Contacts of the strand formed by residues 270 - 281 (chain B) in PDB entry 3C0M
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 270 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B TRP* 3.2 39.0 + - - -
228B SER* 4.1 1.1 - - - -
268B GLN* 3.5 4.8 - - - -
269B ASN* 1.3 80.5 + - - +
271B GLY* 1.3 59.2 + - - -
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Residues in contact with GLY 271 (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 ASN* 3.9 1.3 - - - -
227B TRP* 3.0 39.9 + - - +
270B GLY* 1.3 75.4 - - - -
272B SER* 1.3 59.5 + - - -
273B THR* 4.1 2.7 - - - -
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Residues in contact with SER 272 (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 ALA* 4.1 12.1 - - - +
225B THR 3.4 5.9 + - - -
226B ASN* 2.8 24.7 + - - -
271B GLY* 1.3 72.7 - - - -
273B THR* 1.3 65.1 + - - +
274B THR* 4.2 3.0 + - - +
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Residues in contact with THR 273 (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 ALA* 4.6 1.1 - - - -
225B THR* 3.1 30.3 + - - +
227B TRP* 4.3 20.9 - - + +
256B SER 3.7 18.9 + - - -
257B ILE* 5.3 3.2 - - + -
271B GLY* 4.7 1.1 - - - -
272B SER* 1.3 81.4 + - - +
274B THR* 1.3 68.4 + - - +
275B THR* 3.6 4.2 + - - +
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Residues in contact with THR 274 (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 ASP* 5.2 8.3 - - + +
223B THR 3.6 12.3 - - - -
224B ALA* 4.1 12.8 - - + +
272B SER* 4.2 3.1 + - - +
273B THR* 1.3 77.5 + - - +
275B THR* 1.3 61.6 + - - +
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Residues in contact with THR 275 (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 ASP* 3.5 3.7 - - - -
223B THR* 2.7 52.1 + - + +
224B ALA 4.1 0.7 - - - -
225B THR* 3.1 29.4 - - - +
256B SER* 4.5 20.2 - - - -
273B THR* 3.6 5.8 - - - +
274B THR* 1.3 78.4 - - - +
276B SER* 1.3 74.2 + - - +
277B LEU* 5.2 0.5 - - - +
409B GLN 5.0 3.2 + - - +
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Residues in contact with SER 276 (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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220B ARG* 5.6 1.2 - - - +
221B GLY 3.4 12.7 + - - -
222B ASP* 4.0 9.9 + - - -
275B THR* 1.3 87.2 + - - +
277B LEU* 1.3 82.0 + - - +
278B SER* 5.2 3.2 - - - -
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Residues in contact with LEU 277 (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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219B LEU* 4.0 9.4 - - + -
220B ARG* 3.0 24.7 - - - +
221B GLY* 3.0 32.4 + - - +
222B ASP 3.9 13.0 - - - +
223B THR* 4.1 14.6 - - + -
275B THR* 5.2 0.4 - - - +
276B SER* 1.3 85.5 + - - +
278B SER* 1.3 62.4 + - - +
279B GLN* 4.1 2.2 - - - +
297B LEU* 6.0 1.3 - - + -
409B GLN 4.4 0.2 - - - +
410B PHE* 3.6 16.6 - - + -
411B ALA* 3.5 38.4 - - + +
457B PHE* 4.7 12.6 - - + -
458B ASN 5.4 0.4 - - - +
460B VAL* 5.9 3.4 - - + -
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Residues in contact with SER 278 (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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218B THR* 5.3 1.6 - - - -
219B LEU 3.2 7.6 - - - -
220B ARG* 5.0 14.8 - - - -
276B SER* 5.2 3.6 - - - -
277B LEU* 1.3 75.5 - - - +
279B GLN* 1.3 73.6 + - - +
280B SER* 5.2 1.2 + - - -
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Residues in contact with GLN 279 (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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387A ASN* 5.3 3.1 - - - +
218B THR* 3.2 11.1 + - - +
219B LEU* 3.3 25.9 + - + +
277B LEU* 4.1 2.4 - - - +
278B SER* 1.3 85.8 + - - +
280B SER* 1.3 71.1 + - - +
411B ALA* 4.5 11.7 + - - +
412B GLY 3.6 15.1 + - - +
413B ASN* 2.9 48.5 + - + +
414B ILE* 3.5 24.0 - - + +
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Residues in contact with SER 280 (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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383A SER* 5.2 9.9 - - - -
384A THR* 3.6 14.7 + - - -
216B ASP* 4.9 10.1 + - - +
217B VAL 3.1 9.0 - - - -
218B THR* 2.9 25.6 - - - -
278B SER 5.2 1.0 + - - -
279B GLN* 1.3 79.4 - - - +
281B VAL* 1.3 63.6 + - - +
414B ILE* 3.9 4.4 + - - +
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Residues in contact with VAL 281 (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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122A TYR* 5.5 6.7 - - + +
380A ASN* 5.1 3.6 - - + +
384A THR* 4.5 10.3 - - + +
216B ASP* 2.9 27.0 - - - +
217B VAL* 3.2 16.9 + - + -
280B SER* 1.3 75.6 - - - +
282B ARG* 1.3 69.0 + - - +
283B PRO* 3.7 14.1 - - + -
414B ILE* 4.0 39.5 - - + +
416B ILE* 3.8 32.1 - - + -
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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