Contacts of the strand formed by residues 292 - 300 (chain B) in PDB entry 5UV6
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 292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B LYS* 4.5 6.1 - - - -
290B ASP 3.6 1.4 + - - -
291B TYR* 1.3 75.4 - - - +
293B ASN* 1.3 64.3 + - - -
294B TYR* 3.8 5.9 - - - -
310B THR* 3.3 8.7 - - - +
311B LEU 2.9 34.0 + - - -
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Residues in contact with ASN 293 (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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258B LYS* 3.3 27.4 - - - +
259B GLU* 4.5 3.3 + - - +
292B GLY* 1.3 72.8 - - - -
294B TYR* 1.3 61.4 + - - +
295B THR* 5.5 0.9 - - - +
308B SER* 4.4 4.9 - - - -
309B ILE 3.6 3.5 - - - +
310B THR* 2.6 32.2 + - - +
2005B NAG 1.4 66.2 + - - +
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Residues in contact with TYR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.4 29.4 - - + -
256B TRP* 4.2 12.3 - - + -
257B PHE 3.3 15.0 - - - +
258B LYS* 3.6 34.2 + - + +
263B LEU* 3.8 22.0 - - + -
270B MET* 5.9 0.7 - - - -
281B LEU* 4.1 3.8 - - + -
283B PHE* 3.5 26.1 - + - -
290B ASP* 2.6 38.2 + - - -
292B GLY 3.8 16.2 - - - -
293B ASN* 1.3 76.7 - - - +
295B THR* 1.3 62.8 + - - +
308B SER* 3.3 2.7 - - - -
309B ILE* 2.9 37.4 + - + +
311B LEU* 4.0 6.7 - - + -
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Residues in contact with THR 295 (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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255B GLN 3.5 2.1 - - - +
256B TRP* 3.4 7.0 - - - -
257B PHE* 2.9 44.6 + - - +
258B LYS* 5.2 0.4 - - - +
259B GLU 5.9 0.9 + - - -
260B GLU* 4.7 7.1 + - - -
293B ASN* 5.5 1.0 - - - +
294B TYR* 1.3 72.8 - - - +
296B CYS* 1.3 59.1 + - - +
297B VAL* 3.8 9.4 + - + -
306B ASN* 3.5 35.0 - - + +
307B ALA 3.2 14.4 - - - +
308B SER* 3.0 16.9 + - - +
2004B NAG 4.0 9.2 - - + +
2005B NAG 4.8 3.1 + - - -
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Residues in contact with CYS 296 (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 ILE* 4.2 4.2 - - - +
244B CYS* 2.0 53.6 - - + -
254B PHE* 3.8 9.4 - - + -
255B GLN 3.5 4.7 - - - -
256B TRP* 3.7 19.7 - - + -
294B TYR 4.0 1.6 + - - -
295B THR* 1.3 71.4 - - - +
297B VAL* 1.3 60.6 + - - +
298B ALA 4.0 1.3 + - - -
306B ASN* 3.1 4.4 - - - -
307B ALA* 2.9 42.6 + - - -
309B ILE* 5.4 0.7 - - - -
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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
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253B GLU 3.4 1.9 - - - +
254B PHE* 3.2 7.2 - - - -
255B GLN* 2.9 41.8 + - + +
257B PHE* 3.7 32.1 - - + -
295B THR* 3.8 2.7 - - + -
296B CYS* 1.3 72.3 - - - +
298B ALA* 1.3 59.7 + - - +
299B THR* 3.9 16.1 + - - +
304B ASN* 4.7 13.7 - - - +
305B THR 3.3 14.4 - - - +
306B ASN* 3.6 17.3 - - + +
2004B NAG 3.7 22.7 - - + +
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Residues in contact with ALA 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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224B PRO* 3.5 10.1 - - + +
226B ILE* 4.0 8.3 - - + +
246B ALA* 3.5 32.3 - - + -
252B ALA* 3.6 9.9 - - + -
253B GLU 3.3 4.9 - - - -
254B PHE* 3.8 12.1 - - + -
296B CYS 4.0 1.8 + - - -
297B VAL* 1.3 70.7 - - - +
299B THR* 1.3 63.2 + - - +
304B ASN* 3.3 2.9 - - - +
305B THR* 2.9 33.1 + - + +
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Residues in contact with THR 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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224B PRO* 4.0 0.9 - - - -
251B MET 4.3 0.3 - - - +
252B ALA* 3.1 6.1 - - - -
253B GLU* 2.9 39.2 + - - +
255B GLN* 5.6 2.9 + - - +
297B VAL* 3.9 15.8 + - - +
298B ALA* 1.3 77.3 + - - +
300B ASN* 1.3 69.3 + - - +
303B GLY 3.6 11.2 - - - +
304B ASN* 4.0 10.5 - - + +
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Residues in contact with ASN 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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222B TYR 2.9 25.3 + - - -
223B PRO* 3.7 2.1 - - - +
224B PRO* 3.5 15.9 - - + +
248B ALA* 3.5 8.5 - - - +
249B VAL 3.4 8.3 + - - -
250B PRO* 3.1 31.6 + - + +
251B MET 4.0 6.5 - - - +
252B ALA* 4.3 1.8 - - - -
299B THR* 1.3 82.4 - - - +
301B LYS* 1.3 56.1 + - - +
302B LEU* 2.7 31.9 + - - +
303B GLY 2.9 20.4 + - - +
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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