Contacts of the helix formed by residues 253 - 258 (chain B) in PDB entry 5T0H
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B GLY* 1.3 71.2 - - - -
254B GLU* 1.3 51.2 + - - +
255B LEU* 3.1 8.5 - - - -
256B ILE* 2.7 40.3 + - - +
257B GLN* 3.4 9.1 + - - -
267B VAL* 5.6 4.9 - - - -
287B ILE* 5.4 5.0 - - - +
288B ASP 5.8 0.4 - - - +
289B ALA* 4.6 22.7 - - - +
305B ILE* 6.0 4.0 - - - -
308B THR* 5.0 13.8 + - - +
309B MET* 5.3 5.2 - - - +
312B LEU* 5.0 11.8 - - - +
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Residues in contact with GLU 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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251B VAL* 4.5 11.5 - - - +
252B GLY* 3.2 3.5 + - - -
253B SER* 1.3 76.7 - - - +
255B LEU* 1.3 62.6 + - - +
257B GLN* 3.1 35.6 + - + +
258B LYS* 3.2 10.9 + - + +
229C ARG* 4.1 20.8 - - + +
231C VAL* 4.8 2.6 - - - +
268C GLU* 3.0 43.7 - - + +
271C ARG* 3.9 3.3 - - - +
272C THR* 5.4 0.7 + - - -
275C GLU* 3.1 33.7 - - - +
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Residues in contact with LEU 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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250B VAL* 4.9 11.2 - - + -
251B VAL 6.1 0.4 - - - +
252B GLY 5.0 4.0 - - - +
253B SER 4.3 5.2 - - - +
254B GLU* 1.3 78.6 - - - +
256B ILE* 1.3 80.4 + - + +
258B LYS* 3.1 23.3 - - - +
262B ASP* 3.4 8.7 - - - +
266B LEU* 3.6 23.6 - - + +
267B VAL* 3.6 24.0 - - + -
270B LEU* 3.9 26.7 - - + -
228C ALA 4.0 7.6 - - - +
229C ARG* 3.9 39.8 - - + +
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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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253B SER* 2.7 19.1 + - - +
255B LEU* 1.3 89.0 - - + +
257B GLN* 1.3 56.6 + - - +
258B LYS 3.0 7.9 + - - -
259B TYR 2.8 25.8 + - - +
261B GLY* 5.5 4.3 - - - +
262B ASP* 3.4 19.5 - - - +
263B GLY 3.0 32.8 - - - +
264B PRO* 3.4 23.1 - - + +
266B LEU* 4.3 3.8 - - + +
267B VAL* 4.4 5.6 - - + -
304B GLU* 5.2 4.7 - - + +
305B ILE* 5.8 2.9 - - + -
308B THR* 3.4 34.3 - - + +
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Residues in contact with GLN 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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253B SER* 3.4 6.8 + - - +
254B GLU* 3.1 27.5 + - + +
256B ILE* 1.3 80.1 - - - +
258B LYS* 1.3 59.5 + - - +
259B TYR 3.1 4.0 + - - -
289B ALA* 5.7 1.9 - - - +
292B THR* 5.4 3.3 + - - -
294B ARG 5.0 3.9 + - - +
295B TYR* 4.5 17.3 - - + +
296B ASP* 3.4 17.1 - - + +
298B ASN 3.3 1.2 - - - +
299B SER* 3.2 32.8 - - - +
305B ILE* 5.2 14.7 - - + +
268C GLU* 2.8 44.8 + - + +
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Residues in contact with LYS 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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254B GLU* 3.2 10.6 + - + +
255B LEU* 3.1 26.0 - - - +
256B ILE 4.3 0.9 - - - +
257B GLN* 1.3 76.5 - - - +
259B TYR* 1.3 69.1 + - + +
262B ASP* 4.8 2.9 - - - +
266B LEU* 5.2 3.4 - - + -
296B ASP* 4.3 8.1 - - - -
297B SER* 3.4 17.4 - - - +
298B ASN* 3.1 14.8 - - - +
221C GLN* 6.0 1.6 - - - +
226C GLU 5.2 1.2 + - - -
227C GLY* 4.3 5.9 - - - -
228C ALA 3.7 19.6 + - - +
230C MET* 3.3 36.0 - - + +
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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