Contacts of the helix formed by residues 251 - 261 (chain C) in PDB entry 3A4Y
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 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C THR 5.8 1.0 + - - -
224C ALA* 4.6 6.8 - - - +
228C ALA* 5.3 0.2 - - - +
249C LEU* 3.3 14.0 + - - +
250C ASP* 1.3 79.0 - - - +
252C PRO* 1.3 74.3 - - - +
253C MET* 3.3 2.2 - - - -
254C ALA* 2.9 26.6 - - - +
255C GLY* 3.0 14.0 + - - -
290C VAL* 4.5 1.1 - - - +
291C VAL 3.7 7.3 + - - -
310C LEU 4.6 1.8 + - - -
311C ALA* 5.1 0.5 - - - -
312C GLY* 4.9 9.9 - - - -
320C ARG* 4.4 1.1 - - - +
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Residues in contact with PRO 252 (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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251C SER* 1.3 80.2 - - - +
253C MET* 1.3 54.3 + - - +
255C GLY* 2.7 22.5 + - - +
256C ARG* 2.7 29.6 + - - +
290C VAL* 5.1 3.8 - - + -
291C VAL 4.2 2.7 - - - +
292C GLU* 3.5 35.4 - - + +
320C ARG* 3.7 16.8 - - - +
437C SO4 3.2 40.2 - - - +
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Residues in contact with MET 253 (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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92C ILE* 3.6 20.4 - - + -
93C VAL* 3.7 33.2 - - + +
96C ASP* 3.3 46.9 - - + +
224C ALA* 3.4 23.1 - - + -
225C VAL* 4.9 9.9 - - + -
251C SER* 3.3 2.2 - - - -
252C PRO* 1.3 77.4 - - - +
254C ALA* 1.3 55.8 + - - +
256C ARG* 2.7 44.1 + - - +
257C VAL* 2.8 18.6 + - + +
437C SO4 4.1 2.4 + - - +
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Residues in contact with ALA 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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224C ALA* 3.1 35.8 - - - +
228C ALA* 3.7 20.6 - - + -
229C GLN* 3.5 5.9 - - - +
249C LEU* 4.2 8.6 - - + +
251C SER* 2.9 25.4 + - - +
252C PRO 3.4 0.2 - - - -
253C MET* 1.3 78.9 - - - +
255C GLY* 1.3 60.9 + - - +
257C VAL* 3.5 1.0 + - - +
258C LEU* 3.0 22.5 + - - +
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Residues in contact with GLY 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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249C LEU* 3.9 15.5 - - - +
251C SER 3.0 10.8 + - - -
252C PRO 2.7 11.0 + - - -
254C ALA* 1.3 77.1 - - - +
256C ARG* 1.3 61.2 - - - -
258C LEU* 2.9 16.3 + - - +
259C SER* 3.0 16.8 + - - -
290C VAL* 4.0 13.0 - - - -
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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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92C ILE* 3.9 26.6 - - + +
96C ASP* 3.6 12.9 + - - +
252C PRO* 2.7 36.5 + - - +
253C MET* 2.7 34.5 + - - +
255C GLY* 1.3 71.2 - - - -
257C VAL* 1.3 61.4 + - - +
259C SER* 3.2 20.0 + - - +
260C LEU* 3.2 13.7 + - - +
437C SO4 3.0 30.4 + - - -
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Residues in contact with VAL 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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89C LEU* 4.0 16.6 - - + -
92C ILE* 4.0 19.5 - - + +
93C VAL* 6.4 1.1 - - + -
224C ALA 3.1 23.8 - - - +
225C VAL* 3.4 24.7 - - + +
229C GLN* 3.8 2.7 - - - +
253C MET* 2.8 29.3 + - + +
254C ALA 3.6 6.1 - - - +
256C ARG* 1.3 71.3 - - - +
258C LEU* 1.3 61.7 + - - +
260C LEU* 3.2 5.7 + - - +
261C TYR* 2.9 51.7 + - + -
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Residues in contact with LEU 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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229C GLN* 3.3 16.5 + - + +
232C LEU* 3.9 21.8 - - + -
249C LEU* 4.0 14.6 - - + -
254C ALA 3.0 13.1 + - - +
255C GLY* 2.9 13.9 + - - +
257C VAL* 1.3 76.3 - - - +
259C SER* 1.3 62.0 + - - +
261C TYR* 2.9 24.4 + - + +
262C PRO* 3.2 5.4 - - - +
281C ASN* 5.0 3.6 + - - +
283C PHE* 3.6 37.9 - - + +
284C ARG* 4.1 32.3 - - + +
288C LEU* 4.2 7.0 - - + -
290C VAL* 5.7 2.5 - - + -
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Residues in contact with SER 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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255C GLY 3.0 13.8 + - - -
256C ARG* 3.2 13.7 + - - -
258C LEU* 1.3 76.6 - - - +
260C LEU* 1.3 56.9 + - - +
262C PRO* 3.1 17.5 - - - +
263C ARG* 5.4 3.3 - - - +
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Residues in contact with LEU 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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88C LEU* 3.7 35.9 - - + +
89C LEU* 3.9 13.9 - - + +
92C ILE* 3.6 25.4 - - + -
256C ARG 3.2 8.2 + - - +
257C VAL 3.2 8.9 + - - +
258C LEU 3.1 0.6 - - - -
259C SER* 1.3 75.3 - - - +
261C TYR* 1.3 67.3 + - + +
262C PRO* 3.1 4.0 - - - -
263C ARG* 2.9 55.3 + - - +
264C LEU* 3.5 18.2 - - + +
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Residues in contact with TYR 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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89C LEU* 4.9 3.6 - - + -
143C PRO* 3.7 14.8 - - + +
170C VAL* 5.0 0.9 - - + -
225C VAL 3.8 3.1 + - - -
226C GLU* 2.7 27.9 + - - -
229C GLN* 3.3 32.1 - - + +
257C VAL* 2.9 43.6 + - + -
258C LEU* 2.9 19.0 + - + +
260C LEU* 1.3 77.3 - - - +
262C PRO* 1.3 62.4 - - + +
264C LEU* 3.2 15.5 + - + +
265C VAL 3.8 0.7 + - - -
268C PHE* 3.1 57.8 - + + -
276C PHE* 4.1 3.9 - - + -
281C ASN* 5.5 0.9 - - - +
283C PHE* 3.6 31.0 - + + -
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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