Contacts of the helix formed by residues 269 - 276 (chain A) in PDB entry 4I6J
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 LEU 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ALA 4.4 2.7 - - - +
238A ARG* 3.6 22.4 - - + -
239A LEU* 3.8 20.4 - - + +
242A HIS* 4.2 12.5 - - + +
267A THR 3.4 17.3 - - - +
268A GLY* 1.3 77.4 - - - +
270A SER* 1.3 65.2 + - - +
271A PRO* 3.4 3.6 - - - -
272A TYR* 2.9 21.0 + - + +
273A LEU* 3.0 21.2 + - + +
278A LEU* 3.8 27.4 - - + -
283A PHE* 3.7 35.9 - - + -
307A GLN* 5.1 5.7 + - - +
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Residues in contact with SER 270 (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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228A TRP* 5.3 0.4 - - - -
268A GLY* 4.6 0.4 - - - -
269A LEU* 1.3 77.0 - - - +
271A PRO* 1.3 80.5 - - - +
272A TYR 3.3 0.2 + - - -
273A LEU* 3.3 9.8 + - - +
274A ARG* 3.1 17.3 + - - +
307A GLN* 4.0 21.7 - - - +
370A TRP* 3.5 14.8 + - - -
376A ARG* 5.2 0.2 - - - -
405A ASP* 2.6 37.7 + - - +
428B TRP* 4.1 10.9 - - - -
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Residues in contact with PRO 271 (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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72A PHE* 4.0 20.3 - - + -
228A TRP* 3.9 35.4 - - + -
269A LEU 3.7 2.2 - - - -
270A SER* 1.3 100.2 - - - +
272A TYR* 1.3 62.8 + - + +
274A ARG* 3.3 0.5 + - - +
275A PHE* 3.1 29.9 + - + +
370A TRP* 4.7 5.4 - - + -
404A LEU* 3.9 29.4 - - + +
405A ASP* 4.0 12.6 - - + -
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Residues in contact with TYR 272 (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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72A PHE* 3.4 22.4 - + - -
228A TRP* 3.9 14.2 - + - -
229A GLN 2.7 37.0 + - - -
231A GLY 3.9 9.9 - - - -
234A GLU* 3.4 8.5 - - + +
235A ALA* 3.5 31.4 - - + -
238A ARG* 3.0 43.5 + - - -
268A GLY 3.7 13.0 - - - -
269A LEU* 2.9 17.3 + - + +
271A PRO* 1.3 74.4 - - + +
273A LEU* 1.3 56.9 + - - +
275A PHE 3.4 0.2 + - - -
276A GLY 2.7 31.4 + - - -
277A CYS* 2.9 15.5 + - + -
278A LEU* 3.3 13.0 + - + -
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Residues in contact with LEU 273 (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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148A HIS* 3.6 2.8 - - - -
269A LEU* 3.0 25.0 + - + +
270A SER* 3.5 7.6 - - - +
272A TYR* 1.3 76.7 - - - +
274A ARG* 1.3 62.9 + - - +
276A GLY* 3.1 10.9 + - - -
278A LEU* 3.9 33.4 - - + +
280A CYS* 3.9 28.5 - - + -
283A PHE* 4.2 13.0 - - + -
307A GLN* 4.3 17.7 - - - +
308A LEU* 4.1 20.6 - - + -
311A ARG* 3.3 29.5 + - - +
428B TRP* 4.5 10.5 - - + -
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Residues in contact with ARG 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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29A LYS* 4.1 19.3 - - - +
69A ARG* 3.0 25.5 - - - +
148A HIS* 3.6 15.6 + - - -
270A SER 3.1 10.5 + - - +
271A PRO 3.8 2.2 - - - +
272A TYR 3.3 0.4 - - - -
273A LEU* 1.3 78.9 - - - +
275A PHE* 1.3 86.4 + - - +
311A ARG* 5.0 3.1 - - - +
404A LEU 3.1 15.8 + - - -
405A ASP* 3.6 32.1 - - + +
406A ALA 2.8 38.2 + - - +
407A ASP* 4.0 29.5 - - + +
428B TRP* 5.1 3.3 - - + -
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Residues in contact with PHE 275 (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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28A ARG 6.0 1.1 - - - -
29A LYS* 3.7 11.7 - - - +
30A GLY 3.4 14.7 + - - -
31A LEU* 3.4 18.0 + - + +
69A ARG* 4.3 24.0 - - + -
72A PHE* 3.5 34.5 - + + -
73A LEU* 4.1 35.0 - - + -
271A PRO 3.1 22.1 + - - +
274A ARG* 1.3 105.3 - - - +
276A GLY* 1.3 60.5 + - - +
277A CYS* 3.5 19.0 + - - -
404A LEU* 3.3 26.2 - - + -
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Residues in contact with GLY 276 (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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30A GLY 3.9 7.2 - - - -
31A LEU 3.4 7.3 + - - -
32A ARG* 2.9 41.0 + - - +
148A HIS* 4.8 6.1 - - - -
272A TYR 2.7 11.0 + - - -
273A LEU 3.1 10.7 + - - -
274A ARG 3.7 0.2 + - - -
275A PHE* 1.3 76.0 - - - +
277A CYS* 1.3 63.7 + - - +
278A LEU 3.0 6.3 - - - -
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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