Contacts of the helix formed by residues 240 - 245 (chain A) in PDB entry 5PIJ
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 ALA 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A CYS* 3.1 9.7 - - - -
239A GLY* 1.3 80.4 - - - +
241A PHE* 1.4 59.3 + - - +
242A LEU 3.2 3.8 - - - -
243A ARG* 3.0 30.8 + - + +
308A SER* 4.3 3.6 - - - +
309A GLN 3.4 38.1 + - - +
310A CYS* 3.9 1.7 - - - +
407A EDO 3.2 25.4 - - - +
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Residues in contact with PHE 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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224A GLU 5.4 0.2 - - - -
227A ALA* 3.5 35.4 - - + -
228A ARG* 4.2 12.8 - - + -
231A PHE* 3.8 25.1 - + + -
234A SER* 3.7 24.2 - - - +
235A SER* 3.7 35.4 - - - -
238A CYS* 3.5 7.1 + - + +
239A GLY 5.6 0.7 - - - -
240A ALA* 1.4 76.7 - - - +
242A LEU* 1.4 75.1 + - + +
243A ARG 3.1 0.9 - - - -
244A HIS* 2.9 51.9 + - + +
245A LYS 4.3 0.5 + - - -
246A VAL* 5.3 6.8 + - + +
247A ALA* 4.6 6.1 - - + -
407A EDO 3.3 7.6 + - - -
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Residues in contact with LEU 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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191A TRP* 3.7 25.0 - - + +
192A HIS* 4.3 4.5 - - - +
193A THR 6.1 0.2 - - - -
223A LEU* 4.8 8.7 - - + -
224A GLU* 4.4 11.7 - - + -
227A ALA* 4.1 24.2 - - + -
241A PHE* 1.4 96.8 - - + +
243A ARG* 1.3 55.6 + - - +
245A LYS* 3.0 25.4 + - - +
246A VAL 6.0 0.7 - - - +
247A ALA* 4.0 20.4 - - + -
249A ILE* 6.1 1.6 - - + -
279A TYR* 3.6 35.7 - - + +
407A EDO 3.0 24.2 + - - +
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Residues in contact with ARG 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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192A HIS* 5.9 0.4 - - - -
193A THR* 3.3 18.7 + - - +
194A GLU 2.9 29.5 + - - -
195A ASP* 4.2 7.1 + - - +
196A MET 4.5 4.3 - - - -
197A ASP* 2.9 27.2 + - - +
240A ALA* 3.0 30.0 + - + +
242A LEU* 1.3 76.9 - - - +
244A HIS* 1.4 60.7 + - - +
245A LYS* 3.4 15.0 + - - +
307A ALA* 3.9 10.9 - - - +
308A SER* 2.7 27.5 + - - +
309A GLN* 4.4 7.9 + - - -
310A CYS* 3.9 24.9 - - + +
315A ALA* 3.7 16.4 - - + +
407A EDO 3.8 10.3 - - - -
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Residues in contact with HIS 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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234A SER* 5.5 2.4 - - - -
238A CYS* 3.6 6.6 - - + -
240A ALA 4.4 0.9 - - - -
241A PHE* 2.9 36.7 + - + +
243A ARG* 1.4 78.3 - - - +
245A LYS* 1.4 68.3 + - - +
246A VAL* 3.4 25.4 - - + +
310A CYS* 3.9 6.5 - - - -
312A CYS* 3.4 11.4 - - - -
314A GLU* 3.6 25.9 - - + +
315A ALA* 4.1 7.4 - - - +
401A ZN 2.1 36.6 - - - -
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Residues in contact with LYS 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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88A GLN* 4.9 4.2 + - - +
90A HIS* 5.1 9.0 + - - -
139A ASP* 5.8 1.4 + - - -
190A ALA* 3.4 20.6 + - + +
191A TRP 4.6 2.7 - - - -
192A HIS* 3.7 40.3 + - + +
193A THR 4.9 2.2 - - - +
195A ASP* 5.2 8.8 + - - +
241A PHE 4.3 0.2 + - - -
242A LEU 3.0 16.3 + - - +
243A ARG* 3.5 15.7 - - - +
244A HIS* 1.4 79.2 - - - +
246A VAL* 1.4 60.9 + - - +
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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