Contacts of the strand formed by residues 242 - 252 (chain R) in PDB entry 5C7L
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 ILE 242 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233R ALA* 3.7 38.4 - - + +
236R ILE* 4.1 6.1 - - + -
237R HIS* 3.0 26.3 + - + +
241R GLY* 1.3 71.3 - - - -
243R VAL* 1.3 58.8 - - - +
244R GLU* 3.7 26.2 - - - +
245R GLY 4.3 2.2 - - - +
296R LEU* 3.9 20.4 - - + -
299R LYS* 3.1 27.2 - - + +
300R LEU* 4.5 12.6 - - + -
317R LEU* 5.1 11.0 - - + -
319R CYS* 4.8 5.2 - - + -
320R ARG 3.8 3.4 - - - +
321R LEU* 3.9 17.5 - - + -
322R ALA* 5.8 0.2 - - - -
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Residues in contact with VAL 243 (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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242R ILE* 1.3 71.6 - - - +
244R GLU* 1.3 65.4 + - + +
299R LYS* 3.2 28.8 - - - +
320R ARG* 2.9 57.6 + - + +
321R LEU 3.8 3.8 - - - +
322R ALA* 3.6 29.8 - - + +
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Residues in contact with GLU 244 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242R ILE* 3.5 6.7 - - - -
243R VAL* 1.3 83.1 - - - +
245R GLY* 1.3 57.8 + - - +
299R LYS* 3.4 15.3 - - - +
319R CYS* 3.3 1.7 - - - +
320R ARG* 2.7 68.4 + - + +
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Residues in contact with GLY 245 (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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244R GLU* 1.3 75.9 - - - +
246R LEU* 1.3 66.0 + - - +
299R LYS 2.8 22.0 + - - +
300R LEU* 3.5 17.0 - - - +
301R THR 3.4 17.0 + - - -
317R LEU* 4.6 1.8 - - - -
318R THR 3.1 11.9 - - - -
319R CYS* 3.9 7.0 - - - -
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Residues in contact with LEU 246 (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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245R GLY* 1.3 77.3 - - - +
247R MET* 1.3 58.2 + - - +
248R THR 4.2 0.2 + - - -
301R THR* 3.3 37.5 - - + +
302R GLY* 4.5 3.4 - - - +
316R ASP 3.8 1.2 - - - +
317R LEU* 4.3 2.4 - - - +
318R THR* 2.8 46.9 + - + +
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Residues in contact with MET 247 (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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225R THR* 3.9 28.3 - - + -
229R LEU* 3.8 25.8 - - + -
246R LEU* 1.3 73.6 - - - +
248R THR* 1.3 73.3 + - - +
249R THR* 4.1 6.1 - - + -
283R THR* 4.1 19.7 - - + -
286R ALA* 4.1 22.0 - - + +
300R LEU* 6.4 0.2 - - + -
301R THR 2.9 13.2 + - - +
302R GLY* 3.0 3.3 - - - -
303R MET* 2.9 48.5 + - - +
315R VAL* 4.2 20.2 - - + -
316R ASP 3.4 7.6 - - - +
317R LEU* 4.5 6.7 - - + +
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Residues in contact with THR 248 (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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246R LEU 4.2 0.4 + - - -
247R MET* 1.3 77.7 + - - +
249R THR* 1.3 69.3 + - - +
250R VAL* 4.2 9.6 - - + -
303R MET* 3.2 19.5 - - - +
305R PHE* 3.6 35.0 - - + -
314R VAL 3.9 0.2 - - - +
315R VAL* 3.7 0.9 - - - -
316R ASP* 2.7 55.7 + - + +
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Residues in contact with THR 249 (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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225R THR* 4.3 15.7 - - + +
247R MET* 4.1 13.5 - - + +
248R THR* 1.3 75.1 - - - +
250R VAL* 1.3 63.6 + - - +
251R HIS* 3.5 15.3 + - + +
283R THR* 4.5 3.4 - - + -
303R MET 3.1 7.5 + - - +
304R ALA* 3.6 22.8 - - + +
305R PHE 3.0 24.9 + - - -
314R VAL 3.2 11.9 + - - -
315R VAL* 4.6 3.4 - - - -
386R TYR* 2.7 28.2 + - - +
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Residues in contact with VAL 250 (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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248R THR* 4.2 15.5 - - + +
249R THR* 1.3 71.1 - - - +
251R HIS* 1.3 59.0 + - - +
305R PHE* 3.6 12.3 - - + +
307R VAL* 3.8 33.2 - - + -
312R VAL 4.7 0.3 - - - +
313R SER* 3.4 3.8 - - - -
314R VAL* 2.9 51.1 + - + +
316R ASP* 5.6 6.1 - - + +
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Residues in contact with HIS 251 (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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224R OCS 2.9 25.1 + - - -
225R THR* 3.7 7.9 - - - -
249R THR* 3.8 14.8 - - + +
250R VAL* 1.3 75.6 - - - +
252R SER* 1.3 91.5 + - - +
254R THR* 4.0 13.0 - - + -
304R ALA* 5.2 2.5 - - + -
305R PHE 2.9 11.5 + - - +
306R ARG* 3.3 25.1 + - - +
307R VAL* 2.9 29.1 + - - +
313R SER* 3.2 9.6 + - - -
386R TYR* 3.3 24.2 - - - -
388R ASN* 3.5 25.8 - - - +
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Residues in contact with SER 252 (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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251R HIS* 1.3 100.9 + - - +
253R TYR* 1.3 65.6 + - - +
254R THR* 3.6 0.3 - - - +
306R ARG* 3.4 6.5 - - - -
307R VAL 4.1 1.1 - - - -
309R THR* 2.7 32.1 + - - -
310R PRO 3.7 2.2 - - - -
311R ASP* 2.9 30.2 + - - -
312R VAL 2.7 25.5 + - - -
313R SER* 3.2 4.8 + - - -
388R ASN* 4.1 7.6 - - - -
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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