Contacts of the helix formed by residues 365 - 376 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B LYS* 4.6 7.6 + - - -
364B VAL* 1.3 80.3 - - - +
366B PHE* 1.3 65.7 + - - +
367B ASP* 3.5 9.0 + - - +
368B GLU* 3.1 20.3 + - - +
369B LEU* 2.9 22.2 + - - +
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Residues in contact with PHE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B LYS* 3.8 49.8 - - + -
256B PHE* 3.5 42.6 - + - -
259B GLY* 4.4 7.9 - - - -
364B VAL 3.8 1.0 + - - -
365B SER* 1.3 74.1 - - - +
367B ASP* 1.3 67.3 + - - +
369B LEU* 3.7 15.4 - - + +
370B ILE* 3.0 50.8 + - + +
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Residues in contact with ASP 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B GLY* 4.8 2.6 - - - +
262B SER* 5.0 2.8 + - - -
264B LYS* 3.4 39.1 + - + +
265B VAL* 3.4 28.0 - - + +
268B ARG* 5.1 1.3 - - - +
365B SER* 3.1 4.7 + - - +
366B PHE* 1.3 86.3 - - - +
368B GLU* 1.3 64.8 + - - +
370B ILE* 3.1 22.7 - - - +
371B ALA* 3.1 10.9 + - - +
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B LYS* 5.8 0.2 - - - +
268B ARG* 2.8 50.7 + - - +
272B LEU* 5.3 3.0 - - - +
360B MET* 5.9 3.6 - - - +
364B VAL* 3.1 31.2 - - + -
365B SER* 3.1 14.0 + - - +
367B ASP* 1.3 76.2 - - - +
369B LEU* 1.3 65.6 + - - +
371B ALA* 3.4 3.1 + - - +
372B LEU* 3.0 30.0 + - + +
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B PHE* 5.1 1.8 - - + -
285B VAL* 3.8 28.5 - - + -
320B VAL* 5.8 0.4 - - + -
364B VAL* 3.7 13.9 - - + +
365B SER 2.9 17.0 + - - +
366B PHE* 3.7 24.0 - - + +
368B GLU* 1.3 77.4 - - - +
370B ILE* 1.3 57.5 + - - +
372B LEU* 3.1 10.7 + - + +
373B TYR* 2.8 63.9 + - + +
394B GLU* 4.2 1.1 - - - +
501B UDP 3.3 34.8 - - + +
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B PHE* 3.3 35.4 - - + +
259B GLY 3.9 1.6 - - - -
260B LEU* 3.7 21.9 - - + +
265B VAL* 3.3 23.8 - - + -
366B PHE* 3.0 42.2 + - + +
367B ASP* 3.1 18.8 - - - +
369B LEU* 1.3 75.1 - - - +
371B ALA* 1.3 62.6 + - - +
373B TYR* 3.3 9.7 + - - +
374B ALA* 2.9 29.7 + - - +
398B THR* 3.8 15.6 - - + +
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B VAL* 4.0 3.6 - - + +
268B ARG* 3.5 35.2 - - + -
269B ILE* 3.6 27.2 - - + +
272B LEU* 4.0 4.8 - - + +
367B ASP 3.1 11.6 + - - +
368B GLU 3.8 2.2 - - - +
370B ILE* 1.3 82.7 - - - +
372B LEU* 1.3 57.6 + - - +
374B ALA* 3.2 2.6 + - - +
375B ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 4.1 15.4 - - + +
281B LEU* 4.4 14.6 - - + -
283B VAL* 3.9 16.6 - - + -
285B VAL* 5.1 3.1 - - + -
318B VAL* 4.0 26.0 - - + -
320B VAL* 3.6 29.8 - - + -
360B MET* 4.3 5.4 - - + -
364B VAL* 6.2 2.0 - - + -
368B GLU* 3.0 27.1 + - + +
369B LEU* 3.1 9.6 + - + +
371B ALA* 1.3 73.8 - - - +
373B TYR* 1.3 62.5 + - + +
375B ALA* 3.4 1.6 + - - +
376B SER* 2.7 41.5 + - - +
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Residues in contact with TYR 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B PHE* 4.6 4.5 - + - -
283B VAL* 4.4 10.3 - - + -
285B VAL* 3.8 21.1 - - + +
369B LEU* 2.8 45.0 + - + +
370B ILE* 3.4 9.2 - - - +
372B LEU* 1.3 72.6 - - + +
374B ALA* 1.3 62.4 + - - +
376B SER* 3.0 17.4 + - - -
379B CYS* 5.4 0.9 - - - -
391B VAL* 3.6 26.1 - - + +
394B GLU* 2.9 45.5 + - + +
395B TYR* 3.6 28.7 - + + -
398B THR* 3.2 31.0 - - + +
399B GLN* 2.9 15.3 + - - -
501B UDP 4.2 0.3 + - - -
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LEU* 4.1 9.2 - - + -
269B ILE* 3.6 26.7 - - + +
370B ILE 2.9 17.9 + - - +
371B ALA 3.6 4.7 - - - +
373B TYR* 1.3 76.8 - - - +
375B ALA* 1.3 56.6 + - - +
398B THR* 3.8 14.5 - - - +
399B GLN* 3.6 10.5 + - - +
402B ARG* 2.8 28.8 + - - +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ILE* 4.6 9.8 - - + +
272B LEU* 3.9 30.5 - - + -
273B GLU* 4.7 7.0 - - + +
281B LEU* 4.0 15.7 - - + +
371B ALA 2.9 16.0 + - - +
372B LEU 4.0 4.3 - - - +
373B TYR 3.2 0.4 - - - -
374B ALA* 1.3 76.9 - - - +
376B SER* 1.3 59.4 + - - +
377B ASP* 3.7 5.2 + - - +
402B ARG* 3.3 25.8 + - - +
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Residues in contact with SER 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 3.5 25.8 - - - +
283B VAL* 3.4 37.3 - - - +
372B LEU* 2.7 21.8 + - - +
373B TYR 3.0 5.8 + - - -
374B ALA 3.2 0.2 - - - -
375B ALA* 1.3 78.6 - - - +
377B ASP* 1.3 59.4 + - - +
378B ALA 3.8 2.7 - - - -
395B TYR* 2.9 16.8 + - - -
399B GLN* 3.6 6.6 + - - +
402B ARG* 3.2 12.9 - - - -
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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