0 - - + +
272A LEU* 3.8 31.4 - - + -
273A GLU* 4.7 5.5 - - + +
281A LEU* 3.9 18.1 - - + +
371A ALA 2.9 15.6 + - - +
372A LEU 4.1 2.9 - - - +
373A TYR 3.2 0.4 - - - -
374A ALA* 1.3 77.6 - - - +
376A SER* 1.3 59.4 + - - +
377A ASP* 3.8 2.4 + - - +
402A ARG* 3.5 23.3 + - - +
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LEU* 3.7 19.1 - - - +
283A VAL* 3.1 37.0 + - - +
372A LEU* 2.7 19.9 + - - +
373A TYR 3.1 9.0 + - - -
374A ALA 3.3 0.4 - - - -
375A ALA* 1.3 76.9 - - - +
377A ASP* 1.3 61.0 + - - +
378A ALA 3.6 8.1 - - - -
395A TYR* 3.0 17.1 + - - -
399A GLN* 3.6 4.7 + - - -
402A ARG* 3.1 14.3 - - - -
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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