Contacts of the strand formed by residues 245 - 253 (chain B) in PDB entry 4R95
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 TYR 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ILE* 4.0 13.0 - - + -
241B ASP 3.7 6.5 - - - -
242B HIS* 2.9 63.8 + - - +
243B SER 3.4 3.0 - - - +
244B LEU* 1.3 79.8 - - - +
246B THR* 1.3 67.0 + - - +
247B GLY 3.3 24.7 - - - -
248B SER* 4.8 0.2 - - - -
249B LEU* 3.7 25.9 - - + +
403B TYR* 3.3 27.4 - + + -
416B ALA* 3.5 25.8 - - + -
417B VAL 3.3 14.6 - - - +
419B ALA* 3.9 3.3 - - - +
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Residues in contact with THR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B TYR* 1.3 83.2 - - - +
247B GLY* 1.3 68.9 + - - +
248B SER 3.9 0.5 + - - +
416B ALA* 4.2 0.7 - - - +
417B VAL* 3.1 43.2 + - - +
418B SER 5.0 1.0 + - - -
419B ALA* 5.0 12.3 - - + -
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Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B TYR* 3.3 17.7 - - - -
246B THR* 1.3 78.7 - - - +
248B SER* 1.3 59.4 + - - -
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 4.8 0.4 - - - -
246B THR 4.6 0.5 - - - +
247B GLY* 1.3 73.1 - - - -
249B LEU* 1.3 66.1 + - - +
250B TRP* 3.8 23.1 + - - -
415B PHE 3.7 8.1 - - - +
416B ALA* 3.7 11.9 - - - +
431B VAL* 4.6 6.6 + - - +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ILE* 4.1 20.4 - - + -
242B HIS* 5.8 0.2 - - + -
245B TYR* 3.7 28.7 - - + +
247B GLY 4.2 0.4 + - - -
248B SER* 1.3 76.3 - - - +
250B TRP* 1.3 63.5 + - - +
251B TYR* 3.7 34.6 - - + +
403B TYR* 4.5 4.9 - - + +
405B VAL* 3.7 24.0 - - + -
414B GLY* 3.9 3.6 - - - -
415B PHE 3.5 18.8 - - - +
416B ALA* 3.8 22.0 - - + +
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Residues in contact with TRP 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B SER* 3.9 21.3 - - - -
249B LEU* 1.3 79.3 - - - +
251B TYR* 1.3 63.2 + - - +
355B GLN* 4.1 20.2 - - + -
356B SER 4.8 1.3 - - - -
357B PHE* 3.5 50.3 - + + -
414B GLY* 3.3 0.7 - - - -
415B PHE 2.8 30.0 + - - -
431B VAL* 3.8 28.6 + - + -
432B GLU* 4.5 0.6 - - - +
433B GLY* 3.3 43.7 - - - +
434B PRO* 3.4 17.3 - - + -
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Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ILE* 3.7 24.9 - - - +
249B LEU* 3.7 31.2 - - + +
250B TRP* 1.3 77.6 - - - +
252B THR* 1.3 58.9 + - - +
350B GLY* 3.9 0.7 - - - -
351B GLU* 3.7 40.6 + - + +
357B PHE* 3.4 13.8 - - - -
405B VAL* 4.2 13.2 - - + +
407B ASP* 4.4 3.4 + - + -
412B ARG* 3.5 59.2 + - + -
413B ILE 3.3 3.1 - - - -
414B GLY* 3.3 32.5 - - - -
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B TYR* 1.3 73.7 - - - +
253B PRO* 1.3 67.8 + - - +
262B VAL* 3.6 29.4 - - + +
263B ILE 4.5 3.3 + - - -
348B LEU* 3.6 15.2 - - + +
349B MET* 2.6 23.9 + - - +
351B GLU* 4.9 0.4 - - - -
357B PHE* 3.7 11.2 - - - -
412B ARG* 3.3 4.0 - - - -
413B ILE* 2.8 41.5 + - + +
415B PHE* 4.1 17.0 - - + -
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Residues in contact with PRO 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B THR* 1.3 89.9 + - - +
254B ILE* 1.3 66.9 + - - +
255B ARG* 3.3 6.4 + - - +
261B GLU 3.8 4.3 - - - +
262B VAL* 4.1 12.1 - - - +
263B ILE 5.0 1.0 + - - -
349B MET* 3.4 34.5 - - + +
350B GLY 3.6 18.8 - - - +
351B GLU* 4.6 11.4 - - + +
411B LYS 3.7 9.0 - - - +
412B ARG* 4.2 3.4 - - + -
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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