Contacts of the strand formed by residues 242 - 250 (chain A) in PDB entry 5E2Q
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 SER 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LEU* 3.9 14.7 - - - +
209A LYS* 4.9 0.4 - - - +
210A PRO* 5.0 6.1 - - - +
212A TYR* 4.0 22.7 - - - -
238A GLU* 3.7 3.0 - - - -
239A PHE* 2.8 40.7 + - - +
240A ARG 3.3 3.5 + - - -
241A GLY* 1.3 80.8 - - - +
243A PRO* 1.3 69.6 - - - +
244A PHE* 3.6 10.7 + - - -
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Residues in contact with PRO 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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209A LYS* 3.6 28.9 - - - +
210A PRO 3.5 19.1 - - - +
211A TYR* 3.6 38.9 - - + +
212A TYR* 3.1 27.4 + - + +
236A SER* 6.5 1.1 - - - -
237A TYR 3.3 10.1 - - - +
238A GLU* 3.6 10.3 - - - +
242A SER* 1.3 82.2 - - - +
244A PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 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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183A LEU* 4.0 24.7 - - + -
184A ALA* 3.9 27.8 - - + -
187A PHE* 3.5 42.2 - + + -
200A LEU* 4.4 4.0 - - + -
212A TYR* 3.4 43.7 - + + -
214A VAL* 4.1 9.4 - - + -
236A SER* 3.3 4.2 - - - -
237A TYR* 2.5 41.5 + - + +
239A PHE* 3.9 20.0 - + + -
242A SER* 3.7 22.7 - - - -
243A PRO* 1.3 75.8 - - - +
245A GLN* 1.3 59.1 + - - +
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Residues in contact with GLN 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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212A TYR 2.9 13.7 + - - +
213A GLU* 3.3 11.2 - - + +
214A VAL* 2.8 27.2 + - - -
235A LYS* 3.5 13.2 - - - +
236A SER* 4.6 14.7 - - - +
244A PHE* 1.3 77.5 - - - +
246A VAL* 1.3 67.1 + - - +
247A THR* 3.7 22.6 + - + +
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Residues in contact with VAL 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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187A PHE* 4.2 17.5 - - + -
193A LEU* 4.1 22.4 - - + -
214A VAL* 3.4 8.5 - - + -
216A LEU* 3.8 26.2 - - + -
233A LYS* 3.4 24.7 - - + +
234A LEU* 3.3 30.6 - - + +
235A LYS 3.1 9.6 + - - +
237A TYR* 3.6 20.6 - - + +
245A GLN* 1.3 74.5 - - - +
247A THR* 1.3 65.6 + - - +
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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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213A GLU* 2.8 34.9 + - + +
214A VAL 3.0 5.5 + - - +
215A ARG* 3.3 15.4 - - - +
216A LEU* 2.8 25.2 + - - +
234A LEU* 3.8 6.9 - - - +
245A GLN* 3.7 24.6 + - + +
246A VAL* 1.3 80.2 - - - +
248A ARG* 1.3 66.5 + - - +
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Residues in contact with ARG 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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215A ARG* 4.3 7.7 - - - +
216A LEU* 3.2 23.8 - - + +
218A SER* 3.2 15.7 - - - +
220A LEU* 3.4 21.3 + - - +
221A GLY* 2.7 28.2 + - - +
222A SER 5.4 0.2 + - - -
223A GLU 3.3 24.7 + - - -
224A PRO* 5.2 0.2 - - - +
225A SER* 3.4 17.8 + - - -
230A VAL* 3.9 16.3 - - + +
231A THR* 4.4 8.7 + - - +
234A LEU* 3.5 24.2 - - + +
247A THR* 1.3 80.7 - - - +
249A GLY* 1.3 63.4 + - - +
250A ASP 3.5 0.7 - - - -
287A GLN* 3.1 39.7 + - - +
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Residues in contact with GLY 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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215A ARG* 5.0 1.6 - - - -
216A LEU 3.2 0.8 + - - -
218A SER* 2.9 17.8 + - - -
220A LEU 3.2 19.5 + - - -
221A GLY* 4.3 2.9 - - - -
248A ARG* 1.3 80.7 - - - +
250A ASP* 1.3 64.0 + - - +
251A TYR 3.6 0.3 + - - -
252A ALA* 3.2 18.7 + - - +
718A LEU* 5.6 2.1 - - - +
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Residues in contact with ASP 250 (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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199A ARG* 3.0 45.7 + - - +
215A ARG* 3.2 32.4 + - + +
216A LEU 3.2 19.6 + - - +
217A ALA* 3.7 8.2 - - - +
218A SER 3.3 16.1 + - - +
248A ARG 3.5 1.0 - - - -
249A GLY* 1.3 73.6 - - - +
251A TYR* 1.3 95.9 + - + +
252A ALA 3.0 2.7 + - - -
255A LEU* 3.6 2.4 - - - +
718A LEU* 6.0 0.7 - - - +
722A ASP* 4.7 0.3 - - - +
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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