Contacts of the helix formed by residues 251 - 261 (chain B) in PDB entry 3THY
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 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B TYR* 5.0 1.6 - - - -
250B PHE* 1.3 72.1 - - - +
252B GLU* 1.3 63.7 + - - -
254B ALA* 2.8 20.4 + - - +
255B GLU* 3.3 10.5 + - - +
271B PHE* 3.7 27.8 - - - +
272B MET* 3.4 20.5 + - - +
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Residues in contact with GLU 252 (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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227B TYR* 5.3 1.0 + - - -
231B LYS* 5.4 5.8 - - - +
250B PHE 3.4 0.4 + - - -
251B GLY* 1.3 70.3 - - - -
253B ASP* 1.3 64.4 + - - +
255B GLU* 2.9 16.3 + - - +
256B ILE* 2.8 36.7 + - + +
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Residues in contact with ASP 253 (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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227B TYR* 2.9 25.8 + - - -
231B LYS* 2.9 23.8 + - - +
237B ALA 4.1 0.3 - - - +
238B VAL* 3.3 33.6 - - + +
239B LEU* 3.7 22.6 + - - +
249B PHE* 3.8 6.8 - - + +
250B PHE 2.9 16.5 + - - +
252B GLU* 1.3 77.0 - - - +
254B ALA* 1.3 54.9 + - - +
256B ILE* 3.6 10.5 - - - +
257B ALA* 3.0 28.2 + - - +
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Residues in contact with ALA 254 (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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249B PHE* 3.6 13.0 - - - +
250B PHE 3.2 7.4 + - - -
251B GLY 2.8 12.2 + - - +
253B ASP* 1.3 75.8 - - - +
255B GLU* 1.3 60.4 + - - +
257B ALA* 3.1 3.4 + - - +
258B ALA* 2.9 30.1 + - - +
265B CYS* 3.9 5.6 - - + +
272B MET* 3.7 33.4 - - + +
273B THR* 3.7 16.4 - - - +
274B ALA* 4.5 1.0 - - - +
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Residues in contact with GLU 255 (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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251B GLY 3.3 9.0 + - - +
252B GLU* 2.9 14.8 + - - +
254B ALA* 1.3 77.1 - - - +
256B ILE* 1.3 63.0 + - + +
258B ALA* 3.4 2.9 + - - +
259B ARG* 3.1 38.1 + - - +
265B CYS* 4.3 14.8 - - - -
272B MET* 4.0 28.1 - - + +
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Residues in contact with ILE 256 (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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238B VAL* 4.0 24.2 - - + -
252B GLU* 2.8 31.6 + - + +
253B ASP* 3.6 8.7 - - - +
255B GLU* 1.3 74.5 - - + +
257B ALA* 1.3 60.4 + - - +
259B ARG* 3.0 22.1 + - - +
260B GLU* 2.8 36.9 + - + +
288B LEU* 4.4 9.9 - - + -
293B TYR* 3.6 41.1 - - + +
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Residues in contact with ALA 257 (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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249B PHE* 3.6 37.2 - - + -
253B ASP 3.0 19.6 + - - +
254B ALA 3.1 5.6 + - - +
256B ILE* 1.3 77.1 - - - +
258B ALA* 1.3 57.9 + - - +
260B GLU* 5.1 0.2 - - - -
261B LEU* 3.0 46.8 + - + +
263B ILE* 3.5 10.0 - - + +
274B ALA* 4.5 0.7 - - + -
288B LEU* 5.3 3.6 - - + -
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Residues in contact with ALA 258 (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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83A MET* 4.9 2.4 - - - +
254B ALA 2.9 9.6 + - - +
255B GLU 3.7 4.3 - - - +
256B ILE 3.1 0.2 - - - -
257B ALA* 1.3 77.1 - - - +
259B ARG* 1.3 62.6 + - - +
262B ASN* 3.4 16.8 + - - -
263B ILE* 3.3 31.1 + - + +
265B CYS* 3.5 35.7 - - + +
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Residues in contact with ARG 259 (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 GLU* 3.1 23.7 + - - +
256B ILE* 3.0 32.9 + - - +
258B ALA* 1.3 78.6 - - - +
260B GLU* 1.3 77.5 + - - +
262B ASN* 3.8 12.5 + - - -
293B TYR* 4.6 6.5 + - - -
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Residues in contact with GLU 260 (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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256B ILE* 2.8 20.1 + - + +
259B ARG* 1.3 95.6 + - + +
261B LEU* 1.3 65.6 + - + +
262B ASN* 3.4 4.5 + - - +
287B ARG* 4.0 10.4 + - - +
288B LEU* 3.9 17.7 - - + -
291B LYS* 3.4 37.7 - - + +
293B TYR* 3.0 42.5 + - + +
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Residues in contact with LEU 261 (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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84A ASN* 3.7 2.8 + - - +
249B PHE* 4.2 14.8 - - + -
257B ALA* 3.0 35.2 + - + +
260B GLU* 1.3 81.1 - - + +
262B ASN* 1.3 74.9 + - - +
263B ILE* 3.7 12.3 - - + +
284B HIS* 3.5 47.1 - - + +
287B ARG* 3.1 51.4 + - + +
288B LEU* 4.0 16.8 - - + -
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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