Contacts of the helix formed by residues 359 - 367 (chain D) in PDB entry 6PUO
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 VAL 359 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329D VAL* 5.9 0.9 - - + -
330D LEU 4.8 2.5 - - - +
331D GLU 3.0 15.2 + - - +
332D GLY* 3.8 2.9 - - - -
333D GLY* 3.4 24.5 - - - +
334D PRO* 5.4 0.9 - - + -
336D THR* 3.4 24.0 - - - +
337D LEU* 3.8 30.5 - - + +
340D ILE* 5.9 5.8 - - + -
358D ARG* 1.3 78.9 - - - +
360D ALA* 1.3 65.4 + - - +
361D ASP 3.4 1.8 - - - -
362D VAL* 3.7 13.8 + - + +
363D ILE* 3.4 18.8 + - + +
387D PHE* 4.6 9.4 - - + -
402D TRP* 5.5 4.9 - - + -
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Residues in contact with ALA 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D VAL* 5.1 4.3 - - + -
330D LEU* 4.0 22.2 - - + +
331D GLU 3.6 1.4 + - - -
352D VAL* 4.7 10.3 - - + +
353D VAL 3.8 25.6 - - - +
356D SER 4.7 0.9 - - - +
357D GLY* 3.8 14.1 - - - -
359D VAL* 1.3 81.9 - - - +
361D ASP* 1.3 59.3 + - - +
363D ILE* 3.3 8.8 + - - +
364D ALA* 2.9 26.1 + - - +
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Residues in contact with ASP 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D VAL 4.0 1.0 - - - +
355D GLY* 2.9 36.0 + - - +
356D SER 3.5 5.4 + - - -
357D GLY* 2.8 37.5 + - - +
359D VAL 3.4 0.2 - - - -
360D ALA* 1.3 75.9 - - - +
362D VAL* 1.3 60.4 + - - +
364D ALA* 3.5 7.6 - - + +
365D GLN* 2.9 35.6 + - + +
386D PHE* 3.7 26.6 - - + -
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Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D ARG 3.6 24.5 - - - +
359D VAL* 3.7 15.7 - - + +
360D ALA 3.2 0.2 - - - -
361D ASP* 1.3 76.4 - - - +
363D ILE* 1.3 58.3 + - + +
365D GLN* 3.2 5.3 + - - +
366D VAL* 3.0 34.5 + - + +
379D ILE* 5.2 7.2 - - + -
382D LYS* 4.7 22.7 - - + +
383D LEU* 5.8 1.6 - - - +
386D PHE* 4.6 21.5 - - + -
387D PHE* 4.9 5.6 - - + -
406D ILE* 4.4 20.9 - - + -
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Residues in contact with ILE 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D LEU* 4.1 13.9 - - + -
340D ILE* 5.8 7.6 - - + -
352D VAL* 4.9 13.7 - - + -
359D VAL* 3.4 16.8 - - + +
360D ALA* 3.3 6.7 + - - +
362D VAL* 1.3 76.3 - - + +
364D ALA* 1.3 61.0 + - - +
366D VAL* 3.8 4.0 - - - +
367D ALA* 3.2 24.4 + - - +
406D ILE* 3.8 40.4 - - + -
409D ILE* 4.7 15.0 - - + -
410D VAL* 4.7 6.3 - - + -
416D LEU* 4.3 32.3 - - + -
418D VAL* 5.1 0.2 - - - +
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Residues in contact with ALA 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D VAL* 5.0 2.0 - - + +
354D GLU* 4.2 20.4 - - + -
355D GLY 5.1 0.7 - - - +
360D ALA 2.9 16.6 + - - +
361D ASP* 3.5 12.6 - - + +
362D VAL 3.2 0.2 - - - -
363D ILE* 1.3 79.3 - - - +
365D GLN* 1.3 59.3 + - + +
367D ALA* 4.0 3.5 + - - +
418D VAL* 3.8 24.7 - - + -
420D ARG* 2.4 37.1 + - - +
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Residues in contact with GLN 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D ASP* 2.9 16.2 + - + +
362D VAL* 3.9 3.1 - - - +
364D ALA* 1.3 79.3 - - + +
366D VAL* 1.3 60.6 + - + +
367D ALA 3.2 3.5 + - - -
368D ASN* 4.4 5.5 + - - +
369D LEU* 5.2 1.7 + - - +
382D LYS* 3.3 30.6 - - - +
386D PHE* 3.2 40.4 - - - -
420D ARG* 4.6 3.5 + - - +
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Residues in contact with VAL 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D VAL* 3.0 24.5 + - + +
363D ILE* 3.8 13.2 - - + +
365D GLN* 1.3 74.3 - - + +
367D ALA* 1.3 64.6 + - - +
368D ASN 3.3 3.1 + - - -
369D LEU* 3.6 18.3 + - + +
374D ILE* 3.7 36.6 - - + +
378D LEU* 4.9 10.5 - - + -
382D LYS* 5.7 5.6 - - - +
406D ILE* 3.9 23.1 - - + -
410D VAL* 3.8 16.6 - - + +
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Residues in contact with ALA 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D ILE* 3.2 18.0 + - + +
364D ALA* 4.0 10.3 + - - +
365D GLN 3.2 2.2 - - - -
366D VAL* 1.3 80.0 - - - +
368D ASN* 1.3 68.3 + - - +
369D LEU 4.2 0.9 - - - +
410D VAL* 3.6 22.1 - - + +
416D LEU* 5.3 10.3 - - + -
418D VAL* 4.9 13.7 - - + -
420D ARG* 4.7 3.1 - - - +
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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