Contacts of the strand formed by residues 239 - 244 (chain A) in PDB entry 3QKJ
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 TRP 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TRP* 3.9 3.4 - - - -
231A GLY 2.8 34.2 + - - +
236A PHE* 5.7 2.5 - + - -
237A SER* 3.9 15.5 - - - +
238A TRP* 1.3 73.0 - - - +
240A PRO* 1.4 90.6 - - + +
263A TRP* 3.4 20.9 - + + -
264A PHE 3.4 19.7 + - - -
266A ASP* 4.6 2.6 + - - -
291A THR* 4.7 3.1 - - + -
295A LEU* 4.7 12.6 - - + -
297A SER* 3.8 39.9 - - - -
298A TYR* 3.7 33.7 - + + -
301A ALA* 3.5 8.4 - - + +
356A BTB 3.7 57.0 + - - -
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Residues in contact with PRO 240 (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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229A VAL 3.3 7.0 - - - +
230A TRP* 3.9 5.6 - - + -
238A TRP 4.6 0.2 - - - +
239A TRP* 1.4 102.9 - - + +
241A ALA* 1.3 60.6 - - - +
263A TRP* 3.7 0.7 - - - -
264A PHE* 3.1 22.2 + - + -
280A LEU* 3.9 16.2 - - + -
298A TYR* 5.0 0.7 - - + -
301A ALA* 3.9 25.1 - - + +
302A MET* 3.5 32.8 - - + -
305A ALA* 3.6 21.3 - - + -
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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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228A LEU* 3.6 2.4 - - - +
229A VAL* 2.9 37.0 + - + -
231A GLY 5.2 0.2 - - - +
239A TRP 4.4 0.4 - - - +
240A PRO* 1.3 76.2 - - - +
242A MET* 1.3 59.6 + - - +
261A VAL* 3.9 20.9 - - + -
262A GLN 3.3 16.4 - - - +
263A TRP* 3.7 20.6 - - + -
264A PHE* 3.6 17.0 - - - -
280A LEU* 5.9 0.2 - - - +
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Residues in contact with MET 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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226A GLY* 3.7 23.1 - - - +
227A ASP 3.4 4.5 - - - +
228A LEU* 4.1 4.7 - - + -
241A ALA* 1.3 74.7 - - - +
243A VAL* 1.3 71.5 + - - +
244A VAL* 3.5 5.4 + - + +
261A VAL* 3.3 4.0 - - - -
262A GLN 2.8 33.4 + - - +
264A PHE* 3.7 28.0 - - + -
308A LYS* 3.8 28.5 - - + +
312A ARG* 3.9 13.7 - - - -
255D MET* 4.4 17.3 - - + -
256D SER* 4.0 29.2 - - - +
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Residues in contact with VAL 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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217A TYR* 3.9 20.2 - - + -
223A PHE* 4.2 14.1 - - + -
224A GLY 3.3 32.8 - - - +
225A ILE* 4.0 0.6 - - - +
226A GLY* 2.8 25.9 + - - -
227A ASP* 2.9 19.6 + - + +
229A VAL* 4.0 19.5 - - + -
242A MET* 1.3 73.6 - - - +
244A VAL* 1.4 63.4 + - - +
259A ARG* 4.2 11.0 - - + -
260A TRP 3.5 13.0 - - - +
261A VAL* 4.2 13.0 - - + +
277A LEU* 4.6 4.0 - - + -
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Residues in contact with VAL 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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217A TYR* 2.7 31.5 + - - -
225A ILE* 4.1 8.7 - - - -
242A MET* 3.5 12.8 + - + +
243A VAL* 1.4 77.0 - - - +
245A SER* 1.3 66.6 + - - +
248A ALA* 4.4 7.6 - - + -
249A THR* 4.1 1.8 - - + -
260A TRP* 3.0 29.0 + - + +
261A VAL 4.3 2.5 - - - -
262A GLN* 4.0 17.7 - - + +
269A PHE* 4.0 25.1 - - + -
256D SER* 3.4 26.2 - - - +
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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