Contacts of the helix formed by residues 240 - 249 (chain A) in PDB entry 4CCZ
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 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ILE* 5.2 0.2 - - - -
232A SER 5.7 1.6 - - - +
233A GLY 3.6 9.6 - - - +
234A ARG* 3.8 35.4 - - + +
239A GLN* 1.3 73.8 - - - +
241A GLY* 1.3 54.6 + - - +
242A GLU* 3.9 4.8 + - - +
243A GLY 3.0 15.6 + - - -
244A PHE* 2.7 36.1 + - - +
360A LEU 3.0 7.3 + - - -
361A GLU* 4.1 13.7 - - + -
362A PRO* 3.6 16.0 - - + +
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Residues in contact with GLY 241 (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 ILE* 4.5 11.2 - - - +
233A GLY 3.8 9.1 + - - -
240A THR* 1.3 72.2 - - - +
242A GLU* 1.3 62.7 + - - +
244A PHE* 3.1 10.0 + - - +
245A VAL* 3.0 27.4 + - - +
258A LEU* 5.8 0.4 - - - -
270A PHE* 5.9 2.7 - - - -
273A ILE* 6.5 0.7 - - - -
274A ILE* 4.2 25.4 - - - -
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Residues in contact with GLU 242 (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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240A THR* 3.3 4.5 + - - +
241A GLY* 1.3 75.0 - - - +
243A GLY* 1.3 63.9 + - - +
245A VAL* 3.3 25.3 - - - +
246A ILE* 3.3 12.1 + - - +
273A ILE* 4.7 21.3 - - + +
274A ILE* 4.7 1.5 - - - +
277A CYS* 3.8 20.5 - - + -
362A PRO* 3.7 17.5 - - + +
364A ARG* 2.6 43.3 + - - +
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Residues in contact with GLY 243 (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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239A GLN* 3.6 5.8 + - - -
240A THR* 3.0 14.3 + - - -
242A GLU* 1.3 78.0 - - - +
244A PHE* 1.3 56.6 + - - +
246A ILE* 3.5 4.1 + - - +
247A SER* 2.8 33.4 + - - -
358A SER* 3.8 8.4 - - - -
360A LEU 4.2 7.2 - - - -
362A PRO* 3.8 22.5 - - - +
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Residues in contact with PHE 244 (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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196A ILE* 4.2 20.9 - - + -
199A THR* 3.8 17.7 - - + -
224A ILE* 3.9 19.1 - - + -
225A SER 4.2 0.2 - - - -
226A GLY* 3.6 38.6 - - - -
235A THR* 4.9 13.2 - - + -
239A GLN* 3.5 13.8 - - + +
240A THR 2.7 17.0 + - - +
241A GLY* 3.2 16.8 - - - +
243A GLY* 1.3 72.4 - - - +
245A VAL* 1.3 70.1 + - + +
247A SER* 3.2 12.0 + - - -
248A VAL* 3.3 24.6 + - + +
256A ILE* 3.9 22.7 - - + -
257A GLY 4.1 4.9 - - - -
258A LEU* 5.0 2.5 - - + -
274A ILE* 5.0 5.4 - - + -
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Residues in contact with VAL 245 (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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241A GLY 3.0 14.6 + - - +
242A GLU* 3.3 15.9 - - - +
244A PHE* 1.3 78.9 - - + +
246A ILE* 1.3 68.0 + - + +
248A VAL* 3.3 2.3 + - - +
249A SER* 2.8 38.8 + - - +
256A ILE* 3.7 32.1 - - + +
274A ILE* 3.9 30.1 - - + +
277A CYS* 4.2 26.5 - - + +
278A THR* 5.1 5.8 - - - -
364A ARG* 5.4 0.2 - - - +
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Residues in contact with ILE 246 (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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242A GLU 3.3 8.9 + - - +
243A GLY 3.7 6.3 - - - +
245A VAL* 1.3 83.7 - - + +
247A SER* 1.3 62.1 + - - +
248A VAL 3.2 1.0 + - - -
249A SER* 3.6 14.1 + - - -
250A HIS* 4.9 2.4 + - - -
356A LEU* 3.9 30.5 - - + +
357A LEU 3.5 31.6 - - - +
358A SER* 3.8 4.5 - - - -
362A PRO* 3.4 34.8 - - + -
363A PHE 4.6 0.7 - - - +
364A ARG* 4.1 18.2 - - + +
466A LYS* 4.2 17.2 - - + +
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Residues in contact with SER 247 (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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199A THR* 3.8 10.8 - - - -
203A LYS* 3.7 11.7 - - - +
239A GLN* 2.7 31.4 + - - -
243A GLY 2.8 13.5 + - - -
244A PHE 3.2 7.1 + - - -
246A ILE* 1.3 77.3 - - - +
248A VAL* 1.3 60.0 + - - +
250A HIS* 3.2 20.3 - - - -
358A SER* 3.8 2.8 - - - -
464A GLN 3.7 13.9 - - - -
465A GLY* 3.5 11.9 - - - -
466A LYS* 4.6 8.5 - - - +
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Residues in contact with VAL 248 (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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199A THR* 3.9 19.3 - - + -
202A ALA* 4.6 12.8 - - + +
203A LYS* 4.6 7.4 - - + +
224A ILE* 4.0 27.6 - - + +
244A PHE* 3.3 26.4 + - + +
245A VAL 3.7 4.7 - - - +
246A ILE 3.2 0.2 - - - -
247A SER* 1.3 84.4 - - - +
249A SER* 1.3 63.7 + - - +
250A HIS* 3.2 8.9 - - - -
251A GLY* 3.2 13.8 + - - -
253A PRO* 3.7 9.8 - - + +
256A ILE* 3.8 23.3 - - + -
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Residues in contact with SER 249 (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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245A VAL* 2.8 26.0 + - - +
246A ILE* 3.6 12.4 + - - -
248A VAL* 1.3 77.8 - - - +
250A HIS* 1.3 54.0 + - - +
252A GLU* 2.8 34.5 + - - +
253A PRO* 3.6 7.8 - - - +
256A ILE* 6.0 0.6 - - - +
278A THR* 5.4 4.3 + - - -
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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