Contacts of the helix formed by residues 355 - 365 (chain D) in PDB entry 6NYY
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 THR 355 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354D LYS* 1.3 71.5 - - - +
356D LEU* 1.3 57.8 + - - -
358D ALA* 3.2 6.0 + - - +
359D LYS* 2.9 31.6 + - - +
405D PHE* 4.3 4.6 - - + -
407D ASP* 3.6 13.6 + - - +
801D ANP 2.7 23.3 + - - +
802D MG 2.2 30.3 - - - -
440E GLY* 3.7 27.6 - - - -
441E PHE* 3.9 22.4 - - + +
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Residues in contact with LEU 356 (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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305D VAL* 3.8 27.8 - - + -
309D ASP* 4.0 6.1 - - + +
310D VAL* 3.7 22.0 - - + -
353D GLY* 4.3 5.8 - - - -
354D LYS 3.4 0.2 - - - -
355D THR* 1.3 77.6 - - - +
357D LEU* 1.3 57.3 + - - +
359D LYS* 3.0 14.3 + - + +
360D ALA* 2.9 27.7 + - - +
801D ANP 3.1 80.2 + - + +
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Residues in contact with LEU 357 (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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307D PHE* 4.5 13.5 - - + -
310D VAL* 3.8 18.8 - - + +
313D CYS* 4.8 5.4 - - - -
316D ALA* 3.8 18.4 - - + +
317D LYS* 3.7 29.6 - - + +
320D ILE* 3.7 31.1 - - + +
346D LEU* 4.8 4.0 - - + -
353D GLY 3.3 16.9 + - - +
354D LYS* 3.8 4.7 + - - +
355D THR 3.3 0.6 - - - -
356D LEU* 1.3 77.6 - - - +
358D ALA* 1.3 50.8 + - - +
360D ALA* 4.1 1.9 - - + +
361D THR* 2.7 30.3 + - - -
475D ILE* 3.7 24.5 - - + -
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Residues in contact with ALA 358 (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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346D LEU* 5.0 3.6 - - + +
354D LYS 3.5 6.7 + - - +
355D THR 3.2 9.1 + - - +
356D LEU 3.1 0.6 - - - -
357D LEU* 1.3 77.4 - - - +
359D LYS* 1.3 63.3 + - - +
360D ALA 3.3 0.2 - - - -
361D THR* 3.4 7.3 + - - -
362D ALA* 3.3 15.8 + - - +
369D PHE* 3.6 9.3 - - + -
405D PHE* 3.6 41.1 - - + -
450D LEU* 4.9 6.7 - - + -
441E PHE* 3.4 14.7 - - + -
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Residues in contact with LYS 359 (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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303D ILE* 3.7 17.8 - - + +
305D VAL* 3.9 23.7 - - + +
355D THR* 2.9 23.4 + - - +
356D LEU* 3.0 18.8 + - + +
358D ALA* 1.3 76.1 - - - +
360D ALA* 1.3 64.3 + - - +
362D ALA* 3.3 5.9 + - - +
363D GLY 3.1 15.4 + - - -
801D ANP 5.2 9.1 + - - -
439E ASP* 4.9 7.9 + - - -
440E GLY* 3.3 35.0 + - - -
441E PHE* 3.6 26.9 - - + +
443E THR* 5.1 4.2 + - - -
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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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305D VAL* 3.4 15.0 - - + +
306D LYS 3.5 27.6 - - - +
307D PHE* 3.9 19.9 - - + -
310D VAL* 4.2 8.7 - - + -
356D LEU 2.9 13.9 + - - +
357D LEU* 4.2 5.4 - - - +
359D LYS* 1.3 76.7 - - - +
361D THR* 1.3 61.4 + - - +
363D GLY* 3.1 5.8 + - - -
364D GLU* 2.9 23.4 + - - +
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Residues in contact with THR 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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307D PHE* 4.3 9.3 - - - -
320D ILE* 3.3 22.9 - - + +
323D PHE* 5.5 3.4 - - + -
324D VAL* 3.9 19.9 - - + +
357D LEU 2.7 22.6 + - - -
358D ALA* 3.4 11.9 + - - -
359D LYS 3.2 0.8 - - - -
360D ALA* 1.3 77.2 - - - +
362D ALA* 1.3 59.9 + - - +
363D GLY 3.4 0.3 + - - -
365D ALA* 3.3 25.8 + - - +
369D PHE* 4.9 2.2 - - + -
403D ILE* 4.2 16.3 - - + +
450D LEU* 4.2 20.3 - - + +
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Residues in contact with ALA 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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299D LEU* 4.5 4.4 - - + +
303D ILE* 3.8 24.1 + - + +
358D ALA 3.3 6.6 + - - +
359D LYS* 3.3 10.1 + - - +
361D THR* 1.3 76.7 - - - +
363D GLY* 1.3 63.3 + - - +
365D ALA* 4.1 10.2 - - - +
367D VAL 5.5 1.9 - - - +
369D PHE* 3.6 42.9 - - + +
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Residues in contact with GLY 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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303D ILE 4.0 16.1 - - - +
305D VAL 3.7 15.7 - - - -
306D LYS* 4.1 12.8 + - - -
359D LYS 3.1 9.4 + - - -
360D ALA 3.1 6.3 + - - -
362D ALA* 1.3 80.6 - - - +
364D GLU* 1.3 64.3 + - - +
365D ALA 3.6 3.1 + - - +
366D ASN* 5.5 0.7 - - - +
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Residues in contact with GLU 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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306D LYS* 3.2 33.7 - - + +
307D PHE* 3.0 47.3 + - + +
324D VAL* 4.2 4.9 - - + -
328D LYS* 3.3 26.5 + - - +
360D ALA 2.9 17.4 + - - +
363D GLY* 1.3 74.9 - - - +
365D ALA* 1.3 65.1 + - - +
366D ASN* 3.5 7.4 + - - +
779D TRP* 3.3 31.7 - - + +
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Residues in contact with ALA 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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324D VAL* 3.8 28.6 - - + +
327D LEU* 5.0 3.6 - - + -
328D LYS* 4.7 1.1 - - - +
361D THR 3.3 19.3 + - - +
362D ALA* 4.1 8.4 - - - +
363D GLY 3.4 6.7 - - - +
364D GLU* 1.3 78.9 - - - +
366D ASN* 1.3 58.7 + - - +
367D VAL* 3.2 32.5 + - + +
403D ILE* 4.1 7.0 - - + -
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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