Contacts of the strand formed by residues 249 - 255 (chain B) in PDB entry 5B2G
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 GLN 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B ALA* 4.3 17.6 - - + +
247B THR 3.6 19.2 + - - +
248B GLY* 1.3 82.6 + - - +
250B LYS* 1.3 59.5 + - - +
251B TYR* 3.0 39.0 - - + +
290B SER* 4.9 1.1 - - - -
291B LEU 2.9 26.5 + - - +
318B LYS* 3.5 34.5 + - + +
319B PHE 5.1 4.2 - - - -
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Residues in contact with LYS 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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249B GLN* 1.3 74.8 + - - +
251B TYR* 1.3 63.0 + - - +
288B ASP* 4.5 20.9 - - - +
289B ILE 4.0 5.4 - - - +
290B SER* 4.0 26.0 - - - +
318B LYS* 3.7 6.4 - - - +
319B PHE* 3.3 59.7 + - + +
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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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211B LEU* 4.6 22.7 - - + -
212B THR* 4.0 11.5 + - - -
215B LEU* 4.6 11.0 - - + -
244B ILE* 3.4 33.5 - - + +
246B ALA* 4.0 4.2 + - - +
249B GLN* 3.0 38.5 - - + +
250B LYS* 1.3 76.7 - - - +
252B ARG* 1.3 63.9 + - - +
253B ILE* 5.2 6.1 - - + -
288B ASP* 3.6 4.3 - - - +
289B ILE* 3.0 43.1 + - + +
291B LEU* 3.8 27.8 + - + -
316B PHE* 6.2 3.6 - - + -
317B GLN 3.4 10.3 - - - +
318B LYS* 4.1 22.4 - - + -
319B PHE* 4.3 4.3 - - - -
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Residues in contact with ARG 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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1201A SER 5.0 0.8 + - - -
1202A ASN* 2.8 44.2 + - - +
1204A VAL* 3.7 22.3 - - + +
251B TYR* 1.3 75.1 - - - +
253B ILE* 1.3 68.8 + - - +
254B LEU* 4.7 5.4 - - + +
286B TYR* 3.7 26.9 + - + -
287B VAL 3.2 5.6 - - - +
288B ASP* 2.9 35.9 + - - +
315B LEU 3.6 1.9 - - - +
316B PHE* 3.5 6.8 - - - +
317B GLN* 2.8 52.9 + - + +
319B PHE* 4.3 15.9 - - + -
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Residues in contact with ILE 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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211B LEU* 6.4 0.9 - - + -
242B LEU* 5.4 5.6 - - + -
251B TYR* 5.2 5.4 - - + -
252B ARG* 1.3 76.8 - - - +
254B LEU* 1.3 61.4 + - - +
261B PHE* 3.9 25.8 - - + -
263B ILE* 4.1 27.4 - - + -
286B TYR* 3.6 1.7 - - - -
287B VAL* 2.7 39.8 + - + +
289B ILE* 4.3 14.6 - - + -
291B LEU* 6.1 3.1 - - + -
298B LEU* 4.4 16.6 - - + -
314B ILE* 3.9 11.7 - - + -
315B LEU 4.0 1.8 - - - -
316B PHE* 3.9 33.9 - - + -
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Residues in contact with LEU 254 (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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1202A ASN* 4.9 19.1 - - + +
1203A ILE* 5.8 1.1 - - + -
1316A ALA* 5.8 3.4 - - + -
1319A GLN* 4.2 17.3 - - + +
252B ARG* 4.0 6.5 + - + -
253B ILE* 1.3 73.2 - - - +
255B ALA* 1.3 68.1 + - - +
284B ASP* 4.4 13.2 - - + +
285B HIS 3.2 32.3 - - - +
286B TYR* 3.6 17.7 - - + -
313B SER 4.9 0.2 - - - +
314B ILE* 3.6 6.9 - - - +
315B LEU* 3.0 68.3 + - + +
317B GLN* 6.4 0.7 - - - -
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Residues in contact with ALA 255 (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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1316A ALA* 5.0 2.1 - - - +
253B ILE 4.0 1.8 + - - -
254B LEU* 1.3 85.3 - - - +
256B SER* 1.3 66.8 + - - +
259B VAL* 4.1 11.0 - - + -
261B PHE* 3.6 31.6 - - + -
284B ASP* 4.6 2.4 - - - +
285B HIS* 3.4 27.0 + - + +
313B SER 5.0 1.6 - - - -
314B ILE* 4.0 20.2 - - + -
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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