Contacts of the helix formed by residues 321 - 329 (chain H) in PDB entry 5N9G
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 321 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394F ARG* 5.0 6.9 + - - +
402F PHE* 4.1 14.8 - - + -
406F GLN* 5.8 0.3 + - - -
184G ALA* 5.2 4.9 - - - +
190G ALA 3.5 20.6 + - - +
191G GLU* 3.8 21.0 - - - +
192G TYR 4.1 8.8 + - - +
193G ASN* 4.7 3.0 + - - -
318H VAL* 3.8 14.0 - - + +
319H GLY 3.6 2.6 - - - -
320H THR* 1.4 71.8 - - - +
322H PHE* 1.4 59.2 + - - +
323H SER* 3.5 8.3 + - - -
324H MET* 3.3 24.3 + - - +
325H ILE* 3.3 24.0 + - - +
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Residues in contact with PHE 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G GLU* 3.3 22.4 - - - +
203G ARG* 3.1 35.2 - - - -
315H ILE* 6.1 0.4 - - + -
320H THR* 3.0 25.2 + - - -
321H ASP* 1.4 68.7 - - - +
323H SER* 1.4 59.0 + - - +
325H ILE* 3.8 7.0 - - + +
326H GLY* 2.9 25.1 + - - -
334H ARG* 3.3 27.9 - - + +
337H ILE* 3.9 27.0 - - + +
338H LYS* 3.5 26.7 - - + -
341H PHE* 3.5 50.3 - + + -
342H LYS* 5.6 0.4 - - + -
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Residues in contact with SER 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G GLU* 3.8 2.2 + - - -
193G ASN* 3.1 42.9 + - - -
196G ARG* 5.1 5.5 + - - -
321H ASP* 3.3 4.1 + - - -
322H PHE* 1.4 77.0 - - - +
324H MET* 1.4 62.3 + - - +
326H GLY* 3.3 2.9 + - - -
327H GLN* 3.3 33.1 + - - +
334H ARG* 3.7 20.3 - - - +
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Residues in contact with MET 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F PHE* 3.9 16.2 - - + -
405F ALA* 3.7 28.0 - - + +
406F GLN* 3.5 37.9 - - + +
318H VAL* 3.8 24.5 - - + -
321H ASP* 3.3 25.9 + - - +
323H SER* 1.4 73.4 - - - +
325H ILE* 1.3 64.8 + - - +
327H GLN* 3.2 41.3 + - - +
328H LEU* 3.3 17.3 + - - +
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Residues in contact with ILE 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311H PHE* 4.9 4.9 - - + -
314H ALA* 3.4 39.3 - - + +
315H ILE* 4.5 7.6 - - + +
318H VAL* 3.9 14.6 - - + -
319H GLY 3.6 24.5 - - - +
321H ASP 3.3 20.1 + - - +
322H PHE* 3.9 10.5 - - + +
323H SER 3.3 0.2 - - - -
324H MET* 1.3 76.1 - - - +
326H GLY* 1.3 55.7 + - - +
327H GLN 3.1 1.1 - - - -
328H LEU* 2.9 24.8 + - - +
329H PHE* 3.2 25.2 + - + -
337H ILE* 3.6 26.5 - - + -
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Residues in contact with GLY 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322H PHE 2.9 13.4 + - - -
323H SER 3.3 7.4 + - - -
324H MET 3.3 0.6 - - - -
325H ILE* 1.3 74.3 - - - +
327H GLN* 1.4 55.4 + - - +
329H PHE 2.7 22.6 - - - +
332H ARG 3.1 14.0 - - - +
333H ALA 4.5 5.8 - - - -
334H ARG* 4.8 2.6 + - - -
337H ILE* 3.6 21.0 - - - +
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Residues in contact with GLN 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F ALA 5.6 1.6 + - - -
406F GLN* 5.4 7.5 + - - +
193G ASN* 5.6 0.5 + - - -
323H SER* 3.3 23.6 + - - +
324H MET* 3.2 33.5 + - - +
325H ILE 3.1 0.6 - - - -
326H GLY* 1.4 74.7 - - - +
328H LEU* 1.4 62.1 + - + +
329H PHE 3.3 5.0 - - - +
330H PRO* 4.8 3.5 - - - +
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Residues in contact with LEU 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F ALA* 6.6 0.4 - - + -
314H ALA* 4.2 15.0 - - + -
317H MET* 5.6 9.2 - - - -
318H VAL* 3.6 30.7 - - + -
324H MET* 3.5 18.8 - - - +
325H ILE* 2.9 16.4 + - - +
327H GLN* 1.4 79.4 - - + +
329H PHE* 1.3 61.9 + - + +
330H PRO* 3.7 9.6 - - - +
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Residues in contact with PHE 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H TRP* 3.6 20.4 - + - -
307H GLU* 3.7 28.0 - - + -
310H MET* 3.8 15.7 - - + -
311H PHE* 3.6 33.2 - - - -
314H ALA* 4.3 4.7 - - + -
325H ILE* 3.2 33.7 + - + +
326H GLY 2.7 23.4 - - - +
327H GLN* 4.2 2.3 - - - -
328H LEU* 1.3 81.2 - - + +
330H PRO* 1.3 68.3 - - + +
331H HIS 3.4 0.7 - - - +
332H ARG* 3.3 29.5 - - + +
337H ILE* 3.9 12.3 - - + -
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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