Contacts of the strand formed by residues 241 - 247 (chain A) in PDB entry 1DY7
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ARG* 3.3 17.7 + - - +
217A ASP* 5.9 0.2 - - - -
239A GLY 3.6 0.2 - - - -
240A SER* 1.3 82.2 - - - +
242A ALA* 1.3 64.1 + - - +
243A ARG* 2.9 35.0 + - - +
262A ALA* 3.4 5.0 - - - +
263A TYR* 2.8 42.3 + - + -
264A TRP* 3.2 23.3 + - + +
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Residues in contact with ALA 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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200A HIS* 4.9 0.2 - - - +
214A ILE* 3.7 20.2 - - + -
215A GLY 3.5 3.4 - - - +
216A ARG* 2.9 22.0 + - - -
218A GLY* 3.8 16.8 - - - -
238A ILE* 4.0 8.1 - - + -
239A GLY 5.9 0.2 - - - +
241A GLU* 1.3 76.1 - - - +
243A ARG* 1.3 80.2 + - - +
261A GLY 3.3 19.3 - - - +
262A ALA* 4.1 1.6 - - - +
263A TYR* 4.2 2.7 - - - +
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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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200A HIS* 3.5 43.7 - - + +
201A ILE* 4.3 2.8 - - - +
214A ILE* 4.1 9.6 - - - +
216A ARG* 3.2 33.6 + - - +
241A GLU* 2.9 33.7 + - - +
242A ALA* 1.3 96.1 + - - +
244A SER* 1.3 60.2 + - - +
261A GLY 3.8 2.8 + - - -
263A TYR* 3.5 39.9 - - + -
300A VAL 5.3 1.3 + - - +
602A DHE 2.9 64.5 + - + +
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Residues in contact with SER 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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201A ILE* 5.1 0.2 - - - -
214A ILE* 3.7 8.3 - - - +
243A ARG* 1.3 80.7 - - - +
245A ILE* 1.3 64.4 + - - +
260A ALA* 3.3 5.7 - - - +
261A GLY* 2.9 35.3 + - - -
300A VAL* 4.1 2.1 + - - +
301A ALA 2.9 28.0 + - - -
303A ILE* 3.6 20.4 - - - +
602A DHE 3.6 21.3 - - - -
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Residues in contact with ILE 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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201A ILE* 3.6 18.4 - - + +
203A ARG* 3.2 24.9 + - + +
212A PHE* 3.9 34.1 - - + +
213A VAL 4.4 3.4 - - - +
214A ILE* 3.8 20.4 - - + +
220A VAL* 3.5 41.3 - - + -
244A SER* 1.3 75.5 - - - +
246A GLU* 1.3 72.3 + - - +
258A ALA* 4.9 1.3 - - + -
259A ILE 3.1 16.4 - - - +
260A ALA* 4.6 1.3 - - + -
271A MET* 4.4 8.3 - - + -
303A ILE* 4.4 3.7 - - - +
602A DHE 3.7 5.8 + - - +
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Residues in contact with GLU 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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203A ARG* 3.7 27.5 + - - +
245A ILE* 1.3 77.5 - - - +
247A THR* 1.3 93.4 + - - +
249A LYS* 3.0 35.0 + - - +
258A ALA* 3.3 6.9 - - - +
259A ILE* 2.9 35.7 + - + -
303A ILE* 3.6 26.6 - - + +
304A LEU* 3.7 28.6 - - - +
305A ALA* 3.8 8.1 + - + +
312A PHE* 4.8 0.7 - - + -
565A ASP* 4.3 2.9 - - - +
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Residues in contact with THR 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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203A ARG* 4.8 2.0 - - + -
204A LEU* 2.7 32.2 + - - +
205A SER* 3.7 13.1 - - - -
206A ALA 4.1 0.9 + - - -
212A PHE* 3.6 38.6 - - + -
246A GLU* 1.3 88.8 + - - +
248A SER* 1.3 65.4 + - - +
249A LYS* 3.6 10.4 - - - +
255A ASP* 6.4 0.9 - - - -
257A TYR 3.6 9.6 - - - +
258A ALA* 4.8 0.9 - - + -
305A ALA* 3.1 21.7 - - - +
312A PHE* 3.5 4.7 - - - -
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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