Contacts of the helix formed by residues 269 - 274 (chain A) in PDB entry 3NUI
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 TRP 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 2.8 34.1 + - + -
104A SER* 3.5 9.8 - - - +
105A PRO* 3.9 12.1 - - + -
257A GLU* 3.5 39.7 - - + +
260A CYS 4.7 1.3 - - - -
261A GLY* 3.9 11.4 - - - -
262A PHE* 3.6 31.6 - + - -
265A THR* 4.0 4.7 - - - -
267A ASN* 3.8 1.1 - - - +
268A THR* 1.4 98.7 - - + +
270A GLY* 1.3 63.8 + - - +
271A CYS* 3.7 12.3 - - - -
272A VAL* 3.1 31.1 + - + +
273A THR* 3.2 14.4 + - - +
281A ILE* 3.8 21.8 - - + -
283A SER* 4.5 5.2 - - - -
298A ILE* 4.0 28.0 - - + -
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PRO* 3.5 18.8 - - - -
257A GLU* 2.7 17.3 + - - -
260A CYS* 3.8 12.3 + - - +
265A THR* 3.6 17.6 + - - -
269A TRP* 1.3 71.7 - - - +
271A CYS* 1.3 54.5 + - - -
273A THR* 3.0 2.0 + - - -
274A TYR* 3.0 34.6 + - - -
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Residues in contact with CYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 4.0 15.5 - - - -
224A PRO* 3.4 0.8 - - - +
255A SER* 3.7 3.8 - - - +
257A GLU* 2.9 19.2 + - - +
269A TRP* 3.2 13.2 - - - -
270A GLY* 1.3 76.3 - - - +
272A VAL* 1.3 60.7 + - - +
274A TYR 3.5 0.2 - - - -
275A ASP* 2.9 6.9 + - - -
276A PHE* 2.9 71.3 + - + +
278A PRO* 3.8 24.9 - - + -
281A ILE* 4.3 4.9 - - - -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 4.3 15.3 - - + -
267A ASN* 3.8 25.5 + - + +
268A THR* 5.3 1.3 - - - +
269A TRP* 3.1 38.2 + - + +
271A CYS* 1.3 75.4 - - - +
273A THR* 1.3 67.9 + - - +
275A ASP* 2.9 27.0 + - - +
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A THR* 2.7 38.1 + - - +
267A ASN* 3.0 37.7 - - + +
269A TRP 3.4 3.1 - - - +
270A GLY 3.0 4.7 + - - +
272A VAL* 1.3 79.3 - - - +
274A TYR* 1.3 76.5 + - - +
275A ASP* 3.7 6.4 + - - +
375A ILE* 3.7 19.4 - - - +
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Residues in contact with TYR 274 (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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224A PRO* 4.0 11.2 - - + -
225A VAL* 3.6 24.9 - - + +
233A PRO* 3.5 21.2 - - + +
234A PRO* 3.7 31.0 - - + -
236A LYS* 6.1 3.4 - - - -
239A PHE* 3.8 23.6 - + + +
240A GLN* 3.0 21.0 + - - +
265A THR* 5.3 0.9 - - + -
270A GLY* 3.0 20.1 + - - +
271A CYS 3.5 0.2 - - - -
273A THR* 1.3 93.8 - - - +
275A ASP* 1.3 69.2 + - - +
276A PHE* 3.1 11.1 + - + -
375A ILE* 3.6 20.5 - - + +
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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