Contacts of the strand formed by residues 305 - 314 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170Q VAL* 3.8 30.3 - - + +
171Q GLU* 2.5 34.0 - - - +
248Q VAL* 3.7 25.9 - - - +
249Q LEU 5.3 2.4 + - - -
250Q GLU* 4.2 9.5 + - - +
305Q ARG* 4.6 19.8 - - - +
301R SER* 3.6 0.3 - - - -
302R VAL 2.9 30.1 + - - +
303R GLY 3.3 1.6 + - - -
304R ASP* 1.3 86.6 - - + +
306R GLN* 1.3 57.6 + - - +
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Residues in contact with GLN 306 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171Q GLU* 3.3 9.7 + - - +
247R VAL 4.2 4.2 - - - +
248R VAL* 4.3 14.9 - - - +
249R LEU 4.9 1.9 + - - -
251R LYS 4.2 2.3 - - - +
252R GLN* 3.8 6.2 + - - +
253R ASP* 3.2 19.4 + - - +
254R VAL* 3.0 55.9 + - - +
299R VAL* 3.6 6.4 - - + +
300R MET 3.1 5.6 - - - +
301R SER* 2.9 28.8 + - - +
303R GLY 5.5 0.7 - - - +
304R ASP 4.1 5.3 + - - +
305R ARG* 1.3 80.8 - - - +
307R LEU* 1.3 67.7 + - - +
308R VAL* 4.2 6.0 - - + +
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Residues in contact with LEU 307 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171Q GLU* 3.7 21.2 + - + +
172Q GLY* 3.7 36.6 - - - -
173Q LEU* 3.9 17.4 - - + +
246Q THR 4.0 9.0 - - - +
248Q VAL* 3.7 16.2 - - + -
307Q LEU* 3.9 8.5 - - + -
246R THR* 4.4 12.6 - - + -
247R VAL 3.5 5.8 - - - +
248R VAL* 3.7 28.5 - - + -
298R ARG 4.0 0.3 - - - +
299R VAL* 3.4 4.0 - - - +
300R MET* 2.9 35.3 + - + +
306R GLN* 1.3 73.4 - - - +
308R VAL* 1.3 62.8 + - - +
309R LYS 4.2 0.2 - - - -
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Residues in contact with VAL 308 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173Q LEU* 4.6 0.4 - - - -
163R LEU* 4.8 3.1 - - + -
245R LEU 3.6 0.7 - - - +
246R THR* 3.3 2.8 - - - -
247R VAL* 2.8 51.7 + - + +
249R LEU* 3.8 23.6 - - + +
254R VAL* 4.3 13.0 - - + -
259R VAL* 3.9 30.5 - - + -
297R THR* 5.2 0.9 - - + -
298R ARG 3.6 6.3 - - - +
299R VAL* 4.1 18.8 - - + -
306R GLN* 4.8 7.9 - - + +
307R LEU* 1.3 78.8 - - - +
309R LYS* 1.3 67.2 + - - +
310R VAL* 4.3 3.1 + - + -
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Residues in contact with LYS 309 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173Q LEU* 3.7 29.3 - - + +
174Q MET 2.9 34.1 + - - +
175Q THR* 2.9 18.9 + - - +
230Q GLY* 4.5 5.7 - - - -
231Q GLY 4.7 1.6 - - - +
244R GLU* 4.2 16.7 + - + +
245R LEU 3.1 13.0 - - - +
246R THR* 3.6 18.4 - - - +
296R GLN 4.4 6.3 - - - +
297R THR* 3.3 5.7 - - - +
298R ARG* 2.8 51.9 + - + +
307R LEU 4.2 0.2 + - - -
308R VAL* 1.3 74.7 - - - +
310R VAL* 1.3 72.2 + - - +
311R ALA* 6.4 0.2 - - + -
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Residues in contact with VAL 310 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159R VAL* 3.5 29.2 - - + -
163R LEU* 4.2 11.0 - - + -
244R GLU* 3.3 5.0 - - - +
245R LEU* 2.9 47.5 + - + +
247R VAL* 6.2 0.2 - - + -
259R VAL* 3.6 31.2 - - + -
263R MET* 4.8 2.2 - - + -
292R PHE* 3.6 21.1 - - + -
296R GLN 4.5 5.8 - - - -
297R THR* 4.1 6.1 - - + +
308R VAL* 4.8 5.8 - - + +
309R LYS* 1.3 82.2 - - - +
311R ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 311 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159R VAL* 6.2 0.2 - - - -
242R LEU* 4.0 10.1 - - + -
243R THR 2.9 12.3 - - - +
244R GLU* 4.2 10.8 - - + +
292R PHE* 4.0 6.5 - - - -
293R ASP* 3.1 30.0 + - - +
296R GLN* 3.7 38.6 - - + +
309R LYS* 6.4 0.2 - - + -
310R VAL* 1.3 79.0 - - - +
312R ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 312 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155R SER 3.9 9.9 - - - +
159R VAL* 3.9 15.7 - - + -
242R LEU* 3.7 4.2 - - - -
243R THR* 2.9 35.3 + - + +
290R SER* 3.4 25.6 - - - +
291R LEU 3.2 12.8 - - - +
292R PHE* 4.1 2.0 - - - -
311R ALA* 1.3 75.1 - - - +
313R TRP* 1.3 62.1 - - - +
314R TYR* 4.0 2.8 - - - -
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Residues in contact with TRP 313 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197Q ARG* 4.2 0.2 - - - -
206Q ILE* 3.6 24.2 - - + -
208Q PRO* 3.6 23.3 - - + -
155R SER* 4.8 0.2 - - - -
241R SER 3.4 23.3 - - - -
242R LEU* 3.4 27.1 - - + -
278R ILE* 3.6 40.9 - - + +
279R VAL* 3.9 1.1 - - - -
280R SER* 3.5 33.7 - - - -
283R VAL* 3.8 24.0 - - + -
286R MET* 3.6 2.0 - - - +
290R SER* 3.5 1.6 - - - -
291R LEU* 2.7 45.7 + - + +
293R ASP* 3.0 32.8 + - + +
296R GLN* 3.8 3.3 + - - -
312R ALA* 1.3 74.6 - - - +
314R TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 314 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151R GLY* 3.5 31.6 - - - -
152R THR* 2.7 26.9 + - - -
155R SER* 3.3 15.3 - - - -
176R THR* 2.7 19.3 + - - -
178R HIS* 3.2 8.6 - - - -
241R SER* 2.8 61.7 + - - +
242R LEU 3.8 0.9 - - - -
243R THR* 3.2 20.6 - - - -
283R VAL* 4.1 5.2 - - - -
286R MET* 3.6 7.9 - - - -
289R GLY 3.6 20.2 - - - +
312R ALA 4.0 2.0 - - - -
313R TRP* 1.3 78.2 - - - +
315R ASP* 1.3 59.3 + - - +
316R ASN* 3.2 25.7 + - + -
319R SER* 4.0 4.7 - - - -
320R TYR 6.0 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