Contacts of the helix formed by residues 241 - 249 (chain A) in PDB entry 5I2S
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 6.4 0.2 - - + -
42A GLN* 4.6 6.8 + - - +
239A MET* 3.5 5.9 - - + +
240A ALA* 1.3 76.0 - - - +
242A LYS* 1.3 59.5 + - - +
243A ASP* 3.4 13.9 + - - +
244A LEU* 3.1 39.4 + - + +
245A PHE* 2.9 26.8 + - - +
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Residues in contact with LYS 242 (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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44A LYS* 4.2 20.0 - - - +
238A GLU* 3.2 26.8 + - - +
239A MET 4.0 4.7 - - - +
240A ALA* 3.2 30.5 + - - +
241A ASP* 1.3 73.1 + - - +
243A ASP* 1.3 59.5 + - - +
245A PHE* 3.5 14.2 - - + +
246A ALA* 3.0 28.1 + - - +
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Residues in contact with ASP 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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241A ASP* 3.2 10.1 + - - +
242A LYS* 1.3 77.3 - - - +
244A LEU* 1.3 60.3 + - - +
246A ALA* 3.3 6.7 + - - +
247A ALA* 2.9 30.2 + - - +
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Residues in contact with LEU 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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41A LEU* 4.3 4.0 - - + -
195A LEU* 3.6 56.3 - - + +
196A SER* 4.9 4.3 - - - +
198A LEU* 4.5 6.3 - - + -
239A MET* 3.7 19.7 - - + -
241A ASP* 3.1 31.8 + - + +
243A ASP* 1.3 76.3 - - - +
245A PHE* 1.3 64.9 + - - +
247A ALA* 3.2 9.0 + - + -
248A ALA* 2.9 24.5 + - - +
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Residues in contact with PHE 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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220A LYS* 3.7 31.0 - - + -
227A TRP* 3.8 29.4 - - + -
228A GLY* 3.8 16.8 - - - -
229A VAL* 3.6 14.4 - - + -
238A GLU* 6.2 0.2 - - + -
239A MET* 3.6 30.6 - - + +
241A ASP 2.9 12.9 + - - +
242A LYS* 3.5 18.4 - - + +
244A LEU* 1.3 77.9 - - - +
246A ALA* 1.3 65.5 + - + +
248A ALA* 3.3 12.9 + - - +
249A ARG 3.8 2.9 + - - -
250A PHE* 3.6 32.2 + + + -
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Residues in contact with ALA 246 (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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242A LYS 3.0 18.3 + - - +
243A ASP* 3.7 7.2 - - - +
245A PHE* 1.3 78.8 - - + +
247A ALA* 1.3 62.4 + - - +
249A ARG* 3.1 22.2 + - - +
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Residues in contact with ALA 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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243A ASP 2.9 17.2 + - - +
244A LEU* 3.2 13.2 + - + +
246A ALA* 1.3 73.3 - - - +
248A ALA* 1.3 64.8 + - - +
249A ARG* 3.1 33.4 + - - +
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Residues in contact with ALA 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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196A SER 5.9 1.3 - - - -
198A LEU* 3.6 37.6 - - + +
199A GLY* 4.9 4.3 - - - -
244A LEU* 2.9 11.7 + - - +
245A PHE* 3.6 5.8 - - - +
246A ALA 3.2 0.8 - - - -
247A ALA* 1.3 76.5 - - - +
249A ARG* 1.3 68.2 + - - +
250A PHE* 3.4 34.1 + - + -
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Residues in contact with ARG 249 (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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220A LYS* 6.2 1.1 - - - +
245A PHE 3.8 1.4 + - - -
246A ALA 3.1 16.8 + - - +
247A ALA* 3.1 40.3 + - - +
248A ALA* 1.3 80.7 - - - +
250A PHE* 1.3 68.5 + - - +
251A PRO* 3.4 5.0 - - - +
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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