Contacts of the strand formed by residues 239 - 244 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C TRP* 3.4 4.0 - - - -
231C GLY 2.8 29.9 + - - +
236C PHE* 5.3 3.6 - + + -
237C SER* 3.9 15.7 - - - +
238C TRP* 1.3 73.6 - - - +
240C PRO* 1.4 90.0 - - + +
263C TRP* 3.4 14.1 - + + -
264C PHE 3.4 10.4 + - - -
266C ASP* 4.6 1.3 + - - -
291C THR* 4.7 7.4 - - + -
295C LEU* 4.7 8.1 - - + -
297C SER* 3.8 40.8 - - - -
298C TYR* 3.7 36.3 - + + -
301C ALA* 3.4 17.3 - - + +
356C BTB 3.6 64.2 + - - -
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Residues in contact with PRO 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL 3.4 7.2 - - - +
230C TRP* 3.9 6.7 - - + -
239C TRP* 1.4 102.4 - - + +
241C ALA* 1.3 60.4 + - - +
263C TRP* 3.8 0.5 - - - -
264C PHE* 3.1 22.4 + - + -
280C LEU* 4.0 15.7 - - + -
298C TYR* 5.0 0.9 - - + -
301C ALA* 3.9 25.1 - - + +
302C MET* 3.8 30.7 - - + -
305C ALA* 3.6 22.0 - - + -
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C LEU* 3.6 2.4 - - - +
229C VAL* 2.9 38.9 + - + +
231C GLY 5.2 0.4 - - - +
239C TRP 4.4 0.4 - - - +
240C PRO* 1.3 76.6 - - - +
242C MET* 1.3 60.0 + - - +
261C VAL* 3.9 20.4 - - + -
262C GLN 3.2 15.7 - - - +
263C TRP* 3.7 21.8 - - + -
264C PHE* 3.6 15.3 - - - -
280C LEU* 5.8 0.2 - - - +
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Residues in contact with MET 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A MET* 4.3 17.0 - - + -
256A SER* 4.3 28.0 - - - +
226C GLY* 3.7 22.0 - - - +
227C ASP 3.4 4.3 - - - +
228C LEU* 4.0 5.2 - - + -
241C ALA* 1.3 75.0 - - - +
243C VAL* 1.3 72.6 + - - +
244C VAL* 3.5 4.7 + - + +
261C VAL* 3.2 4.3 - - - -
262C GLN 2.8 30.2 + - - -
264C PHE* 3.7 28.7 - - + -
308C LYS* 3.8 26.5 - - + -
312C ARG* 3.8 15.9 - - - -
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Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C TYR* 3.8 19.7 - - + -
223C PHE* 4.1 13.5 - - + -
224C GLY* 3.4 32.3 - - - +
225C ILE* 4.1 1.0 - - - +
226C GLY* 2.8 27.1 + - - -
227C ASP* 2.9 19.2 + - + +
229C VAL* 4.1 19.3 - - + -
242C MET* 1.3 72.5 - - - +
244C VAL* 1.3 63.4 + - - +
259C ARG* 4.3 11.7 - - + -
260C TRP 3.5 12.6 - - - +
261C VAL* 4.3 12.6 - - + +
277C LEU* 4.5 4.9 - - + -
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A SER* 3.9 32.1 - - - +
217C TYR* 2.7 32.4 + - - -
225C ILE* 4.1 10.5 - - - -
242C MET* 3.7 13.9 - - + +
243C VAL* 1.3 78.4 - - - +
245C SER* 1.3 66.1 + - - +
248C ALA* 4.4 2.7 - - + -
249C THR* 4.0 1.3 - - + -
260C TRP* 3.0 28.6 + - + +
261C VAL 4.3 1.8 - - - -
262C GLN* 4.0 15.9 - - + +
269C PHE* 4.0 25.6 - - + -
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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