Contacts of the helix formed by residues 253 - 262 (chain C) in PDB entry 2Y1M
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 SER 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C HIS* 5.1 0.9 - - - -
250C PRO* 2.9 14.4 + - - +
252C SER* 1.3 76.7 - - - +
254C LEU* 1.3 52.1 + - - +
255C LEU 3.5 1.6 - - - -
256C ARG* 3.2 38.5 + - - +
257C ASN* 2.6 66.7 + - - -
352C LEU 4.1 6.1 + - - -
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C LEU* 4.3 10.8 - - + -
213C HIS* 3.8 18.6 - - + +
241C PHE* 5.9 0.2 - - + -
244C PHE* 3.8 35.4 - - + -
245C THR* 4.4 14.6 - - + +
248C PHE* 3.4 31.9 - - + +
250C PRO 3.3 1.9 + - - -
251C TRP* 3.3 48.3 + - + +
252C SER 3.5 0.6 + - - -
253C SER* 1.3 75.8 - - - +
255C LEU* 1.3 64.5 + - + +
257C ASN* 3.1 4.5 + - - +
258C TRP* 2.9 26.2 + - - +
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C LEU* 4.5 5.2 - - + -
213C HIS* 3.8 41.7 + - + +
214C PRO 4.3 7.2 - - - +
215C ILE* 3.9 18.6 - - + -
220C GLU* 4.6 9.0 - - - +
224C LEU* 3.8 36.8 - - + -
244C PHE* 4.4 5.2 - - + -
254C LEU* 1.3 92.6 - - + +
256C ARG* 1.3 61.0 + - - +
258C TRP* 3.6 12.7 - - + +
259C ASN* 2.9 41.5 + - - +
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Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C SER* 3.2 32.8 + - - +
255C LEU* 1.3 77.6 - - - +
257C ASN* 1.3 63.2 + - - +
259C ASN* 3.6 6.6 + - - +
260C SER* 3.0 33.6 + - - +
351C GLY 3.9 21.8 + - - -
352C LEU* 3.9 23.6 + - + +
354C GLU* 4.5 16.2 - - - +
359C ASP 6.1 0.2 - - - -
360C HIS* 4.3 27.5 - - + +
361C ILE* 4.9 13.0 - - + +
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Residues in contact with ASN 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C PHE* 3.4 16.6 + - + +
249C GLN 3.5 0.4 - - - -
250C PRO* 3.2 33.1 + - - +
253C SER* 2.6 51.3 + - - +
254C LEU 3.4 5.4 - - - +
256C ARG* 1.3 73.7 - - - +
258C TRP* 1.3 56.1 + - - +
260C SER 3.5 0.3 + - - -
261C LEU* 3.1 44.0 + - + +
325C PHE* 3.4 22.8 - - + -
352C LEU* 3.5 18.8 - - - +
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Residues in contact with TRP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C GLU* 3.6 31.4 - - + -
223C ALA* 3.6 11.2 - - + -
224C LEU* 3.3 45.5 - - + -
227C THR* 3.6 16.5 + - - -
244C PHE* 4.0 15.7 - + + -
248C PHE* 3.6 29.8 - + + -
254C LEU 2.9 15.1 + - - +
255C LEU* 3.2 21.3 + - + +
257C ASN* 1.3 75.6 - - - +
259C ASN* 1.3 85.6 + - - +
262C ALA* 2.9 37.1 + - + +
263C VAL* 3.3 28.0 + - + +
368C TYR* 4.1 0.9 - + - -
371C TYR* 3.6 8.2 + + - -
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Residues in contact with ASN 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C GLU* 3.4 18.6 + - - -
255C LEU* 2.9 30.4 + - - +
256C ARG* 4.1 6.2 - - - +
258C TRP* 1.3 87.9 - - - +
260C SER* 1.3 61.2 + - - +
261C LEU 3.5 0.2 + - - -
263C VAL* 3.8 5.1 - - - +
264C THR* 3.2 32.2 + - - +
361C ILE* 4.2 13.9 + - + +
363C VAL* 4.1 15.9 - - + +
368C TYR* 2.8 30.8 + - - -
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Residues in contact with SER 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ARG* 3.0 18.6 + - - +
257C ASN 4.1 0.7 - - - -
259C ASN* 1.3 76.8 - - - +
261C LEU* 1.3 60.0 + - - +
264C THR* 4.3 8.8 + - - -
265C HIS* 3.6 21.7 + - - +
347C PRO* 5.5 1.6 - - - +
349C LEU* 4.1 12.2 - - - +
352C LEU* 3.9 29.5 - - - +
361C ILE* 3.8 24.8 - - - +
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Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LEU 5.1 2.9 - - - +
248C PHE* 4.4 17.7 - - + -
249C GLN 5.7 0.9 - - - +
257C ASN* 3.1 27.6 + - + +
260C SER* 1.3 82.8 - - - +
262C ALA* 1.3 59.4 + - - +
265C HIS* 3.4 15.1 - - - +
268C TYR* 3.5 2.9 - - - +
293C PHE* 3.4 24.0 - - + -
303C TRP* 5.4 0.6 - - - -
324C LEU* 4.0 31.9 - - + +
325C PHE* 4.2 22.0 - - + +
328C LEU* 3.6 30.3 - - + -
349C LEU* 3.8 16.6 - - + -
352C LEU* 4.5 5.8 - - + -
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C PHE* 4.0 11.4 - - + -
258C TRP* 2.9 30.1 + - + +
261C LEU* 1.3 79.7 - - - +
263C VAL* 1.3 66.2 + - - +
264C THR 3.1 3.0 + - - -
265C HIS 3.6 6.9 + - - +
268C TYR* 3.3 45.1 - - + +
371C TYR* 4.0 9.0 - - - +
374C MET* 5.8 0.2 - - - +
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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