Contacts of the strand formed by residues 241 - 249 (chain Q) in PDB entry 3K9Q
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 241 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177Q ILE 3.4 11.4 - - - -
178Q HIS* 3.4 8.9 + - - -
179Q ALA 3.0 16.8 + - - -
240Q GLY* 1.3 69.5 - - - -
242Q LEU* 1.3 60.6 - - - +
283Q VAL* 4.7 1.8 - - - +
313Q TRP* 3.3 14.2 - - - -
314Q TYR* 2.9 59.6 + - - -
316Q ASN* 2.7 24.6 + - - -
206R ILE* 4.4 2.9 - - - -
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Residues in contact with LEU 242 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175Q THR 3.9 0.5 - - - +
176Q THR* 2.9 5.1 + - - -
177Q ILE* 2.7 48.0 + - + +
241Q SER* 1.3 75.7 - - - +
243Q THR* 1.3 68.7 + - - +
244Q GLU* 4.2 8.3 - - + +
296Q GLN* 3.8 17.5 - - - +
311Q ALA* 4.0 3.6 - - + -
312Q ALA 3.5 25.1 - - - +
313Q TRP* 3.5 43.1 - - + +
314Q TYR* 4.2 0.2 - - - -
206R ILE* 4.7 4.3 - - + -
233R GLN* 3.4 39.7 - - - +
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Residues in contact with THR 243 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152Q THR* 4.0 1.6 - - - +
155Q SER* 2.7 28.3 + - - +
156Q LEU* 4.5 18.2 - - + -
174Q MET* 3.9 29.4 - - + -
175Q THR 3.7 2.7 - - - -
176Q THR* 3.6 7.2 + - - +
242Q LEU* 1.3 70.5 - - - +
244Q GLU* 1.3 65.9 + - - +
245Q LEU* 5.1 2.4 - - + +
310Q VAL 3.9 0.3 - - - +
311Q ALA* 3.0 7.3 - - - +
312Q ALA* 2.9 39.1 + - + -
314Q TYR* 3.0 12.8 - - - -
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Residues in contact with GLU 244 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173Q LEU 3.9 0.3 - - - +
174Q MET* 3.2 6.2 - - - +
175Q THR* 2.7 47.5 + - - +
177Q ILE* 3.9 17.6 - - + +
242Q LEU* 4.4 3.6 - - + -
243Q THR* 1.3 76.3 - - - +
245Q LEU* 1.3 61.3 + - - +
246Q THR* 4.3 1.6 - - - +
296Q GLN* 4.0 4.5 + - - -
309Q LYS* 4.2 17.0 - - + +
310Q VAL 3.4 4.9 - - - +
311Q ALA* 4.4 9.4 - - + -
175R THR* 2.6 38.1 + - - +
233R GLN* 2.7 32.0 + - - +
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Residues in contact with LEU 245 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156Q LEU* 3.7 32.5 - - + -
159Q VAL* 4.0 11.9 - - + -
160Q ALA* 4.8 6.5 - - + -
163Q LEU* 3.8 26.2 - - + -
173Q LEU 3.5 18.2 - - - +
174Q MET* 4.1 8.7 - - + -
228Q LEU* 3.9 26.0 - - + -
243Q THR* 5.2 3.6 - - + +
244Q GLU* 1.3 75.4 - - - +
246Q THR* 1.3 61.4 + - - +
247Q VAL* 3.5 14.7 - - + +
308Q VAL 3.7 0.9 - - - +
309Q LYS* 3.2 4.7 - - - +
310Q VAL* 2.9 41.0 + - + +
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Residues in contact with THR 246 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172Q GLY* 3.1 2.1 - - - -
173Q LEU 2.7 43.8 + - - -
244Q GLU* 5.3 1.9 - - - +
245Q LEU* 1.3 73.0 - - - +
247Q VAL* 1.3 61.8 + - - +
307Q LEU* 4.4 15.3 - - + -
308Q VAL 3.3 4.5 - - - +
309Q LYS* 3.7 20.1 - - - +
173R LEU* 3.9 32.2 - - + +
246R THR* 4.4 28.7 + - + -
307R LEU* 4.0 3.5 - - + +
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Residues in contact with VAL 247 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Q LEU* 4.1 15.0 - - + -
169Q LEU* 3.8 19.3 - - + -
171Q GLU 3.4 7.6 - - - +
172Q GLY* 4.0 6.3 - - - -
228Q LEU* 4.5 0.9 - - + -
245Q LEU* 3.5 31.2 - - + +
246Q THR* 1.3 81.0 - - - +
248Q VAL* 1.3 63.8 + - - +
249Q LEU* 3.7 26.7 - - + -
306Q GLN 4.1 0.3 - - - +
307Q LEU* 3.5 9.9 - - - +
308Q VAL* 2.7 50.7 + - + +
310Q VAL* 6.2 0.7 - - + -
307R LEU* 4.9 0.9 - - - -
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Residues in contact with VAL 248 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169Q LEU* 4.0 0.7 - - - +
170Q VAL* 2.9 38.9 + - + +
171Q GLU* 2.8 28.5 + - + +
247Q VAL* 1.3 73.8 - - - +
249Q LEU* 1.3 70.5 + - - +
306Q GLN 4.4 11.0 - - - +
307Q LEU* 3.6 25.1 - - + -
171R GLU* 6.0 0.2 - - - +
248R VAL* 4.6 6.3 - - + -
305R ARG* 3.7 27.8 - - - +
307R LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 249 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Q LEU* 4.3 17.0 - - + +
167Q PHE* 3.7 39.3 - - + +
168Q GLY 3.1 12.1 - - - +
169Q LEU* 4.2 11.9 - - + -
170Q VAL* 3.7 6.6 - - - +
247Q VAL* 3.7 23.5 + - + -
248Q VAL* 1.3 84.6 - - - +
250Q GLU* 1.3 64.9 + - - +
251Q LYS 3.6 13.7 + - - +
252Q GLN* 3.8 6.4 - - - +
254Q VAL* 4.3 8.7 - - + -
259Q VAL* 5.3 0.2 - - + -
306Q GLN 5.0 2.6 + - - -
308Q VAL* 3.8 31.6 - - + +
305R ARG* 5.3 2.1 + - - -
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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