Contacts of the strand formed by residues 248 - 252 (chain B) in PDB entry 6RQT
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 ASN 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ILE* 2.9 37.9 + - + +
238B SER* 3.1 23.0 + - - -
246B GLN* 3.7 1.4 - - - +
247B THR* 1.3 76.8 + - - +
249B VAL* 1.3 66.0 + - - +
260B PHE* 5.4 2.3 - - + -
261B ARG 3.9 3.8 + - - -
262B PHE* 3.8 17.8 - - - -
357B ILE 3.2 26.0 + - - +
358B VAL* 3.5 25.9 - - + +
359B LEU* 3.3 8.3 + - + +
377B MET* 3.6 15.3 - - + +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 5.9 3.1 - - + -
233B GLY 6.4 0.2 - - - -
234B ILE 3.7 0.9 - - - +
235B GLN* 3.4 36.3 - - + +
247B THR* 3.8 12.8 - - + -
248B ASN* 1.3 77.2 - - - +
250B LEU* 1.3 83.3 + - - +
251B HIS* 3.5 16.2 - - + +
260B PHE* 4.1 3.6 - - - +
261B ARG* 3.4 63.5 + - + +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLY* 4.3 11.3 - - - -
234B ILE* 2.9 48.3 + - + +
249B VAL* 1.3 89.1 - - - +
251B HIS* 1.3 80.8 + - - +
258B VAL* 4.7 10.1 - - + -
259B THR 3.7 5.6 - - - +
260B PHE* 3.6 31.2 - - + -
273B VAL* 5.1 0.4 - - + -
374B LEU* 5.0 3.4 - - + -
377B MET* 3.8 30.3 - - + +
378B ILE* 4.6 11.2 - - + -
381B LEU* 4.4 17.9 - - + -
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Residues in contact with HIS 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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222B PHE* 3.3 53.1 + + + +
225B ARG* 3.1 31.4 + - - -
229B TYR* 3.6 22.0 - + + -
230B SER* 5.3 0.7 - - - -
232B TYR 4.6 8.1 - - - -
233B GLY* 5.2 0.4 - - - -
249B VAL* 3.5 19.5 - - + +
250B LEU* 1.3 90.5 + - - +
252B TYR* 1.3 60.3 + - - +
253B LEU 3.3 4.1 + - - -
258B VAL* 3.3 9.3 - - - +
259B THR* 3.0 46.4 + - + +
260B PHE 5.1 0.9 + - - +
261B ARG* 3.8 6.3 + - - +
381B LEU* 5.1 0.9 - - - -
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Residues in contact with TYR 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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1484A LEU* 5.4 1.6 - - - +
229B TYR* 2.9 25.1 - - - +
230B SER* 3.1 34.8 + - - +
232B TYR* 3.7 27.3 + + + -
233B GLY* 5.4 0.2 - - - -
251B HIS* 1.3 71.7 - - - +
253B LEU* 1.3 70.7 + - - +
254B ASN* 4.2 14.2 + - + -
257B GLN 4.7 5.4 - - - -
258B VAL* 4.9 2.5 - - + -
305B ARG* 2.7 48.7 + - - -
381B LEU* 3.6 25.7 - - + +
382B TYR* 5.4 4.7 - + - -
385B VAL* 4.0 29.4 - - + +
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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