Contacts of the strand formed by residues 270 - 281 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A TRP* 3.6 38.4 + - - -
228A SER* 3.9 1.8 - - - -
268A GLN* 3.2 8.9 + - - -
269A ASN* 1.3 80.9 + - - +
271A GLY* 1.3 58.8 + - - -
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Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASN* 3.4 5.4 - - - +
227A TRP* 2.9 45.4 + - - +
270A GLY* 1.3 74.2 - - - -
272A SER* 1.3 60.0 + - - -
273A THR* 5.0 1.1 - - - -
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ALA* 4.5 8.8 - - - +
225A THR 3.3 9.9 + - - -
226A ASN* 3.9 18.4 - - - +
271A GLY* 1.3 71.9 - - - -
273A THR* 1.3 65.2 + - - +
274A THR* 5.0 4.2 - - - +
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ALA* 3.3 4.5 - - - +
225A THR* 2.9 36.2 + - - -
227A TRP* 4.3 22.8 - - + +
256A SER* 3.6 21.4 + - - +
257A ILE* 5.9 2.2 - - + -
271A GLY* 5.0 0.4 - - - -
272A SER* 1.3 77.8 - - - +
274A THR* 1.3 68.0 + - - +
275A THR* 4.8 2.6 + - - -
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Residues in contact with THR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASP* 4.6 15.1 - - - +
223A THR 3.1 11.2 - - - +
224A ALA* 4.6 8.1 - - + -
256A SER* 5.7 0.2 + - - -
272A SER* 5.0 3.8 - - - +
273A THR* 1.3 83.7 + - - +
275A THR* 1.3 63.7 + - - +
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASP* 2.9 9.0 - - - +
223A THR* 2.5 58.0 + - + +
225A THR* 4.3 9.4 + - - -
256A SER* 3.5 32.4 + - - +
273A THR* 4.8 2.1 + - - -
274A THR* 1.3 75.7 - - - +
276A SER* 1.3 82.9 + - - +
410A PHE* 6.6 0.2 - - + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLY 3.3 7.0 - - - -
222A ASP* 4.4 1.8 - - - +
223A THR* 4.9 0.2 - - - +
275A THR* 1.3 88.1 - - - +
277A LEU* 1.3 77.9 + - - +
278A SER* 4.2 5.4 - - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 3.2 30.0 - - + +
220A ARG* 3.3 16.2 - - - +
221A GLY* 2.9 42.0 + - - +
222A ASP* 3.6 14.1 - - - +
223A THR* 3.9 11.0 - - + +
275A THR 3.8 2.5 - - - +
276A SER* 1.3 92.9 - - - +
278A SER* 1.3 63.1 + - - +
279A GLN* 5.4 2.7 - - - +
297A LEU* 5.2 1.8 - - + -
410A PHE* 6.0 0.4 - - - -
411A ALA* 4.0 30.3 - - + +
457A PHE* 4.7 16.4 - - + -
460A VAL* 5.4 7.0 - - + -
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A THR* 5.2 2.9 - - - -
219A LEU 3.9 1.8 - - - -
220A ARG* 5.7 0.4 - - - -
276A SER* 4.2 6.2 - - - -
277A LEU* 1.3 75.5 - - - +
279A GLN* 1.3 70.2 + - - +
280A SER* 3.9 2.8 + - - -
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A THR* 3.1 6.6 + - - -
219A LEU* 3.0 41.8 + - + +
277A LEU* 5.4 2.2 - - - +
278A SER* 1.3 83.6 - - - +
280A SER* 1.3 61.6 + - - +
281A VAL* 5.2 3.4 - - + -
411A ALA* 5.2 4.8 + - - +
412A GLY 2.8 11.0 + - - +
413A ASN* 2.8 42.6 + - + +
414A ILE* 3.5 34.1 - - + +
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASP* 3.9 21.4 - - - +
217A VAL 3.1 5.9 + - - -
218A THR* 2.9 24.8 + - - -
278A SER 3.9 3.0 + - - -
279A GLN* 1.3 77.0 - - - +
281A VAL* 1.3 64.2 + - - +
282A ARG* 4.1 0.3 + - - +
384B THR* 5.6 1.0 + - - -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASP* 3.4 2.3 - - - -
217A VAL* 2.6 43.8 + - + +
279A GLN* 4.2 2.9 - - + -
280A SER* 1.3 78.4 - - - +
282A ARG* 1.3 61.7 + - - +
283A PRO* 3.7 16.9 - - + +
414A ILE* 3.4 47.5 - - + +
416A ILE* 4.3 24.9 - - + -
384B THR* 5.8 5.4 - - - +
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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