Contacts of the strand formed by residues 305 - 314 (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 ARG 305 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301Q SER* 3.5 1.0 - - - -
302Q VAL 2.8 28.3 + - - +
303Q GLY 3.3 0.8 - - - -
304Q ASP* 1.3 83.9 - - + +
306Q GLN* 1.3 56.8 + - - +
170R VAL* 3.7 34.0 - - + +
171R GLU* 2.6 34.7 - - - +
248R VAL* 3.4 26.3 - - - +
249R LEU 5.0 3.0 + - - -
250R GLU* 5.5 2.8 - - - +
305R ARG* 4.6 19.4 - - - +
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Residues in contact with GLN 306 (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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247Q VAL 4.1 4.0 - - - +
248Q VAL* 4.4 14.9 - - - +
249Q LEU 5.0 1.7 + - - -
251Q LYS 4.1 3.3 - - - +
252Q GLN* 3.8 3.6 + - - +
253Q ASP* 3.2 19.3 + - - +
254Q VAL* 2.8 56.5 + - - +
299Q VAL* 3.6 6.4 - - + +
300Q MET 3.1 6.3 - - - +
301Q SER* 3.0 27.8 + - - +
303Q GLY 5.5 0.4 - - - +
304Q ASP 3.9 7.6 + - - +
305Q ARG* 1.3 80.1 - - - +
307Q LEU* 1.3 68.0 + - - +
308Q VAL* 4.3 5.4 + - + +
171R GLU* 3.4 8.3 + - - +
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Residues in contact with LEU 307 (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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246Q THR* 4.4 11.7 - - + -
247Q VAL 3.5 7.4 - - - +
248Q VAL* 3.6 29.2 - - + -
298Q ARG 3.9 0.3 - - - +
299Q VAL* 3.5 3.5 - - - +
300Q MET* 2.9 35.2 + - + +
306Q GLN* 1.3 75.2 - - - +
308Q VAL* 1.3 61.9 + - - +
171R GLU* 4.0 16.5 + - + +
172R GLY* 3.8 37.9 - - - +
173R LEU* 3.8 21.4 - - + +
246R THR 4.0 7.9 - - - +
248R VAL* 4.0 7.0 - - + -
307R LEU* 3.9 14.6 - - + -
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Residues in contact with VAL 308 (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* 5.0 2.0 - - + -
245Q LEU 3.7 0.5 - - - +
246Q THR* 3.3 2.1 - - - +
247Q VAL* 2.7 54.2 + - + +
249Q LEU* 3.8 24.2 - - + +
254Q VAL* 4.2 12.8 - - + -
259Q VAL* 4.0 24.5 - - + -
297Q THR* 5.1 0.9 - - + -
298Q ARG 3.5 8.1 - - - +
299Q VAL* 4.1 19.1 - - + -
306Q GLN* 4.8 7.0 - - + -
307Q LEU* 1.3 78.8 - - - +
309Q LYS* 1.3 67.2 + - - +
310Q VAL* 4.6 8.5 - - + -
173R LEU* 4.6 1.3 - - - -
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Residues in contact with LYS 309 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244Q GLU* 4.2 16.2 - - + +
245Q LEU 3.2 12.3 - - - +
246Q THR* 3.7 17.7 - - - +
296Q GLN 4.5 8.7 - - - +
297Q THR* 3.3 5.2 - - - +
298Q ARG* 2.8 46.1 + - + +
307Q LEU 4.1 0.6 + - - -
308Q VAL* 1.3 73.7 - - - +
310Q VAL* 1.3 74.8 + - - +
311Q ALA* 6.3 0.7 - - + -
173R LEU* 3.9 25.6 - - + +
174R MET 2.9 26.2 + - - +
175R THR* 2.9 26.3 + - - -
230R GLY* 4.4 6.1 - - - -
231R GLY 4.5 2.6 - - - +
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Residues in contact with VAL 310 (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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159Q VAL* 3.6 28.0 - - + -
163Q LEU* 4.2 11.9 - - + -
243Q THR 3.9 0.2 - - - +
244Q GLU* 3.4 2.4 - - - -
245Q LEU* 2.9 41.7 + - + +
247Q VAL* 6.2 0.4 - - + -
259Q VAL* 3.7 30.5 - - + -
263Q MET* 4.9 2.0 - - + -
292Q PHE* 3.6 20.2 - - + -
296Q GLN 4.4 6.3 - - - -
297Q THR* 4.0 6.5 - - + +
308Q VAL* 4.6 7.2 - - + +
309Q LYS* 1.3 81.8 - - - +
311Q ALA* 1.3 63.6 + - - +
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Residues in contact with ALA 311 (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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159Q VAL* 5.8 0.4 - - - -
242Q LEU* 4.0 8.3 - - + -
243Q THR 3.0 10.8 - - - +
244Q GLU* 4.4 9.4 - - + -
292Q PHE* 4.1 5.7 - - - -
293Q ASP* 3.1 28.7 + - - +
296Q GLN* 3.5 40.8 - - + +
309Q LYS* 6.0 0.9 - - + -
310Q VAL* 1.3 81.2 - - - +
312Q ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 312 (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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155Q SER 4.0 6.3 - - - +
159Q VAL* 3.9 21.1 - - + -
242Q LEU* 3.6 4.2 - - - -
243Q THR* 2.9 37.2 + - + +
290Q SER* 3.6 23.3 - - - +
291Q LEU 3.2 13.7 - - - +
292Q PHE* 4.2 2.0 - - - -
311Q ALA* 1.3 75.3 - - - +
313Q TRP* 1.3 62.5 + - - +
314Q TYR* 4.0 2.3 - - - -
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Residues in contact with TRP 313 (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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155Q SER* 4.8 0.3 - - - -
241Q SER 3.3 23.6 - - - -
242Q LEU* 3.5 26.5 - - + -
278Q ILE* 3.6 41.9 - - + +
279Q VAL* 3.9 1.1 - - - -
280Q SER* 3.6 35.4 - - - -
283Q VAL* 3.8 22.9 - - + -
286Q MET* 3.7 1.4 - - - +
290Q SER* 3.6 1.9 - - - -
291Q LEU* 2.8 42.5 + - + +
293Q ASP* 2.9 35.6 + - + +
296Q GLN* 3.7 14.8 + - - -
312Q ALA* 1.3 73.5 - - - +
314Q TYR* 1.3 64.6 + - - +
206R ILE* 3.6 25.1 - - + -
208R PRO* 3.9 10.8 - - + -
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Residues in contact with TYR 314 (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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151Q GLY* 3.4 32.3 - - - -
152Q THR* 2.7 27.1 + - - -
155Q SER* 3.2 14.6 - - - -
176Q THR* 2.8 19.3 + - - -
178Q HIS* 3.2 7.3 - - - -
241Q SER* 2.9 55.2 + - - -
242Q LEU 3.8 3.8 - - - -
243Q THR* 3.0 21.1 - - - -
283Q VAL* 4.2 3.4 - - - -
286Q MET* 3.6 8.7 - - - -
289Q GLY 3.7 20.4 - - - +
312Q ALA 4.0 1.6 - - - -
313Q TRP* 1.3 78.0 - - - +
315Q ASP* 1.3 61.5 + - - +
316Q ASN* 3.1 21.4 + - + -
319Q SER* 4.0 4.5 - - - +
337Q GOL 3.8 6.1 - - - -
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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