Contacts of the helix formed by residues 243 - 254 (chain A) in PDB entry 4I2C
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 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ASN* 4.7 7.2 + - - +
181A LEU* 5.3 0.2 - - - +
239A ALA 3.1 12.2 + - - +
240A VAL* 3.0 17.3 + - - +
242A ASN* 1.3 76.9 - - - +
244A GLU* 1.3 59.4 + - - +
245A ARG* 3.3 14.1 + - - +
246A TYR* 2.9 28.9 + - + +
247A LYS* 3.0 31.4 + - - +
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Residues in contact with GLU 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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242A ASN 3.5 5.3 + - - +
243A ASP* 1.3 71.5 + - - +
245A ARG* 1.3 60.2 + - - +
247A LYS* 2.8 35.0 + - - +
248A SER* 3.1 33.6 + - - -
267A PHE* 4.0 13.2 - - + -
272A ARG* 4.5 19.4 + - - +
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Residues in contact with ARG 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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181A LEU* 3.4 47.8 + - + +
182A ARG* 5.1 13.9 - - - +
183A GLU* 6.0 0.2 + - - -
243A ASP* 3.3 12.3 + - - +
244A GLU* 1.3 73.5 - - - +
246A TYR* 1.3 60.2 + - - +
248A SER* 3.4 2.4 + - - -
249A PHE* 2.9 28.8 + - - +
264A GLU* 3.7 41.8 + - - +
267A PHE* 3.7 44.4 - - + +
268A ARG* 4.4 11.1 - - - +
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Residues in contact with TYR 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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174A ILE* 4.1 19.0 - - + +
177A GLU* 3.0 41.2 + - + -
178A ASN* 3.9 22.2 - - - +
181A LEU* 3.7 13.2 - - + +
240A VAL* 3.2 46.4 - - + +
241A LEU* 3.9 25.7 - - + +
243A ASP* 2.9 15.1 + - + +
244A GLU 3.4 0.2 - - - -
245A ARG* 1.3 76.4 - - - +
247A LYS* 1.3 66.0 + - + +
249A PHE* 3.3 5.2 + + - +
250A LYS* 3.0 46.5 + - + +
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Residues in contact with LYS 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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241A LEU 3.4 22.9 - - - +
242A ASN* 3.4 24.8 + - - +
243A ASP 3.0 12.9 + - - +
244A GLU* 2.8 38.4 + - - +
246A TYR* 1.3 79.1 - - + +
248A SER* 1.4 57.7 + - - +
250A LYS* 3.5 4.9 + - - +
251A LEU* 3.0 31.0 + - - +
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Residues in contact with SER 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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244A GLU* 3.1 18.2 + - - -
245A ARG 3.7 2.0 - - - -
247A LYS* 1.4 74.2 - - - +
249A PHE* 1.3 59.9 + - - +
251A LEU* 3.4 5.0 + - - -
252A PHE* 2.9 56.5 + - - -
263A ALA 5.7 0.4 - - - -
267A PHE* 3.6 20.2 - - - -
272A ARG* 3.4 29.8 + - - -
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Residues in contact with PHE 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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177A GLU* 4.0 28.5 - - + -
180A GLU* 4.2 16.8 - - - -
181A LEU* 3.6 42.8 - - + -
245A ARG 2.9 18.3 + - - +
246A TYR* 3.3 7.8 + + - +
248A SER* 1.3 75.8 - - - +
250A LYS* 1.3 68.3 + - + +
252A PHE* 5.2 0.2 - - - -
253A THR* 2.7 63.1 + - + +
260A LEU* 3.6 27.6 - - + -
263A ALA* 4.5 15.3 - - + -
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Residues in contact with LYS 250 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLU* 2.7 43.4 + - - +
246A TYR* 3.0 43.9 + - + +
247A LYS* 3.8 5.6 - - - +
249A PHE* 1.3 85.2 - - + +
251A LEU* 1.3 62.5 + - - +
253A THR* 3.5 6.7 + - - +
254A SER* 3.2 23.7 + - - -
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Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A LYS 3.0 17.6 + - - +
248A SER* 3.8 4.9 - - - +
250A LYS* 1.3 76.5 - - - +
252A PHE* 1.3 66.2 + - + +
254A SER* 2.6 25.4 + - - +
272A ARG 3.4 25.8 - - - +
273A THR* 4.1 13.0 - - + -
274A LEU* 3.9 32.8 - - + +
296A TYR* 4.4 7.0 - - - +
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Residues in contact with PHE 252 (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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248A SER* 2.9 37.6 + - - +
251A LEU* 1.3 82.3 - - + +
253A THR* 1.3 60.6 + - - +
254A SER 3.1 0.2 - - - -
255A VAL* 3.2 17.3 + - - +
258A VAL* 3.4 20.9 - - + +
263A ALA* 3.5 32.3 - - + -
266A TRP* 3.7 28.9 - + + -
267A PHE 3.8 7.6 - - - -
271A PHE 3.3 33.7 - - - -
272A ARG* 3.8 20.2 - - - -
273A THR 4.1 0.9 - - - -
274A LEU* 4.0 9.9 - - + -
277A ILE* 3.4 23.6 - - + -
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Residues in contact with THR 253 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A PHE* 2.7 53.7 + - + +
250A LYS* 3.5 10.0 + - - +
252A PHE* 1.3 70.8 - - - +
254A SER* 1.4 58.0 + - - +
255A VAL 3.0 5.6 - - - -
258A VAL 3.5 11.7 - - - +
259A GLY* 3.7 31.0 - - - +
263A ALA* 3.8 5.2 - - + -
601A NA 2.4 25.7 - - - -
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Residues in contact with SER 254 (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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250A LYS 3.2 14.2 + - - -
251A LEU* 2.6 22.1 + - - +
252A PHE 3.1 1.2 - - - -
253A THR* 1.4 74.9 - - - +
255A VAL* 1.3 57.8 + - - +
256A PHE 3.9 1.6 + - - -
296A TYR* 2.6 39.9 + - - -
299A LEU* 6.0 1.6 - - - +
300A VAL* 4.9 14.2 - - - +
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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