Contacts of the helix formed by residues 240 - 247 (chain A) in PDB entry 3PEY
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 GLU 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LYS* 6.3 0.4 - - - -
170A PRO* 3.7 19.5 - - + -
174A LEU* 3.7 23.6 - - + +
239A ASP* 1.3 87.3 + - - +
241A ALA* 1.3 65.3 + - - +
242A ASP* 3.3 6.1 - - - -
243A ASN* 3.1 5.2 + - + +
244A MET 3.0 17.3 + - - -
270A PHE 2.9 7.1 + - - -
271A SER* 3.9 5.9 + - - -
272A ALA 5.0 0.2 + - - -
392A ARG* 2.9 38.7 + - + +
393A GLY* 3.3 14.2 + - - -
422A HIS* 3.3 15.1 + - - -
1001A MG 3.9 2.4 - - - -
1002A BEF 3.3 26.8 - - - -
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Residues in contact with ALA 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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238A LEU* 3.5 12.8 - - + +
239A ASP 3.8 4.0 - - - -
240A GLU* 1.3 76.0 - - - +
242A ASP* 1.3 64.3 + - - +
244A MET* 3.6 6.6 - - - +
245A LEU* 3.0 30.1 + - - +
269A LEU* 3.5 41.5 - - + -
270A PHE 3.0 10.1 + - - +
271A SER* 3.9 1.0 - - - -
274A PHE* 3.9 9.2 - - + -
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Residues in contact with ASP 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 GLU 3.8 0.2 - - - +
241A ALA* 1.3 75.0 - - - +
243A ASN* 1.3 61.3 + - - -
245A LEU* 5.2 0.4 - - - -
246A ASP* 3.1 27.7 + - - +
271A SER* 2.7 20.4 + - - -
273A THR* 2.7 40.8 + - - +
274A PHE* 3.9 10.9 - - + -
275A ALA 5.0 1.7 + - - -
278A VAL* 3.8 33.2 - - + +
392A ARG* 2.9 24.5 + - - -
418A ALA* 4.6 4.2 - - - +
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Residues in contact with ASN 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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170A PRO* 3.4 32.3 - - - +
240A GLU 3.1 6.8 + - - +
242A ASP* 1.3 78.8 + - - +
244A MET* 1.3 66.2 + - - +
246A ASP* 4.6 3.8 - - - +
247A GLN* 2.9 53.2 + - - +
250A LEU* 3.8 8.1 - - - +
392A ARG* 3.3 39.4 + - - +
419A THR* 5.8 0.2 + - - -
3B U 5.2 1.6 + - - -
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Residues in contact with MET 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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168A LEU* 3.4 38.4 - - + +
169A ALA 3.4 17.7 - - - +
170A PRO* 3.5 30.1 - - + -
216A PRO* 3.7 11.4 - - + -
238A LEU* 4.3 11.2 - - + -
239A ASP 3.1 23.3 - - - +
240A GLU 3.0 9.1 + - - +
241A ALA* 3.6 9.4 - - - +
243A ASN* 1.3 76.8 - - - +
245A LEU* 1.3 59.5 + - - +
250A LEU* 3.3 18.8 - - - +
251A GLY* 3.1 28.6 + - - -
254A CYS* 3.8 15.7 - - - -
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Residues in contact with LEU 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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238A LEU* 4.1 22.4 - - + -
241A ALA 3.0 21.6 + - - +
242A ASP* 4.0 3.1 - - - +
243A ASN 3.2 0.2 - - - -
244A MET* 1.3 77.4 - - - +
246A ASP* 1.3 59.4 + - - +
251A GLY* 3.5 16.4 - - - +
254A CYS* 5.0 5.2 - - + -
255A ILE* 4.5 11.7 - - + -
269A LEU* 4.1 15.3 - - + -
274A PHE* 5.6 0.4 - - + -
278A VAL* 4.4 6.3 - - + -
281A TYR* 3.9 36.7 + - + +
282A ALA* 3.7 36.1 - - + +
285A ILE* 4.4 19.7 - - + -
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Residues in contact with ASP 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 ASP 3.1 15.3 + - - +
243A ASN* 4.2 2.7 - - - +
245A LEU* 1.3 78.3 - - - +
247A GLN* 1.3 69.0 + - + +
248A GLN 3.6 1.0 + - - -
278A VAL* 3.2 34.8 - - - +
281A TYR* 5.8 1.3 - - - -
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Residues in contact with GLN 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 ASN* 2.9 44.6 + - - +
245A LEU 3.8 0.2 - - - -
246A ASP* 1.3 82.0 - - + +
248A GLN* 1.3 76.2 + - - +
249A GLY 3.4 0.3 + - - -
250A LEU* 3.9 13.7 - - + -
251A GLY* 2.9 23.7 + - - -
1B U 4.0 12.0 + - - -
2B U 3.3 33.4 + - - +
3B U 3.9 9.5 - - - +
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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