Contacts of the strand formed by residues 309 - 316 (chain Q) in PDB entry 2D2I
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 LEU 309 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248Q VAL* 3.8 32.3 - - + -
249Q VAL 3.9 13.2 - - - +
250Q GLN* 4.1 11.2 - - + +
303Q LEU* 3.6 3.3 - - + +
304Q VAL* 4.7 0.8 - - - +
305Q MET* 2.9 55.8 + - + +
307Q GLY 3.8 0.8 - - - -
308Q ASP* 1.3 77.1 - - - +
310Q VAL* 1.3 60.0 + - - +
311Q LYS* 5.7 0.4 - - + -
175R LYS* 3.9 21.3 - - + -
176R GLY* 4.9 3.1 - - - -
177R THR* 4.3 18.8 - - + +
248R VAL* 5.6 1.8 - - + +
250R GLN* 5.8 4.7 - - + +
309R LEU* 4.9 12.1 - - + -
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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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167Q LEU* 4.3 15.7 - - + -
171Q PHE* 5.9 1.3 - - + -
247Q LEU 3.6 0.9 - - - +
248Q VAL* 3.3 4.3 - - - +
249Q VAL* 2.8 64.0 + - + +
251Q VAL* 4.2 13.0 - - + -
255Q THR* 4.0 19.7 - - + -
260Q VAL* 4.1 9.9 - - + -
303Q LEU 3.5 4.7 - - - +
304Q VAL* 3.5 28.5 - - + -
309Q LEU* 1.3 77.2 - - - +
311Q LYS* 1.3 61.2 + - - +
312Q VAL* 5.2 3.4 - - + -
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Residues in contact with LYS 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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246Q ASP* 3.1 30.2 + - - +
247Q LEU 3.0 5.8 - - - +
248Q VAL* 3.9 10.1 - - + +
301Q LEU 5.2 3.8 - - - +
302Q THR* 3.6 4.9 - - - +
303Q LEU* 2.9 46.7 + - + +
309Q LEU* 5.3 0.7 - - + +
310Q VAL* 1.3 74.0 - - - +
312Q VAL* 1.3 67.6 + - - +
313Q ILE* 4.3 11.9 - - + -
177R THR* 3.4 39.9 + - + +
178R MET* 3.8 10.9 + - - +
179R THR* 3.0 26.9 + - - -
232R GLY* 5.8 0.4 - - - -
233R ILE* 4.3 14.1 - - + -
246R ASP* 5.3 1.0 + - - -
248R VAL* 5.8 1.0 - - - +
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Residues in contact with VAL 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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163Q VAL* 4.1 22.7 - - + -
167Q LEU* 4.1 23.1 - - + -
245Q VAL* 3.6 1.6 - - - +
247Q LEU* 2.9 38.2 + - + +
260Q VAL* 4.5 11.2 - - + -
264Q LEU* 4.1 25.1 - - + -
297Q VAL* 4.3 12.6 - - + -
302Q THR* 4.6 6.7 - - + +
310Q VAL* 5.2 3.1 - - + -
311Q LYS* 1.3 83.6 - - - +
313Q ILE* 1.3 76.5 + - - +
314Q ALA* 4.2 3.1 + - + -
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Residues in contact with ILE 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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244Q VAL* 3.3 28.9 - - + -
245Q VAL 3.4 1.3 - - - -
246Q ASP* 3.5 34.3 - - + +
297Q VAL* 3.5 2.3 - - - -
298Q ASP* 2.8 33.3 + - + +
301Q LEU* 3.7 46.6 - - + +
302Q THR* 5.4 1.4 + - - +
311Q LYS* 4.3 5.8 - - + -
312Q VAL* 1.3 84.0 - - - +
314Q ALA* 1.3 60.7 + - - +
315Q TRP* 5.2 2.2 - - + +
233R ILE* 4.0 20.4 - - + -
235R LEU* 5.3 9.2 - - + -
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Residues in contact with ALA 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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159Q CYS* 3.7 12.8 - - - -
163Q VAL* 4.5 11.9 - - + -
244Q VAL* 3.3 5.5 - - - -
245Q VAL* 2.8 52.3 + - + +
295Q SER* 4.3 5.2 - - - -
296Q ILE 3.1 19.7 - - - +
297Q VAL* 4.1 5.4 - - + +
298Q ASP 4.4 0.2 - - - +
312Q VAL* 4.2 3.1 - - + -
313Q ILE* 1.3 77.7 - - - +
315Q TRP* 1.3 61.2 + - - +
316Q TYR* 3.8 0.2 - - - -
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Residues in contact with TRP 315 (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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242Q VAL* 4.2 5.8 - - + -
243Q SER 3.3 13.0 - - - -
244Q VAL* 3.7 28.0 - - + +
283Q LEU 4.5 3.3 + - - -
284Q VAL 4.5 1.3 - - - -
285Q SER* 3.6 33.7 - - - -
288Q PHE* 3.2 40.5 - + + -
295Q SER* 3.5 1.7 - - - -
296Q ILE* 2.7 49.6 + - + +
298Q ASP* 3.1 30.3 + - + +
301Q LEU* 5.5 0.7 - - + -
313Q ILE* 5.2 1.3 - - + +
314Q ALA* 1.3 74.1 - - - +
316Q TYR* 1.3 65.9 + - - +
208R ILE* 3.5 42.8 - - + -
210R PRO* 3.5 28.5 - - + -
235R LEU* 5.4 1.6 - - + -
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Residues in contact with TYR 316 (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 CYS* 3.6 32.3 - - + -
156Q THR* 3.1 20.2 + - - -
159Q CYS* 3.6 13.0 - - + -
180Q THR* 2.8 24.4 + - - -
182Q HIS* 3.3 6.3 - - - -
242Q VAL* 3.4 5.4 - - - +
243Q SER* 2.8 64.2 + - - -
244Q VAL* 3.5 4.7 - - - -
245Q VAL* 3.6 17.6 - - + +
288Q PHE* 5.6 0.9 - - - -
293Q GLU 4.9 2.5 - - - +
294Q SER* 3.3 20.9 - - - +
296Q ILE* 4.2 8.1 - - - -
314Q ALA 3.8 1.3 - - - -
315Q TRP* 1.3 79.8 - - - +
317Q ASP* 1.3 59.8 + - - +
318Q ASN* 3.1 23.2 + - + -
321Q GLY* 6.4 0.2 - - - -
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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