Contacts of the helix formed by residues 255 - 264 (chain B) in PDB entry 5EJC
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 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B CYS* 4.2 6.4 - - - -
253B LEU 3.9 0.4 - - - -
254B ASN* 1.3 79.8 - - - +
256B ALA* 1.3 65.9 + - - +
257B GLU* 3.3 15.9 + - - +
258B LYS* 3.0 34.5 + - - +
259B ILE* 2.9 27.9 + - - +
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Residues in contact with ALA 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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195B CYS* 3.4 23.9 + - - +
196B SER* 3.6 7.4 - - - +
197B ALA* 3.7 16.8 - - - -
200B LYS* 3.4 33.4 - - + -
255B SER* 1.3 71.9 + - - +
257B GLU* 1.3 56.3 + - - +
259B ILE* 3.8 0.7 - - - +
260B THR* 3.0 36.5 + - - +
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Residues in contact with GLU 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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200B LYS* 6.1 0.2 - - - -
255B SER* 3.1 9.8 + - - +
256B ALA* 1.3 79.9 - - - +
258B LYS* 1.3 61.2 + - + +
260B THR* 2.9 18.9 + - - +
261B LYS* 3.1 36.8 + - + +
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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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253B LEU* 3.4 34.6 - - + +
254B ASN* 2.9 31.3 + - - +
255B SER* 3.0 24.2 + - - +
257B GLU* 1.3 80.9 - - + +
259B ILE* 1.3 61.4 + - - +
261B LYS* 4.1 5.9 - - - +
262B PHE* 3.3 16.1 + - - +
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Residues in contact with ILE 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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191B HIS* 4.3 12.8 - - + +
192B LEU* 4.2 18.6 - - + -
195B CYS* 5.2 2.7 - - - -
197B ALA* 4.4 15.3 - - + -
201B LEU* 4.6 3.6 - - + -
250B VAL* 3.6 41.7 - - + +
253B LEU* 3.7 20.2 - - + -
255B SER 2.9 25.8 + - - +
256B ALA 3.8 4.5 - - - +
258B LYS* 1.3 75.2 - - - +
260B THR* 1.3 65.6 + - - +
262B PHE* 3.2 5.7 + - - +
263B LEU* 3.1 40.0 + - + +
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Residues in contact with THR 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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197B ALA* 5.0 3.6 - - + +
200B LYS* 3.0 42.4 - - + +
201B LEU* 4.4 7.6 - - + +
202B PRO* 4.9 2.9 - - + -
256B ALA 3.0 14.7 + - - +
257B GLU* 2.9 17.0 + - - +
259B ILE* 1.3 76.8 - - + +
261B LYS* 1.3 69.3 + - - +
263B LEU* 3.1 8.9 + - - +
264B GLU* 3.0 37.9 + - - +
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Residues in contact with LYS 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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257B GLU* 3.1 35.3 + - + +
258B LYS* 4.1 6.3 - - - +
259B ILE 3.3 0.2 - - - -
260B THR* 1.3 83.1 + - - +
262B PHE* 1.3 62.2 + - - +
264B GLU* 3.7 11.2 + - - +
265B ASN* 3.6 30.5 + - - +
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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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246B PHE* 3.9 42.6 - + + -
249B LYS* 3.8 38.1 - - + -
250B VAL* 4.2 15.7 - - + -
253B LEU* 4.1 13.5 - - + -
258B LYS 3.3 11.7 + - - +
259B ILE 3.2 8.4 + - - +
260B THR 3.2 0.6 - - - -
261B LYS* 1.3 78.4 - - - +
263B LEU* 1.3 79.4 + - + +
265B ASN 3.1 32.3 + - - +
266B ILE* 3.5 4.8 + - + +
267B PRO* 4.1 24.0 - - + -
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Residues in contact with LEU 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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192B LEU* 5.8 0.2 - - + -
201B LEU* 3.5 32.5 - - + -
202B PRO* 4.2 17.3 - - + +
205B LEU* 4.6 6.4 - - - +
206B TRP* 4.4 17.6 + - + -
214B CYS* 4.8 6.9 - - - -
242B ILE* 4.1 26.0 - - + +
243B LEU* 4.2 18.8 - - + -
246B PHE* 6.1 0.2 - - + -
250B VAL* 4.9 6.1 - - + -
259B ILE* 3.1 30.7 + - + +
260B THR* 3.1 4.9 + - - +
262B PHE* 1.3 95.0 - - + +
264B GLU* 1.3 61.3 + - - +
265B ASN 3.3 0.2 - - - -
266B ILE* 3.5 14.8 - - + +
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Residues in contact with GLU 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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202B PRO* 4.0 27.6 - - + +
205B LEU* 4.5 16.6 - - + +
213B GLY 5.2 5.7 - - - +
214B CYS* 5.8 2.7 - - - -
260B THR* 3.0 28.9 + - - +
261B LYS* 4.1 11.8 - - - +
262B PHE 3.2 0.4 - - - -
263B LEU* 1.3 75.9 - - - +
265B ASN* 1.3 74.3 + - - +
266B ILE 3.9 0.9 - - - -
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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