Contacts of the strand formed by residues 294 - 302 (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 GLY 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B THR* 5.2 0.8 - - - +
244B ILE* 3.2 33.7 + - - +
267B ASN* 4.6 12.6 - - - -
293B ALA* 1.3 78.6 - - - +
295B GLN* 1.3 61.2 + - - +
296B TYR* 4.1 8.1 - - - -
1147C LYS* 3.5 23.7 - - - +
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Residues in contact with GLN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 5.8 2.2 - - - +
241B HIS* 4.3 22.9 - - + +
242B LEU 3.3 17.7 - - - +
243B THR* 3.5 27.7 + - + +
266B ASN* 3.3 40.0 + - + +
267B ASN* 5.0 4.9 + - - +
294B GLY* 1.3 73.2 - - - +
296B TYR* 1.3 62.2 + - - +
297B VAL* 6.3 0.2 - - + -
1147C LYS* 4.0 9.3 + - - +
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B HIS* 3.6 1.6 - - - -
242B LEU* 2.9 42.0 + - + +
244B ILE* 3.9 26.5 - - + -
263B ILE* 5.2 4.3 - - + -
264B TYR 3.6 8.7 - - - +
265B SER* 3.8 13.9 - - - -
266B ASN 4.2 2.7 - - - +
267B ASN* 5.8 3.1 - - - -
274B LEU* 3.6 32.8 - - + -
291B LEU* 3.6 28.6 - - + +
292B ASP* 3.2 32.4 + - - +
293B ALA 3.4 13.2 + - - -
294B GLY* 4.1 10.8 - - - -
295B GLN* 1.3 78.3 - - - +
297B VAL* 1.3 73.0 + - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASN* 4.4 19.5 - - + +
240B LEU 3.4 7.4 - - - +
241B HIS* 3.8 20.9 - - + +
242B LEU* 5.4 0.7 - - - -
262B ASN 3.7 0.9 - - - +
263B ILE* 3.9 3.7 - - - +
264B TYR* 3.0 44.7 + - + +
266B ASN* 3.6 33.8 - - + +
271B LEU* 5.3 4.3 - - + -
295B GLN* 6.3 0.2 - - + -
296B TYR* 1.3 82.9 - - - +
298B LEU* 1.3 64.1 + - - +
299B VAL* 4.1 20.6 - - + -
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Residues in contact with LEU 298 (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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238B LEU 3.2 4.5 - - - +
240B LEU* 2.9 43.3 + - + +
242B LEU* 4.2 13.0 - - + -
253B ILE* 4.4 14.6 - - + -
261B PHE* 3.6 35.2 - - + -
262B ASN 3.5 4.9 - - - +
263B ILE* 3.7 22.7 - - + -
297B VAL* 1.3 74.3 - - - +
299B VAL* 1.3 59.5 + - - +
300B MSE 3.5 25.8 + - + +
314B ILE* 4.7 4.0 - - + -
316B PHE* 4.1 29.4 - - + -
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Residues in contact with VAL 299 (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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237B LYS* 3.5 33.9 - - + +
238B LEU 3.4 5.4 - - - +
239B ASN* 3.4 31.6 - - - +
261B PHE* 3.1 3.4 - - - -
262B ASN* 2.8 47.4 + - + +
264B TYR* 4.3 24.0 - - + -
297B VAL* 4.2 11.4 - - + -
298B LEU* 1.3 70.1 - - - +
300B MSE 1.3 62.7 + - - +
301B LYS* 5.5 0.6 - - + +
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Residues in contact with MSE 300 (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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226B TRP* 4.0 7.2 - - + -
237B LYS* 3.3 4.9 - - - +
238B LEU* 3.0 43.3 + - + +
240B LEU* 3.8 29.6 - - + -
259B VAL* 4.4 7.9 - - + -
260B ASP 3.2 9.9 - - - +
261B PHE* 4.1 7.9 - - + +
298B LEU* 3.5 23.2 + - + +
299B VAL* 1.3 73.0 - - - +
301B LYS* 1.3 66.4 - - - +
312B TYR* 3.8 45.8 + - + -
314B ILE* 3.8 32.3 - - + -
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Residues in contact with LYS 301 (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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234B TRP* 2.6 38.5 + - - +
235B THR* 3.8 12.7 + - - +
236B GLN 4.8 4.7 - - - +
237B LYS* 4.0 27.8 - - + +
259B VAL* 4.4 3.2 - - - +
260B ASP* 2.9 45.4 + - + +
299B VAL 5.5 0.7 - - - +
300B MSE 1.3 78.1 - - - +
302B ALA* 1.3 82.7 + - - +
303B ASN* 5.0 2.9 - - - +
312B TYR* 4.1 6.0 + - - -
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Residues in contact with ALA 302 (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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1314A LEU* 4.8 2.7 - - + -
234B TRP* 3.8 9.8 - - + +
258B ILE* 3.8 11.0 - - + +
259B VAL* 4.5 9.0 - - + +
301B LYS* 1.3 101.9 + - - +
303B ASN* 1.3 60.7 + - - +
304B SER 4.3 7.9 - - - +
306B TYR* 4.0 26.5 - - + -
312B TYR* 3.6 23.1 + - + +
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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