Contacts of the helix formed by residues 257 - 265 (chain B) in PDB entry 4RE1
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 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B PRO* 3.5 20.9 - - - -
253B GLU* 4.9 1.3 - - - -
254B LYS* 3.6 11.8 + - - +
255B LYS 3.4 3.6 + - - -
256B GLY* 1.3 80.5 - - - +
258B LEU* 1.3 55.8 + - - -
259B LYS 3.4 2.0 - - - -
260B GLU* 3.2 6.2 + - - +
261B LEU* 2.8 34.5 + - - +
310B LYS* 5.2 4.3 - - - -
373B LEU* 5.3 2.2 - - - -
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Residues in contact with LEU 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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244B ILE* 4.2 13.0 - - + -
247B ILE* 4.2 18.8 - - + -
248B TYR* 4.2 17.7 - - + +
251B PHE* 3.9 41.5 - - + +
252B PRO* 3.5 7.7 + - - +
257B GLY* 1.3 70.5 - - - -
259B LYS* 1.3 54.2 + - - +
261B LEU* 3.1 4.7 + - + -
262B PHE* 2.8 37.6 + - - +
270B PHE* 4.1 13.7 - - + -
373B LEU* 4.0 19.0 - - + +
387B CYS* 3.8 28.9 - - - -
389B ALA* 4.8 3.4 - - + -
408B LEU* 5.2 3.4 - - + -
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Residues in contact with LYS 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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248B TYR* 3.4 59.7 + - + +
252B PRO 4.9 1.8 + - - -
253B GLU* 3.4 43.6 + - + +
257B GLY 3.4 0.6 - - - -
258B LEU* 1.3 78.7 - - - +
260B GLU* 1.3 62.6 + - - +
262B PHE* 3.9 1.6 - - - +
263B GLY* 3.0 21.1 + - - -
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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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253B GLU* 6.0 0.4 - - - +
254B LYS 4.1 4.6 - - - +
255B LYS* 3.6 13.0 - - - +
256B GLY* 3.0 30.0 + - - -
257B GLY* 3.2 14.1 + - - +
259B LYS* 1.3 79.6 - - - +
261B LEU* 1.3 65.3 + - + +
263B GLY* 3.3 1.4 + - - -
264B LYS* 3.1 27.1 + - + +
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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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256B GLY* 3.9 20.4 - - - +
257B GLY 2.8 22.5 + - - +
258B LEU* 3.6 7.0 - - - +
260B GLU* 1.3 75.5 - - + +
262B PHE* 1.3 59.2 + - - +
264B LYS* 3.3 32.1 + - - +
265B GLY* 2.9 24.1 + - - +
270B PHE* 3.4 22.6 - - + -
373B LEU* 5.3 2.2 - - + -
375B VAL* 3.7 40.2 - - + -
384B THR* 3.8 13.6 + - - +
387B CYS* 5.2 1.1 - - - -
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Residues in contact with PHE 262 (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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244B ILE* 3.5 36.6 - - + -
248B TYR* 3.6 15.7 - - - +
258B LEU 2.8 19.5 + - - +
259B LYS 3.9 3.4 - - - +
261B LEU* 1.3 71.0 - - - +
263B GLY* 1.3 68.7 + - - +
265B GLY* 3.1 12.8 + - - -
267B GLN* 3.5 53.4 + - + +
270B PHE* 3.6 29.1 - + + -
408B LEU 3.7 18.6 - - - -
409B VAL 3.9 5.6 - - - -
410B LYS* 3.8 25.8 - - + -
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Residues in contact with GLY 263 (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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259B LYS 3.0 16.3 + - - -
260B GLU* 3.3 2.0 + - - -
262B PHE* 1.3 81.3 - - - +
264B LYS* 1.3 62.5 + - - +
265B GLY 3.5 0.2 + - - -
267B GLN* 5.3 4.8 + - - -
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Residues in contact with LYS 264 (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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260B GLU* 3.1 18.7 + - + +
261B LEU* 3.5 29.0 - - - +
263B GLY* 1.3 78.6 - - - +
265B GLY* 1.3 64.0 + - - +
266B PRO* 4.8 0.2 - - - +
382B GLN* 3.9 23.9 + - - +
383B GLU* 5.7 1.1 - - - +
384B THR* 4.3 11.6 + - - +
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Residues in contact with GLY 265 (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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261B LEU 2.9 15.2 + - - +
262B PHE 3.1 12.4 + - - -
263B GLY 4.5 0.2 - - - -
264B LYS* 1.3 88.8 - - - +
266B PRO* 1.3 76.2 - - - +
267B GLN* 3.8 3.1 - - - -
270B PHE* 4.2 5.8 - - - -
383B GLU* 5.5 0.3 - - - +
384B THR* 4.1 14.6 + - - -
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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