Contacts of the helix formed by residues 298 - 305 (chain A) in PDB entry 4N0N
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 GLY 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A PHE* 1.3 77.5 - - - +
299A ALA* 1.3 65.1 + - - -
300A ALA 3.3 4.2 + - - -
301A VAL* 3.3 12.1 + - - +
302A CYS* 3.3 9.9 + - - -
314A PRO* 3.7 3.8 - - - -
315A ALA 3.7 7.6 - - - -
317A HIS* 3.1 24.8 + - - -
319A THR* 3.0 20.7 + - - -
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Residues in contact with ALA 299 (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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298A GLY* 1.3 72.3 - - - -
300A ALA* 1.3 53.2 + - - +
302A CYS* 3.6 3.1 - - - +
303A ASP* 2.7 47.5 + - - +
314A PRO* 3.5 25.4 - - + +
315A ALA 4.7 0.4 + - - -
317A HIS 4.6 0.4 + - - -
318A THR* 5.7 0.6 - - - +
319A THR 5.2 0.6 - - - +
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Residues in contact with ALA 300 (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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298A GLY 3.3 1.2 + - - -
299A ALA* 1.3 78.8 - - - +
301A VAL* 1.3 60.1 + - - +
303A ASP* 3.5 10.9 - - - +
304A LEU* 3.4 20.3 + - - +
319A THR 3.3 25.5 + - - +
320A LYS* 5.3 0.2 - - - -
321A VAL* 3.8 21.4 - - + +
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Residues in contact with VAL 301 (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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297A PHE* 3.5 38.8 - - + -
298A GLY 3.3 3.1 + - - +
299A ALA 3.3 0.2 - - - -
300A ALA* 1.3 73.6 - - - +
302A CYS* 1.3 61.3 + - - +
304A LEU* 2.9 32.0 + - + +
305A ILE* 3.1 9.7 + - + +
319A THR* 3.6 30.5 - - + -
321A VAL* 3.7 14.1 - - + -
379A VAL* 3.2 28.3 - - + +
380A THR* 4.1 7.4 - - - +
382A ALA 4.6 3.4 - - - +
386A LEU* 5.0 4.0 - - + -
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Residues in contact with CYS 302 (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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294A CYS* 4.4 1.3 - - - -
297A PHE* 3.8 21.3 - - - -
298A GLY 3.3 7.3 + - - +
299A ALA* 3.3 8.0 + - - +
301A VAL* 1.3 77.5 - - - +
303A ASP* 1.3 58.1 + - - +
305A ILE* 3.3 10.2 + - - +
306A LYS* 2.9 37.0 + - - +
312A TYR* 4.2 26.5 - - + +
313A GLU 4.4 0.9 - - - -
314A PRO* 3.6 39.9 - - + -
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Residues in contact with ASP 303 (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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299A ALA* 2.7 34.7 + - - +
300A ALA* 3.5 11.4 - - - +
302A CYS* 1.3 73.1 - - - +
304A LEU* 1.3 61.3 + - - +
306A LYS* 3.2 29.2 + - - +
400A LYS 4.5 7.4 - - - +
401A PHE* 5.4 3.9 - - - -
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Residues in contact with LEU 304 (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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300A ALA 3.4 8.2 + - - +
301A VAL* 2.9 17.9 + - - +
303A ASP* 1.3 81.4 - - - +
305A ILE* 1.3 56.9 + - - +
306A LYS 3.8 0.5 + - - -
307A GLY 4.9 0.3 + - - -
321A VAL* 4.1 26.9 - - + -
323A PHE* 5.4 1.8 - - + -
379A VAL* 3.8 37.0 - - + +
386A LEU* 4.5 4.3 - - + -
388A ILE* 4.3 8.7 - - + -
395A LEU* 6.0 1.3 - - + -
399A LEU* 3.4 31.4 - - + +
400A LYS 4.4 6.6 - - - +
401A PHE* 3.3 46.1 - - + +
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Residues in contact with ILE 305 (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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160A PRO* 4.4 3.1 - - + -
297A PHE* 4.1 20.9 - - + -
301A VAL* 3.1 11.6 + - + +
302A CYS* 3.7 8.5 - - - +
304A LEU* 1.3 74.9 - - - +
306A LYS* 1.3 63.8 + - - +
307A GLY 3.2 3.1 - - - -
308A ILE* 3.0 11.1 + - + -
309A TYR* 3.0 51.4 + - + +
312A TYR* 4.2 14.8 - - + -
376A VAL* 4.7 8.7 - - + +
379A VAL* 3.8 28.0 - - + -
380A THR* 4.0 18.8 - - - +
399A LEU* 4.6 10.1 - - + -
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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